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USC Norris Comprehensive Cancer Center
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Publications for Norris Cancer Center Members in the Molecular Genetics Program

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Total Number of Publications: 584 (At least 1 author in this program)
Inter Programmatic Publications: 109 (A collaboration outside the program...at least 1 author in the program, and at least 1 author out of the program)
Intra Programmatic Publications: 77 (A collaboration within the program...at least 2 authors in the program)

1: Viggiani CJ, Aparicio JG, Aparicio OM
ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays.
Methods Mol Biol 521: 255-78 (2009)
PM ID: 19563111
2: Toleno DM, Renaud G, Wolfsberg TG, Islam M, Wildman DE, Siegmund KD, Hacia JG
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.
BMC Bioinformatics 10: 77 (2009)
PM ID: 19265541 PMC2660304
3: Green MD, Sabatinos SA, Forsburg SL
Microscopy techniques to examine DNA replication in fission yeast.
Methods Mol Biol 521: 463-82 (2009)
PM ID: 19563123
4: Sabatinos SA, Forsburg SL
Measuring DNA content by flow cytometry in fission yeast.
Methods Mol Biol 521: 449-61 (2009)
PM ID: 19563122
5: Luche DD, Forsburg SL
Cell-cycle synchrony for analysis of S. pombe DNA replication.
Methods Mol Biol 521: 437-48 (2009)
PM ID: 19563121
6: Dey R, Ji K, Liu Z, Chen L
A cytokine-cytokine interaction in the assembly of higher-order structure and activation of the interleukine-3:receptor complex.
PLoS One 4: e5188 (2009)
PM ID: 19352505 PMC2662821
7: Kuramochi H, Uchida K, Peters JH, Shimizu D, Vallbohmer D, Schneider S, Danenberg KD, Danenberg PV
Loss of heterozygosity at thymidylate synthase locus in Barrett's metaplasia, dysplasia, and carcinoma sequences.
BMC Cancer 9: 157 (2009)
PM ID: 19460136 PMC2694818
8: Knott SR, Viggiani CJ, Aparicio OM, Tavaré S
Strategies for analyzing highly enriched IP-chip datasets.
BMC Bioinformatics 10: 305 (2009)
PM ID: 19772646 PMC2759964
9: Grimminger PP, Stöhlmacher J, Vallböhmer D, Schneider PM, Hölscher AH, Metzger R, Danenberg PV, Brabender J
Prognostic Significance and Clinicopathological Associations of COX-2 SNP in Patients with Nonsmall Cell Lung Cancer.
J Oncol 2009: 139590 (2009)
PM ID: 20016751 PMC2793422
10: Li B, Jog S, Candelario J, Reddy S, Comai L
Altered nuclear functions in progeroid syndromes: a paradigm for aging research.
ScientificWorldJournal 9: 1449-62 (2009)
PM ID: 20024518
11: Paoloni M, Davis S, Lana S, Withrow S, Sangiorgi L, Picci P, Hewitt S, Triche T, Meltzer P, Khanna C
Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.
BMC Genomics 10: 625 (2009)
PM ID: 20028558 PMC2803201
12: Longo VD
Linking sirtuins, IGF-I signaling, and starvation.
Exp Gerontol 44: 70-4 (2009)
PM ID: 18638538
13: Mori R, Xiong S, Wang Q, Tarabolous C, Shimada H, Panteris E, Danenberg KD, Danenberg PV, Pinski JK
Gene profiling and pathway analysis of neuroendocrine transdifferentiated prostate cancer cells.
Prostate 69: 12-23 (2009)
PM ID: 18814146
14: Yuksek K, Chen WL, Chien D, Ou JH
Ubiquitin-independent degradation of hepatitis C virus F protein.
J Virol 83: 612-21 (2009)
PM ID: 18971267 PMC2612388
15: Haga K, Tomioka A, Liao CP, Kimura T, Matsumoto H, Ohno I, Hermann K, Logg CR, Jiao J, Tanaka M, Hirao Y, Wu H, Kruse CA, Roy-Burman P, Kasahara N
PTEN knockout prostate cancer as a model for experimental immunotherapy.
J Urol 181: 354-62 (2009)
PM ID: 19010487 PMC2838731 NIHMS175651
16: Wu L, Fossum E, Joo CH, Inn KS, Shin YC, Johannsen E, Hutt-Fletcher LM, Hass J, Jung JU
Epstein-Barr virus LF2: an antagonist to type I interferon.
J Virol 83: 1140-6 (2009)
PM ID: 18987133 PMC2612359
17: Kim RH, Coates JM, Bowles TL, McNerney GP, Sutcliffe J, Jung JU, Gandour-Edwards R, Chuang FY, Bold RJ, Kung HJ
Arginine deiminase as a novel therapy for prostate cancer induces autophagy and caspase-independent apoptosis.
Cancer Res 69: 700-8 (2009)
PM ID: 19147587 PMC2629384 NIHMS79278
18: Ohta S, Uemura H, Matsui Y, Ishiguro H, Fujinami K, Kondo K, Miyamoto H, Yazawa T, Danenberg K, Danenberg PV, Tohnai I, Kubota Y
Alterations of p16 and p14ARF genes and their 9p21 locus in oral squamous cell carcinoma.
Oral Surg Oral Med Oral Pathol Oral Radiol Endod 107: 81-91 (2009)
PM ID: 19101490
19: Machida K, Tsukamoto H, Mkrtchyan H, Duan L, Dynnyk A, Liu HM, Asahina K, Govindarajan S, Ray R, Ou JH, Seki E, Deshaies R, Miyake K, Lai MM
Toll-like receptor 4 mediates synergism between alcohol and HCV in hepatic oncogenesis involving stem cell marker Nanog.
Proc Natl Acad Sci U S A 106: 1548-53 (2009)
PM ID: 19171902 PMC2635765
20: Chen JL, Lin HH, Kim KJ, Lin A, Ou JH, Ann DK
PKC delta signaling: a dual role in regulating hypoxic stress-induced autophagy and apoptosis.
Autophagy 5: 244-6 (2009)
PM ID: 19098423 PMC2743529 NIHMS123596
21: Choudhary B, Zhou J, Li P, Thomas S, Kaartinen V, Sucov HM
Absence of TGFbeta signaling in embryonic vascular smooth muscle leads to reduced lysyl oxidase expression, impaired elastogenesis, and aneurysm.
Genesis 47: 115-21 (2009)
PM ID: 19165826
22: Myong S, Cui S, Cornish PV, Kirchhofer A, Gack MU, Jung JU, Hopfner KP, Ha T
Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA.
Science 323: 1070-4 (2009)
PM ID: 19119185 PMC3567915 NIHMS437732
23: de Villartay JP, Shimazaki N, Charbonnier JB, Fischer A, Mornon JP, Lieber MR, Callebaut I
A histidine in the beta-CASP domain of Artemis is critical for its full in vitro and in vivo functions.
DNA Repair (Amst) 8: 202-8 (2009)
PM ID: 19022407
24: Gasparyan HJ, Xu L, Petreaca RC, Rex AE, Small VY, Bhogal NS, Julius JA, Warsi TH, Bachant J, Aparicio OM, Nugent CI
Yeast telomere capping protein Stn1 overrides DNA replication control through the S phase checkpoint.
Proc Natl Acad Sci U S A 106: 2206-11 (2009)
PM ID: 19171895 PMC2650133
25: Davicioni E, Anderson MJ, Finckenstein FG, Lynch JC, Qualman SJ, Shimada H, Schofield DE, Buckley JD, Meyer WH, Sorensen PH, Triche TJ
Molecular classification of rhabdomyosarcoma--genotypic and phenotypic determinants of diagnosis: a report from the Children's Oncology Group.
Am J Pathol 174: 550-64 (2009)
PM ID: 19147825 PMC2630563
26: Kamerlin SC, Haranczyk M, Warshel A
Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.
J Phys Chem B 113: 1253-72 (2009)
PM ID: 19055405 PMC2679392 NIHMS86597
27: Yu X, Wang Y, Jiang M, Bierie B, Roy-Burman P, Shen MM, Taketo MM, Wills M, Matusik RJ
Activation of beta-Catenin in mouse prostate causes HGPIN and continuous prostate growth after castration.
Prostate 69: 249-62 (2009)
PM ID: 18991257
28: Asahina K, Tsai SY, Li P, Ishii M, Maxson RE, Sucov HM, Tsukamoto H
Mesenchymal origin of hepatic stellate cells, submesothelial cells, and perivascular mesenchymal cells during mouse liver development.
Hepatology 49: 998-1011 (2009)
PM ID: 19085956 PMC2673117 NIHMS98872
29: Tsai AG, Engelhart AE, Hatmal MM, Houston SI, Hud NV, Haworth IS, Lieber MR
Conformational variants of duplex DNA correlated with cytosine-rich chromosomal fragile sites.
J Biol Chem 284: 7157-64 (2009)
PM ID: 19106104 PMC2652318
30: Ren C, Finkel SE, Tower J
Conditional inhibition of autophagy genes in adult Drosophila impairs immunity without compromising longevity.
Exp Gerontol 44: 228-35 (2009)
PM ID: 18955126 PMC2664319 NIHMS99063
31: Yik WY, Steinberg SJ, Moser AB, Moser HW, Hacia JG
Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders.
Hum Mutat 30: E467-80 (2009)
PM ID: 19105186 PMC2649967 NIHMS86157
32: Wies E, Hahn AS, Schmidt K, Viebahn C, Rohland N, Lux A, Schellhorn T, Holzer A, Jung JU, Neipel F
The Kaposi's Sarcoma-associated Herpesvirus-encoded vIRF-3 Inhibits Cellular IRF-5.
J Biol Chem 284: 8525-38 (2009)
PM ID: 19129183 PMC2659211
33: Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D
Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers.
Proc Natl Acad Sci U S A 106: 4828-33 (2009)
PM ID: 19261858 PMC2651202
34: Jiang X, Castelao JE, Groshen S, Cortessis VK, Shibata D, Conti DV, Yuan JM, Pike MC, Gago-Dominguez M
Urinary tract infections and reduced risk of bladder cancer in Los Angeles.
Br J Cancer 100: 834-9 (2009)
PM ID: 19174821 PMC2653778
35: Woo YJ, Siegmund KD, Tavaré S, Shibata D
Older individuals appear to acquire mitotically older colorectal cancers.
J Pathol 217: 483-8 (2009)
PM ID: 19165870
36: Rausch JW, Chelico L, Goodman MF, Le Grice SF
Dissecting APOBEC3G substrate specificity by nucleoside analog interference.
J Biol Chem 284: 7047-58 (2009)
PM ID: 19136562 PMC2652320
37: Chelico L, Pham P, Goodman MF
Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G.
Philos Trans R Soc Lond B Biol Sci 364: 583-93 (2009)
PM ID: 19022738 PMC2660917
38: Fujino Y, Liao CP, Zhao YS, Pan J, Mathes LE, Hayes KA, Ohno K, Tsujimoto H, Roy-Burman P
Identification of a novel common proviral integration site, flit-1, in feline leukemia virus induced thymic lymphoma.
Virology 386: 16-22 (2009)
PM ID: 19203775
39: Kondo Y, Machida K, Liu HM, Ueno Y, Kobayashi K, Wakita T, Shimosegawa T, Lai MM
Hepatitis C virus infection of T cells inhibits proliferation and enhances fas-mediated apoptosis by down-regulating the expression of CD44 splicing variant 6.
J Infect Dis 199: 726-36 (2009)
PM ID: 19199548
40: Kraigsley AM, Finkel SE
Adaptive evolution in single species bacterial biofilms.
FEMS Microbiol Lett 293: 135-40 (2009)
PM ID: 19239496
41: Liu HM, Aizaki H, Choi KS, Machida K, Ou JJ, Lai MM
SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interacting protein) is a host factor involved in hepatitis C virus RNA replication.
Virology 386: 249-56 (2009)
PM ID: 19232660 PMC3099193 NIHMS296131
42: Shao C, Lacey M, Dubeau L, Ehrlich M
Hemimethylation footprints of DNA demethylation in cancer.
Epigenetics 4: 165-75 (2009)
PM ID: 19287214
43: Vardi-Kilshtain A, Roca M, Warshel A
The empirical valence bond as an effective strategy for computer-aided enzyme design.
Biotechnol J 4: 495-500 (2009)
PM ID: 19229886 PMC2671572 NIHMS96908
44: Roca M, Vardi-Kilshtain A, Warshel A
Toward accurate screening in computer-aided enzyme design.
Biochemistry 48: 3046-56 (2009)
PM ID: 19161327 PMC2832760 NIHMS91570
45: Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR
DNA binding site sequence directs glucocorticoid receptor structure and activity.
Science 324: 407-10 (2009)
PM ID: 19372434 PMC2777810 NIHMS153427
46: Indiani C, Langston LD, Yurieva O, Goodman MF, O'Donnell M
Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase.
Proc Natl Acad Sci U S A 106: 6031-8 (2009)
PM ID: 19279203 PMC2654394
47: Kobayashi H, Sugihara K, Uetake H, Higuchi T, Yasuno M, Enomoto M, Iida S, Lenz HJ, Danenberg KD, Danenberg PV
Messenger RNA expression of COX-2 and angiogenic factors in primary colorectal cancer and corresponding liver metastasis.
Int J Oncol 34: 1147-53 (2009)
PM ID: 19287974
48: Rohs R, West SM, Liu P, Honig B
Nuance in the double-helix and its role in protein-DNA recognition.
Curr Opin Struct Biol 19: 171-7 (2009)
PM ID: 19362815 PMC2701566
49: Knott SR, Viggiani CJ, Tavaré S, Aparicio OM
Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae.
Genes Dev 23: 1077-90 (2009)
PM ID: 19417103 PMC2682954
50: Singh N, Warshel A
Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects.
J Phys Chem B 113: 7372-82 (2009)
PM ID: 19402609 PMC2738853 NIHMS114340
51: Kamerlin SC, Haranczyk M, Warshel A
Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.
Chemphyschem 10: 1125-34 (2009)
PM ID: 19301306
52: Gack MU, Albrecht RA, Urano T, Inn KS, Huang IC, Carnero E, Farzan M, Inoue S, Jung JU, García-Sastre A
Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I.
Cell Host Microbe 5: 439-49 (2009)
PM ID: 19454348 PMC2737813 NIHMS119750
53: Evdokimova V, Tognon C, Ng T, Ruzanov P, Melnyk N, Fink D, Sorokin A, Ovchinnikov LP, Davicioni E, Triche TJ, Sorensen PH
Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition.
Cancer Cell 15: 402-15 (2009)
PM ID: 19411069
54: MacCarthy T, Kalis SL, Roa S, Pham P, Goodman MF, Scharff MD, Bergman A
V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment.
Proc Natl Acad Sci U S A 106: 8629-34 (2009)
PM ID: 19443686 PMC2682541
55: Chelico L, Pham P, Goodman MF
Mechanisms of APOBEC3G-catalyzed processive deamination of deoxycytidine on single-stranded DNA.
Nat Struct Mol Biol 16: 454-5; author reply 455-6 (2009)
PM ID: 19421154 PMC2764237 NIHMS141527
56: Upton TG, Kashemirov BA, McKenna CE, Goodman MF, Prakash GK, Kultyshev R, Batra VK, Shock DD, Pedersen LC, Beard WA, Wilson SH
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function.
Org Lett 11: 1883-6 (2009)
PM ID: 19351147 PMC2722935 NIHMS108641
57: Wei M, Fabrizio P, Madia F, Hu J, Ge H, Li LM, Longo VD
Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension.
PLoS Genet 5: e1000467 (2009)
PM ID: 19424415 PMC2669710
58: Liu H, Shi Y, Chen XS, Warshel A
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.
Proc Natl Acad Sci U S A 106: 7449-54 (2009)
PM ID: 19383795 PMC2678657
59: Oh DS, DeMeester SR, Dunst CM, Mori R, Lehman BJ, Kuramochi H, Danenberg K, Danenberg P, Hagen JA, Chandrasoma P, DeMeester TR
Validation of a rodent model of Barrett's esophagus using quantitative gene expression profiling.
Surg Endosc 23: 1346-52 (2009)
PM ID: 18813976
60: Biffinger JC, Ray R, Little BJ, Fitzgerald LA, Ribbens M, Finkel SE, Ringeisen BR
Simultaneous analysis of physiological and electrical output changes in an operating microbial fuel cell with Shewanella oneidensis.
Biotechnol Bioeng 103: 524-31 (2009)
PM ID: 19189395
61: Palchevskiy V, Finkel SE
A role for single-stranded exonucleases in the use of DNA as a nutrient.
J Bacteriol 191: 3712-6 (2009)
PM ID: 19329645 PMC2681894
62: Roy D, Lieber MR
G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter.
Mol Cell Biol 29: 3124-33 (2009)
PM ID: 19307304 PMC2682002
63: Shimazaki N, Tsai AG, Lieber MR
H3K4me3 stimulates the V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in cis: implications for translocations.
Mol Cell 34: 535-44 (2009)
PM ID: 19524534 PMC2920491 NIHMS226375
64: Reinen J, Okun J, Rabinowitz D, Rybak D, Stadheim L, Shah V, Wiesner R, Faulk D, Bynon JS, Eckhoff D, Singh H, Tanikella R, Perry T, Forman L, Nielsen C, Shrestha R, Ahya V, Michael M, Palevsky H, Reddy R, Kaplowitz N, Roberts KE, Fallon MB, Krowka MJ, Benza RL, Knowles JA, Badesch DB, Brown RS, Taichman DB, Trotter J, Zacks S, Horn EM, Kawut SM, Pulmonary Vascular Complications of Liver Disease Study Group
Serotonin transporter polymorphisms in patients with portopulmonary hypertension.
Chest 135: 1470-5 (2009)
PM ID: 19141529 PMC2716711
65: Kamerlin SC, McKenna CE, Goodman MF, Goondman MF, Warshel A
A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.
Biochemistry 48: 5963-71 (2009)
PM ID: 19391628 PMC2775081 NIHMS152678
66: Kotoglou P, Kalaitzakis A, Vezyraki P, Tzavaras T, Michalis LK, Dantzer F, Jung JU, Angelidis C
Hsp70 translocates to the nuclei and nucleoli, binds to XRCC1 and PARP-1, and protects HeLa cells from single-strand DNA breaks.
Cell Stress Chaperones 14: 391-406 (2009)
PM ID: 19089598 PMC2728274
67: Lee HR, Toth Z, Shin YC, Lee JS, Chang H, Gu W, Oh TK, Kim MH, Jung JU
Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 targets MDM2 to deregulate the p53 tumor suppressor pathway.
J Virol 83: 6739-47 (2009)
PM ID: 19369353 PMC2698538
68: Sucov HM, Gu Y, Thomas S, Li P, Pashmforoush M
Epicardial control of myocardial proliferation and morphogenesis.
Pediatr Cardiol 30: 617-25 (2009)
PM ID: 19277768
69: Siegmund KD, Marjoram P, Tavaré S, Shibata D
Many colorectal cancers are "flat" clonal expansions.
Cell Cycle 8: 2187-93 (2009)
PM ID: 19556889
70: Kim H, Heo K, Kim JH, Kim K, Choi J, An W
Requirement of histone methyltransferase SMYD3 for estrogen receptor-mediated transcription.
J Biol Chem 284: 19867-77 (2009)
PM ID: 19509295 PMC2740412
71: Tiemann-Boege I, Curtis C, Shinde DN, Goodman DB, Tavaré S, Arnheim N
Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel.
Anal Chem 81: 5770-6 (2009)
PM ID: 19601653 PMC2733210 NIHMS124813
72: Yoon SR, Qin J, Glaser RL, Jabs EW, Wexler NS, Sokol R, Arnheim N, Calabrese P
The ups and downs of mutation frequencies during aging can account for the Apert syndrome paternal age effect.
PLoS Genet 5: e1000558 (2009)
PM ID: 19593369 PMC2700275
73: Arnheim N, Calabrese P
Understanding what determines the frequency and pattern of human germline mutations.
Nat Rev Genet 10: 478-88 (2009)
PM ID: 19488047 PMC2744436 NIHMS135635
74: Jiang Q, Karata K, Woodgate R, Cox MM, Goodman MF
The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP.
Nature 460: 359-63 (2009)
PM ID: 19606142 PMC2731490 NIHMS133217
75: Knott SR, Viggiani CJ, Aparicio OM
To promote and protect: coordinating DNA replication and transcription for genome stability.
Epigenetics 4: 362-5 (2009)
PM ID: 19736523
76: Kamerlin SC, Cao J, Rosta E, Warshel A
On unjustifiably misrepresenting the EVB approach while simultaneously adopting it.
J Phys Chem B 113: 10905-15 (2009)
PM ID: 19606825 PMC2736350 NIHMS125551
77: Madia F, Wei M, Yuan V, Hu J, Gattazzo C, Pham P, Goodman MF, Longo VD
Oncogene homologue Sch9 promotes age-dependent mutations by a superoxide and Rev1/Polzeta-dependent mechanism.
J Cell Biol 186: 509-23 (2009)
PM ID: 19687253 PMC2733759
78: Hoffmann AC, Hoffman AC, Danenberg KD, Taubert H, Danenberg PV, Wuerl P
A three-gene signature for outcome in soft tissue sarcoma.
Clin Cancer Res 15: 5191-8 (2009)
PM ID: 19671876
79: Klemm L, Duy C, Iacobucci I, Kuchen S, von Levetzow G, Feldhahn N, Henke N, Li Z, Hoffmann TK, Kim YM, Hofmann WK, Jumaa H, Groffen J, Heisterkamp N, Martinelli G, Lieber MR, Casellas R, Müschen M
The B cell mutator AID promotes B lymphoid blast crisis and drug resistance in chronic myeloid leukemia.
Cancer Cell 16: 232-45 (2009)
PM ID: 19732723 PMC2931825 NIHMS138671
80: Sutch BT, Chambers EJ, Bayramyan MZ, Gallaher TK, Haworth IS
Similarity of protein-RNA interfaces based on motif analysis.
J Chem Inf Model 49: 2139-46 (2009)
PM ID: 19731952
81: Dhillon N, Raab J, Guzzo J, Szyjka SJ, Gangadharan S, Aparicio OM, Andrews B, Kamakaka RT
DNA polymerase epsilon, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator.
EMBO J 28: 2583-600 (2009)
PM ID: 19629037 PMC2738695
82: Lee HR, Kim MH, Lee JS, Liang C, Jung JU
Viral interferon regulatory factors.
J Interferon Cytokine Res 29: 621-7 (2009)
PM ID: 19715458 PMC2956608
83: Xu L, Haworth IS, Kulkarni AA, Bolger MB, Davies DL
Mutagenesis and cysteine scanning of transmembrane domain 10 of the human dipeptide transporter.
Pharm Res 26: 2358-66 (2009)
PM ID: 19685173 PMC2861424 NIHMS155693
84: Pisliakov AV, Cao J, Kamerlin SC, Warshel A
Enzyme millisecond conformational dynamics do not catalyze the chemical step.
Proc Natl Acad Sci U S A 106: 17359-64 (2009)
PM ID: 19805169 PMC2762662
85: Choi J, Heo K, An W
Cooperative action of TIP48 and TIP49 in H2A.Z exchange catalyzed by acetylation of nucleosomal H2A.
Nucleic Acids Res 37: 5993-6007 (2009)
PM ID: 19696079 PMC2764430
86: Stroud JC, Oltman A, Han A, Bates DL, Chen L
Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR.
J Mol Biol 393: 98-112 (2009)
PM ID: 19683540 PMC2753696 NIHMS139292
87: E X, Hwang S, Oh S, Lee JS, Jeong JH, Gwack Y, Kowalik TF, Sun R, Jung JU, Liang C
Viral Bcl-2-mediated evasion of autophagy aids chronic infection of gammaherpesvirus 68.
PLoS Pathog 5: e1000609 (2009)
PM ID: 19816569 PMC2752191
88: Chang H, Wachtman LM, Pearson CB, Lee JS, Lee HR, Lee SH, Vieira J, Mansfield KG, Jung JU
Non-human primate model of Kaposi's sarcoma-associated herpesvirus infection.
PLoS Pathog 5: e1000606 (2009)
PM ID: 19798430 PMC2745662
89: Chelico L, Pham P, Petruska J, Goodman MF
Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G.
J Biol Chem 284: 27761-5 (2009)
PM ID: 19684020 PMC2788826
90: Landsberg D, Gill J, Shapiro RJ, Günther OP, Balshaw RF, Scherer A, Hollander Z, Mui A, Triche TJ, Freue GC, Li G, Ng RT, Wilson-McManus J, McMaster WR, McManus BM, Keown PA, Biomarkers in Transplantation Team
Functional genomic analysis of peripheral blood during early acute renal allograft rejection.
Transplantation 88: 942-51 (2009)
PM ID: 19935467
91: Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B
The role of DNA shape in protein-DNA recognition.
Nature 461: 1248-53 (2009)
PM ID: 19865164 PMC2793086 NIHMS143859
92: Kilshtain AV, Warshel A
On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes.
Proteins 77: 536-50 (2009)
PM ID: 19480013 PMC2767396 NIHMS130536
93: Widschwendter M, Apostolidou S, Jones AA, Fourkala EO, Arora R, Pearce CL, Frasco MA, Ayhan A, Zikan M, Cibula D, Iyibozkurt CA, Yavuz E, Hauser-Kronberger C, Dubeau L, Menon U, Jacobs IJ
HOXA methylation in normal endometrium from premenopausal women is associated with the presence of ovarian cancer: a proof of principle study.
Int J Cancer 125: 2214-8 (2009)
PM ID: 19621443
94: Lee JS, Li Q, Lee JY, Lee SH, Jeong JH, Lee HR, Chang H, Zhou FC, Gao SJ, Liang C, Jung JU
FLIP-mediated autophagy regulation in cell death control.
Nat Cell Biol 11: 1355-62 (2009)
PM ID: 19838173 PMC2802862 NIHMS165792
95: Xu TX, Sotnikova TD, Liang C, Zhang J, Jung JU, Spealman RD, Gainetdinov RR, Yao WD
Hyperdopaminergic tone erodes prefrontal long-term potential via a D2 receptor-operated protein phosphatase gate.
J Neurosci 29: 14086-99 (2009)
PM ID: 19906957 PMC2818669 NIHMS163955
96: Hu K, Lee C, Qiu D, Fotovati A, Davies A, Abu-Ali S, Wai D, Lawlor ER, Triche TJ, Pallen CJ, Dunn SE
Small interfering RNA library screen of human kinases and phosphatases identifies polo-like kinase 1 as a promising new target for the treatment of pediatric rhabdomyosarcomas.
Mol Cancer Ther 8: 3024-35 (2009)
PM ID: 19887553 PMC2783569 NIHMS150149
97: Kamerlin SC, Warshel A
On the energetics of ATP hydrolysis in solution.
J Phys Chem B 113: 15692-8 (2009)
PM ID: 19888735
98: Vicatos S, Roca M, Warshel A
Effective approach for calculations of absolute stability of proteins using focused dielectric constants.
Proteins 77: 670-84 (2009)
PM ID: 19856460
99: Waskar M, Landis GN, Shen J, Curtis C, Tozer K, Abdueva D, Skvortsov D, Tavaré S, Tower J
Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy.
Aging (Albany NY) 1: 903-36 (2009)
PM ID: 20157574 PMC2815744
100: Sumiyoshi T, Holt NG, Hollis RP, Ge S, Cannon PM, Crooks GM, Kohn DB
Stable transgene expression in primitive human CD34+ hematopoietic stem/progenitor cells, using the Sleeping Beauty transposon system.
Hum Gene Ther 20: 1607-26 (2009)
PM ID: 19689196
101: Machida K, Liu JC, McNamara G, Levine A, Duan L, Lai MM
Hepatitis C virus causes uncoupling of mitotic checkpoint and chromosomal polyploidy through the Rb pathway.
J Virol 83: 12590-600 (2009)
PM ID: 19793824 PMC2786750
102: Safdie FM, Dorff T, Quinn D, Fontana L, Wei M, Lee C, Cohen P, Longo VD
Fasting and cancer treatment in humans: A case series report.
Aging (Albany NY) 1: 988-1007 (2009)
PM ID: 20157582 PMC2815756
103: Calabrese P, Shibata D
A simple algebraic cancer equation: calculating how cancers may arise with normal mutation rates.
BMC Cancer 10: 3 (2010)
PM ID: 20051132 PMC2829925
104: Lieber MR, Gu J, Lu H, Shimazaki N, Tsai AG
Nonhomologous DNA end joining (NHEJ) and chromosomal translocations in humans.
Subcell Biochem 50: 279-96 (2010)
PM ID: 20012587 PMC3079314 NIHMS263118
105: Lieber MR
The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway.
Annu Rev Biochem 79: 181-211 (2010)
PM ID: 20192759 PMC3079308 NIHMS263377
106: Tsai AG, Lieber MR
Mechanisms of chromosomal rearrangement in the human genome.
BMC Genomics 11 Suppl 1: S1 (2010)
PM ID: 20158866 PMC2822523
107: Yang SJ, Lopez LA, Hauser H, Exline CM, Haworth KG, Cannon PM
Anti-tetherin activities in Vpu-expressing primate lentiviruses.
Retrovirology 7: 13 (2010)
PM ID: 20167081 PMC2831821
108: Christodoulopoulos I, Droniou-Bonzom ME, Oldenburg JE, Cannon PM
Vpu-dependent block to incorporation of GaLV Env into lentiviral vectors.
Retrovirology 7: 4 (2010)
PM ID: 20102634 PMC2831008
109: Nugent RL, Johnsson A, Fleharty B, Gogol M, Xue-Franzén Y, Seidel C, Wright AP, Forsburg SL
Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation.
BMC Genomics 11: 59 (2010)
PM ID: 20096118 PMC2823694
110: Parrella E, Longo VD
Insulin/IGF-I and related signaling pathways regulate aging in nondividing cells: from yeast to the mammalian brain.
ScientificWorldJournal 10: 161-77 (2010)
PM ID: 20098959
111: Hauser H, Lopez LA, Yang SJ, Oldenburg JE, Exline CM, Guatelli JC, Cannon PM
HIV-1 Vpu and HIV-2 Env counteract BST-2/tetherin by sequestration in a perinuclear compartment.
Retrovirology 7: 51 (2010)
PM ID: 20529266 PMC2890665
112: Jiang X, Gwye Y, Russell D, Cao C, Douglas D, Hung L, Kovar H, Triche TJ, Lawlor ER
CD133 expression in chemo-resistant Ewing sarcoma cells.
BMC Cancer 10: 116 (2010)
PM ID: 20346143 PMC2851692
113: Hong YJ, Marjoram P, Shibata D, Siegmund KD
Using DNA methylation patterns to infer tumor ancestry.
PLoS One 5: e12002 (2010)
PM ID: 20711251 PMC2918495
114: Toth Z, Maglinte DT, Lee SH, Lee HR, Wong LY, Brulois KF, Lee S, Buckley JD, Laird PW, Marquez VE, Jung JU
Epigenetic analysis of KSHV latent and lytic genomes.
PLoS Pathog 6: e1001013 (2010)
PM ID: 20661424 PMC2908616
115: Watkins PA, Moser AB, Toomer CB, Steinberg SJ, Moser HW, Karaman MW, Ramaswamy K, Siegmund KD, Lee DR, Ely JJ, Ryder OA, Hacia JG
Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions.
BMC Physiol 10: 19 (2010)
PM ID: 20932325 PMC2964658
116: Brewster AS, Slaymaker IM, Afif SA, Chen XS
Mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and DNA binding.
BMC Mol Biol 11: 62 (2010)
PM ID: 20716382 PMC2933578
117: Kapranov P, St Laurent G, Raz T, Ozsolak F, Reynolds CP, Sorensen PH, Reaman G, Milos P, Arceci RJ, Thompson JF, Triche TJ
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA.
BMC Biol 8: 149 (2010)
PM ID: 21176148 PMC3022773
118: Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS
Origins of specificity in protein-DNA recognition.
Annu Rev Biochem 79: 233-69 (2010)
PM ID: 20334529 PMC3285485 NIHMS355508
119: Roy D, Zhang Z, Lu Z, Hsieh CL, Lieber MR
Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site.
Mol Cell Biol 30: 146-59 (2010)
PM ID: 19841062 PMC2798282
120: Ge H, Wei M, Fabrizio P, Hu J, Cheng C, Longo VD, Li LM
Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant.
Nucleic Acids Res 38: 143-58 (2010)
PM ID: 19880387 PMC2800218
121: Martin VK, Droniou-Bonzom ME, Reignier T, Oldenburg JE, Cox AU, Cannon PM
Investigation of clade B New World arenavirus tropism by using chimeric GP1 proteins.
J Virol 84: 1176-82 (2010)
PM ID: 19889757 PMC2798354
122: Liu R, Li X, Tulpule A, Zhou Y, Scehnet JS, Zhang S, Lee JS, Chaudhary PM, Jung J, Gill PS
KSHV-induced notch components render endothelial and mural cell characteristics and cell survival.
Blood 115: 887-95 (2010)
PM ID: 19965636 PMC2815507
123: Wolkenhauer O, Auffray C, Baltrusch S, Blüthgen N, Byrne H, Cascante M, Ciliberto A, Dale T, Drasdo D, Fell D, Ferrell JE, Gallahan D, Gatenby R, Günther U, Harms BD, Herzel H, Junghanss C, Kunz M, van Leeuwen I, Lenormand P, Levi F, Linnebacher M, Lowengrub J, Maini PK, Malik A, Rateitschak K, Sansom O, Schäfer R, Schürrle K, Sers C, Schnell S, Shibata D, Tyson J, Vera J, White M, Zhivotovsky B, Jaster R
Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.
Cancer Res 70: 12-3 (2010)
PM ID: 20028868 PMC2802734
124: Sir D, Ou JH
Autophagy in viral replication and pathogenesis.
Mol Cells 29: 1-7 (2010)
PM ID: 20077024 PMC3115743 NIHMS295695
125: Hong H, Yen HY, Brockmeyer A, Liu Y, Chodankar R, Pike MC, Stanczyk FZ, Maxson R, Dubeau L
Changes in the mouse estrus cycle in response to BRCA1 inactivation suggest a potential link between risk factors for familial and sporadic ovarian cancer.
Cancer Res 70: 221-8 (2010)
PM ID: 20028858 PMC2805040 NIHMS157376
126: Oh S, E X, Hwang S, Liang C
Autophagy evasion in herpesviral latency.
Autophagy 6: 151-2 (2010)
PM ID: 19923915 PMC2847627 NIHMS188706
127: Bertram JG, Oertell K, Petruska J, Goodman MF
DNA polymerase fidelity: comparing direct competition of right and wrong dNTP substrates with steady state and pre-steady state kinetics.
Biochemistry 49: 20-8 (2010)
PM ID: 20000359 PMC2803633 NIHMS164418
128: Rucker R, Oelschlaeger P, Warshel A
A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.
Proteins 78: 671-80 (2010)
PM ID: 19842163 PMC2966340 NIHMS143734
129: Lim M, Zhong C, Yang S, Bell AM, Cohen MB, Roy-Burman P
Runx2 regulates survivin expression in prostate cancer cells.
Lab Invest 90: 222-33 (2010)
PM ID: 19949374 PMC2815261 NIHMS145799
130: Viggiani CJ, Knott SR, Aparicio OM
Genome-wide analysis of DNA synthesis by BrdU immunoprecipitation on tiling microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae.
Cold Spring Harb Protoc 2010: pdb.prot5385 (2010)
PM ID: 20150148
131: Chen Y, Dey R, Chen L
Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.
Structure 18: 246-56 (2010)
PM ID: 20159469 PMC2824536 NIHMS169893
132: Chen L
In pursuit of the high-resolution structure of nicotinic acetylcholine receptors.
J Physiol 588: 557-64 (2010)
PM ID: 19995851 PMC2828130
133: Lee C, Safdie FM, Raffaghello L, Wei M, Madia F, Parrella E, Hwang D, Cohen P, Bianchi G, Longo VD
Reduced levels of IGF-I mediate differential protection of normal and cancer cells in response to fasting and improve chemotherapeutic index.
Cancer Res 70: 1564-72 (2010)
PM ID: 20145127 PMC2836202 NIHMS167060
134: Longo VD, Fontana L
Calorie restriction and cancer prevention: metabolic and molecular mechanisms.
Trends Pharmacol Sci 31: 89-98 (2010)
PM ID: 20097433 PMC2829867 NIHMS173014
135: Punj V, Matta H, Chaudhary PM
X-linked ectodermal dysplasia receptor is downregulated in breast cancer via promoter methylation.
Clin Cancer Res 16: 1140-8 (2010)
PM ID: 20145163 PMC2822888 NIHMS166027
136: Wang M, Ye R, Barron E, Baumeister P, Mao C, Luo S, Fu Y, Luo B, Dubeau L, Hinton DR, Lee AS
Essential role of the unfolded protein response regulator GRP78/BiP in protection from neuronal apoptosis.
Cell Death Differ 17: 488-98 (2010)
PM ID: 19816510 PMC2822118 NIHMS143864
137: Jiang M, Fernandez S, Jerome WG, He Y, Yu X, Cai H, Boone B, Yi Y, Magnuson MA, Roy-Burman P, Matusik RJ, Shappell SB, Hayward SW
Disruption of PPARgamma signaling results in mouse prostatic intraepithelial neoplasia involving active autophagy.
Cell Death Differ 17: 469-81 (2010)
PM ID: 19834493 PMC2821953 NIHMS143868
138: Wang A, Alimova IN, Luo P, Jong A, Triche TJ, Wu L
Loss of CAK phosphorylation of RAR{alpha} mediates transcriptional control of retinoid-induced cancer cell differentiation.
FASEB J 24: 833-43 (2010)
PM ID: 19917671 PMC2830139
139: Wang XM, Greiner TC, Bibikova M, Pike BL, Siegmund KD, Sinha UK, Müschen M, Jaeger EB, Weisenburger DD, Chan WC, Shibata D, Fan JB, Hacia JG
Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations.
J Cell Biochem 109: 818-27 (2010)
PM ID: 20069569 PMC3122883 NIHMS305118
140: Sir D, Tian Y, Chen WL, Ann DK, Yen TS, Ou JH
The early autophagic pathway is activated by hepatitis B virus and required for viral DNA replication.
Proc Natl Acad Sci U S A 107: 4383-8 (2010)
PM ID: 20142477 PMC2840127
141: Naik AK, Lieber MR, Raghavan SC
Cytosines, but not purines, determine recombination activating gene (RAG)-induced breaks on heteroduplex DNA structures: implications for genomic instability.
J Biol Chem 285: 7587-97 (2010)
PM ID: 20051517 PMC2844206
142: Kamerlin SC, Sharma PK, Chu ZT, Warshel A
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization.
Proc Natl Acad Sci U S A 107: 4075-80 (2010)
PM ID: 20150513 PMC2840163
143: Lucas TM, Lyddon TD, Cannon PM, Johnson MC
Pseudotyping incompatibility between HIV-1 and gibbon ape leukemia virus Env is modulated by Vpu.
J Virol 84: 2666-74 (2010)
PM ID: 20042505 PMC2826068
144: Wu Y, Dey R, Han A, Jayathilaka N, Philips M, Ye J, Chen L
Structure of the MADS-box/MEF2 domain of MEF2A bound to DNA and its implication for myocardin recruitment.
J Mol Biol 397: 520-33 (2010)
PM ID: 20132824 PMC2952653 NIHMS176218
145: Wu CC, Asgharzadeh S, Triche TJ, D'Argenio DZ
Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning.
Bioinformatics 26: 807-13 (2010)
PM ID: 20134029 PMC2832827
146: Davicioni E, Anderson JR, Buckley JD, Meyer WH, Triche TJ
Gene expression profiling for survival prediction in pediatric rhabdomyosarcomas: a report from the children's oncology group.
J Clin Oncol 28: 1240-6 (2010)
PM ID: 20124188 PMC3040045
147: Punj V, Matta H, Schamus S, Tamewitz A, Anyang B, Chaudhary PM
Kaposi's sarcoma-associated herpesvirus-encoded viral FLICE inhibitory protein (vFLIP) K13 suppresses CXCR4 expression by upregulating miR-146a.
Oncogene 29: 1835-44 (2010)
PM ID: 20023696 PMC2845732 NIHMS159454
148: Grimminger PP, Schneider PM, Metzger R, Vallböhmer D, Danenberg KD, Danenberg PV, Hölscher AH, Brabender J
Ornithine decarboxylase mRNA expression in curatively resected non-small-cell lung cancer.
Clin Lung Cancer 11: 114-9 (2010)
PM ID: 20199977
149: Kuramochi H, Hayashi K, Nakajima G, Kamikozuru H, Yamamoto M, Danenberg KD, Danenberg PV
Epidermal growth factor receptor (EGFR) mRNA levels and protein expression levels in primary colorectal cancer and corresponding liver metastases.
Cancer Chemother Pharmacol 65: 825-31 (2010)
PM ID: 19701635
150: Gu J, Li S, Zhang X, Wang LC, Niewolik D, Schwarz K, Legerski RJ, Zandi E, Lieber MR
DNA-PKcs regulates a single-stranded DNA endonuclease activity of Artemis.
DNA Repair (Amst) 9: 429-37 (2010)
PM ID: 20117966 PMC2847011 NIHMS171326
151: Gack MU, Nistal-Villán E, Inn KS, García-Sastre A, Jung JU
Phosphorylation-mediated negative regulation of RIG-I antiviral activity.
J Virol 84: 3220-9 (2010)
PM ID: 20071582 PMC2838087
152: Liang C, Jung JU
Autophagy genes as tumor suppressors.
Curr Opin Cell Biol 22: 226-33 (2010)
PM ID: 19945837 PMC2854193 NIHMS159173
153: van Doorninck JA, Ji L, Schaub B, Shimada H, Wing MR, Krailo MD, Lessnick SL, Marina N, Triche TJ, Sposto R, Womer RB, Lawlor ER
Current treatment protocols have eliminated the prognostic advantage of type 1 fusions in Ewing sarcoma: a report from the Children's Oncology Group.
J Clin Oncol 28: 1989-94 (2010)
PM ID: 20308669 PMC2860404
154: Tsai AG, Lu Z, Lieber MR
The t(14;18)(q32;q21)/IGH-MALT1 translocation in MALT lymphomas is a CpG-type translocation, but the t(11;18)(q21;q21)/API2-MALT1 translocation in MALT lymphomas is not.
Blood 115: 3640-1; author reply 3641-2 (2010)
PM ID: 20430965 PMC2867271
155: Lieber MR
NHEJ and its backup pathways in chromosomal translocations.
Nat Struct Mol Biol 17: 393-5 (2010)
PM ID: 20368722 PMC3074614 NIHMS263440
156: Messer BM, Roca M, Chu ZT, Vicatos S, Kilshtain AV, Warshel A
Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.
Proteins 78: 1212-27 (2010)
PM ID: 20052756 PMC2822134 NIHMS159971
157: Cuesta I, Núñez-Ramírez R, Scheres SH, Gai D, Chen XS, Fanning E, Carazo JM
Conformational rearrangements of SV40 large T antigen during early replication events.
J Mol Biol 397: 1276-86 (2010)
PM ID: 20219473 PMC2862297 NIHMS190866
158: Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.
Nat Struct Mol Biol 17: 423-9 (2010)
PM ID: 20364130 PMC3280089 NIHMS299653
159: Singh N, Warshel A
Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions.
Proteins 78: 1705-23 (2010)
PM ID: 20186976 PMC2868600 NIHMS188138
160: Singh N, Warshel A
A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes.
Proteins 78: 1724-35 (2010)
PM ID: 20186973 PMC3064472 NIHMS281237
161: Kamerlin SC, Warshel A
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
Proteins 78: 1339-75 (2010)
PM ID: 20099310 PMC2841229 NIHMS161376
162: Dolan WP, Le AH, Schmidt H, Yuan JP, Green M, Forsburg SL
Fission yeast Hsk1 (Cdc7) kinase is required after replication initiation for induced mutagenesis and proper response to DNA alkylation damage.
Genetics 185: 39-53 (2010)
PM ID: 20176980 PMC2870973
163: McKenna CE, Kashemirov BA, Peterson LW, Goodman MF
Modifications to the dNTP triphosphate moiety: from mechanistic probes for DNA polymerases to antiviral and anti-cancer drug design.
Biochim Biophys Acta 1804: 1223-30 (2010)
PM ID: 20079885
164: Romero RM, Eriksen SP, Haworth IS
Quantitative assessment of assisted problem-based learning in a pharmaceutics course.
Am J Pharm Educ 74: 66 (2010)
PM ID: 20585427 PMC2879117
165: Wu MH, Ma WL, Hsu CL, Chen YL, Ou JH, Ryan CK, Hung YC, Yeh S, Chang C
Androgen receptor promotes hepatitis B virus-induced hepatocarcinogenesis through modulation of hepatitis B virus RNA transcription.
Sci Transl Med 2: 32ra35 (2010)
PM ID: 20484730 PMC3032595 NIHMS265454
166: Sir D, Ann DK, Ou JH
Autophagy by hepatitis B virus and for hepatitis B virus.
Autophagy 6: 548-9 (2010)
PM ID: 20305390
167: Christensen GB, Baffoe-Bonnie AB, George A, Powell I, Bailey-Wilson JE, Carpten JD, Giles GG, Hopper JL, Severi G, English DR, Foulkes WD, Maehle L, Moller P, Eeles R, Easton D, Badzioch MD, Whittemore AS, Oakley-Girvan I, Hsieh CL, Dimitrov L, Xu J, Stanford JL, Johanneson B, Deutsch K, McIntosh L, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Isaacs WB, Thibodeau SN, McDonnell SK, Hebbring S, Schaid DJ, Lange EM, Cooney KA, Tammela TL, Schleutker J, Paiss T, Maier C, Grönberg H, Wiklund F, Emanuelsson M, Farnham JM, Cannon-Albright LA, Camp NJ, International Consortium for Prostate Cancer Genetics
Genome-wide linkage analysis of 1,233 prostate cancer pedigrees from the International Consortium for Prostate Cancer Genetics using novel sumLINK and sumLOD analyses.
Prostate 70: 735-44 (2010)
PM ID: 20333727 PMC3428045 NIHMS398194
168: Luo P, Yang X, Ying M, Chaudhry P, Wang A, Shimada H, May WA, Adams GB, Mock D, Triche TJ, He Q, Wu L
Retinoid-suppressed phosphorylation of RARalpha mediates the differentiation pathway of osteosarcoma cells.
Oncogene 29: 2772-83 (2010)
PM ID: 20190807
169: Chelico L, Prochnow C, Erie DA, Chen XS, Goodman MF
Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G.
J Biol Chem 285: 16195-205 (2010)
PM ID: 20212048 PMC2871487
170: Kang HG, Jenabi JM, Liu XF, Reynolds CP, Triche TJ, Sorensen PH
Inhibition of the insulin-like growth factor I receptor by epigallocatechin gallate blocks proliferation and induces the death of Ewing tumor cells.
Mol Cancer Ther 9: 1396-407 (2010)
PM ID: 20423994
171: Wu AH, Siegmund KD, Long TI, Cozen W, Wan P, Tseng CC, Shibata D, Laird PW
Hormone therapy, DNA methylation and colon cancer.
Carcinogenesis 31: 1060-7 (2010)
PM ID: 20064828 PMC2878358
172: Jao CC, Hegde BG, Gallop JL, Hegde PB, McMahon HT, Haworth IS, Langen R
Roles of amphipathic helices and the bin/amphiphysin/rvs (BAR) domain of endophilin in membrane curvature generation.
J Biol Chem 285: 20164-70 (2010)
PM ID: 20418375 PMC2888429
173: Okitsu CY, Hsieh JC, Hsieh CL
Transcriptional activity affects the H3K4me3 level and distribution in the coding region.
Mol Cell Biol 30: 2933-46 (2010)
PM ID: 20404096 PMC2876678
174: Brewster AS, Chen XS
Insights into the MCM functional mechanism: lessons learned from the archaeal MCM complex.
Crit Rev Biochem Mol Biol 45: 243-56 (2010)
PM ID: 20441442 PMC2953368 NIHMS194950
175: Nistal-Villán E, Gack MU, Martínez-Delgado G, Maharaj NP, Inn KS, Yang H, Wang R, Aggarwal AK, Jung JU, García-Sastre A
Negative role of RIG-I serine 8 phosphorylation in the regulation of interferon-beta production.
J Biol Chem 285: 20252-61 (2010)
PM ID: 20406818 PMC2888438
176: Tolstov YL, Arora R, Scudiere SC, Busam K, Chaudhary PM, Chang Y, Moore PS
Lack of evidence for direct involvement of Merkel cell polyomavirus (MCV) in chronic lymphocytic leukemia (CLL).
Blood 115: 4973-4 (2010)
PM ID: 20538816 PMC2890166
177: Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues.
J Am Chem Soc 132: 7617-25 (2010)
PM ID: 20465217 PMC2891752 NIHMS204944
178: Patel M, Jiang Q, Woodgate R, Cox MM, Goodman MF
A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V.
Crit Rev Biochem Mol Biol 45: 171-84 (2010)
PM ID: 20441441 PMC2874081 NIHMS191044
179: West SM, Rohs R, Mann RS, Honig B
Electrostatic interactions between arginines and the minor groove in the nucleosome.
J Biomol Struct Dyn 27: 861-6 (2010)
PM ID: 20232938 PMC2946858 NIHMS232253
180: Liu R, Gong M, Li X, Zhou Y, Gao W, Tulpule A, Chaudhary PM, Jung J, Gill PS
Induction, regulation, and biologic function of Axl receptor tyrosine kinase in Kaposi sarcoma.
Blood 116: 297-305 (2010)
PM ID: 20442363 PMC2910613
181: Kamerlin SC, Mavri J, Warshel A
Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues.
FEBS Lett 584: 2759-66 (2010)
PM ID: 20433839 PMC2886715 NIHMS200597
182: Lopez LA, Yang SJ, Hauser H, Exline CM, Haworth KG, Oldenburg J, Cannon PM
Ebola virus glycoprotein counteracts BST-2/Tetherin restriction in a sequence-independent manner that does not require tetherin surface removal.
J Virol 84: 7243-55 (2010)
PM ID: 20444895 PMC2898217
183: Abdueva D, Wing M, Schaub B, Triche T, Davicioni E
Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays.
J Mol Diagn 12: 409-17 (2010)
PM ID: 20522636 PMC2893624
184: Maeda K, Singh SK, Eda K, Kitabatake M, Pham P, Goodman MF, Sakaguchi N
GANP-mediated recruitment of activation-induced cytidine deaminase to cell nuclei and to immunoglobulin variable region DNA.
J Biol Chem 285: 23945-53 (2010)
PM ID: 20507984 PMC2911284
185: Michán S, Li Y, Chou MM, Parrella E, Ge H, Long JM, Allard JS, Lewis K, Miller M, Xu W, Mervis RF, Chen J, Guerin KI, Smith LE, McBurney MW, Sinclair DA, Baudry M, de Cabo R, Longo VD
SIRT1 is essential for normal cognitive function and synaptic plasticity.
J Neurosci 30: 9695-707 (2010)
PM ID: 20660252 PMC2921958 NIHMS223303
186: Fabrizio P, Hoon S, Shamalnasab M, Galbani A, Wei M, Giaever G, Nislow C, Longo VD
Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation.
PLoS Genet 6: e1001024 (2010)
PM ID: 20657825 PMC2904796
187: Holt N, Wang J, Kim K, Friedman G, Wang X, Taupin V, Crooks GM, Kohn DB, Gregory PD, Holmes MC, Cannon PM
Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo.
Nat Biotechnol 28: 839-47 (2010)
PM ID: 20601939 PMC3080757 NIHMS216984
188: Chen YC, Su WC, Huang JY, Chao TC, Jeng KS, Machida K, Lai MM
Polo-like kinase 1 is involved in hepatitis C virus replication by hyperphosphorylating NS5A.
J Virol 84: 7983-93 (2010)
PM ID: 20534861 PMC2916529
189: Shibata D, Lieber MR
Is there any genetic instability in human cancer?
DNA Repair (Amst) 9: 858; discussion 859-60 (2010)
PM ID: 20605538 PMC2914198 NIHMS206531
190: Machida K, Tsukamoto H, Liu JC, Han YP, Govindarajan S, Lai MM, Akira S, Ou JH
c-Jun mediates hepatitis C virus hepatocarcinogenesis through signal transducer and activator of transcription 3 and nitric oxide-dependent impairment of oxidative DNA repair.
Hepatology 52: 480-92 (2010)
PM ID: 20683948 PMC3107125 NIHMS295838
191: Reddy S, Li B, Comai L
Processing of human telomeres by the Werner syndrome protein.
Cell Cycle 9: 3137-8 (2010)
PM ID: 20814240 PMC3050012 NIHMS275746
192: Lieber MR, Wilson TE
SnapShot: Nonhomologous DNA end joining (NHEJ).
Cell 142: 496-496.e1 (2010)
PM ID: 20691907
193: Finch CE, Morgan TE, Longo VD, de Magalhaes JP
Cell resilience in species life spans: a link to inflammation?
Aging Cell 9: 519-26 (2010)
PM ID: 20415721 PMC2952360 NIHMS200282
194: Hoffmann AC, Wild P, Leicht C, Bertz S, Danenberg KD, Danenberg PV, Stöhr R, Stöckle M, Lehmann J, Schuler M, Hartmann A
MDR1 and ERCC1 expression predict outcome of patients with locally advanced bladder cancer receiving adjuvant chemotherapy.
Neoplasia 12: 628-36 (2010)
PM ID: 20689757 PMC2915407
195: Zhang Z, Sun E, Ou JH, Liang TJ
Inhibition of cellular proteasome activities mediates HBX-independent hepatitis B virus replication in vivo.
J Virol 84: 9326-31 (2010)
PM ID: 20592087 PMC2937595
196: Liao CP, Adisetiyo H, Liang M, Roy-Burman P
Cancer-associated fibroblasts enhance the gland-forming capability of prostate cancer stem cells.
Cancer Res 70: 7294-303 (2010)
PM ID: 20807814 PMC2940948 NIHMS226495
197: Tsai AG, Yoda A, Weinstock DM, Lieber MR
t(X;14)(p22;q32)/t(Y;14)(p11;q32) CRLF2-IGH translocations from human B-lineage ALLs involve CpG-type breaks at CRLF2, but CRLF2/P2RY8 intrachromosomal deletions do not.
Blood 116: 1993-4 (2010)
PM ID: 20847213
198: Frushicheva MP, Cao J, Chu ZT, Warshel A
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase.
Proc Natl Acad Sci U S A 107: 16869-74 (2010)
PM ID: 20829491 PMC2947920
199: Lee HR, Lee S, Chaudhary PM, Gill P, Jung JU
Immune evasion by Kaposi's sarcoma-associated herpesvirus.
Future Microbiol 5: 1349-65 (2010)
PM ID: 20860481 PMC3076960 NIHMS267783
200: Molyneux SD, Di Grappa MA, Beristain AG, McKee TD, Wai DH, Paderova J, Kashyap M, Hu P, Maiuri T, Narala SR, Stambolic V, Squire J, Penninger J, Sanchez O, Triche TJ, Wood GA, Kirschner LS, Khokha R
Prkar1a is an osteosarcoma tumor suppressor that defines a molecular subclass in mice.
J Clin Invest 120: 3310-25 (2010)
PM ID: 20697156 PMC2929719
201: Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.
Proc Natl Acad Sci U S A 107: 15693-8 (2010)
PM ID: 20724659 PMC2936638
202: Grimminger PP, Schneider PM, Metzger R, Vallböhmer D, Hölscher AH, Danenberg PV, Brabender J
Low thymidylate synthase, thymidine phosphorylase, and dihydropyrimidine dehydrogenase mRNA expression correlate with prolonged survival in resected non-small-cell lung cancer.
Clin Lung Cancer 11: 328-34 (2010)
PM ID: 20837458
203: Grimminger PP, Schneider PM, Metzger R, Vallböhmer D, Danenberg KD, Danenberg PV, Hölscher AH, Brabender J
The prognostic role of Bcl-2 mRNA expression in curatively resected non-small cell lung cancer (NSCLC).
Lung Cancer 70: 82-7 (2010)
PM ID: 20064672
204: Gonidakis S, Finkel SE, Longo VD
Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA.
Aging Cell 9: 868-81 (2010)
PM ID: 20707865 PMC2941539 NIHMS226667
205: Gonidakis S, Finkel SE, Longo VD
E. coli hypoxia-inducible factor ArcA mediates lifespan extension in a lipoic acid synthase mutant by suppressing acetyl-CoA synthetase.
Biol Chem 391: 1139-47 (2010)
PM ID: 20707605
206: Rychkova A, Vicatos S, Warshel A
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes.
Proc Natl Acad Sci U S A 107: 17598-603 (2010)
PM ID: 20876127 PMC2955132
207: Dryga A, Warshel A
Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules.
J Phys Chem B 114: 12720-8 (2010)
PM ID: 20836533 PMC2948080 NIHMS230420
208: Kamerlin SC, Chu ZT, Warshel A
On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models.
J Org Chem 75: 6391-401 (2010)
PM ID: 20825150 PMC2945449 NIHMS227935
209: Anderson JR, Barr FG, Hawkins DS, Parham DM, Skapek SX, Triche TJ
Fusion-negative alveolar rhabdomyosarcoma: modification of risk stratification is premature.
J Clin Oncol 28: e587-8; author reply e589-90 (2010)
PM ID: 20697086
210: Balasubramanian P, Longo VD
Linking Klotho, Nrf2, MAP kinases and aging.
Aging (Albany NY) 2: 632-3 (2010)
PM ID: 21076180 PMC2993790
211: Popova AM, Qin PZ
A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA.
Biophys J 99: 2180-9 (2010)
PM ID: 20923652 PMC3042557
212: Mori R, Dorff TB, Xiong S, Tarabolous CJ, Ye W, Groshen S, Danenberg KD, Danenberg PV, Pinski JK
The relationship between proangiogenic gene expression levels in prostate cancer and their prognostic value for clinical outcomes.
Prostate 70: 1692-700 (2010)
PM ID: 20564320
213: Potratz JC, Saunders DN, Wai DH, Ng TL, McKinney SE, Carboni JM, Gottardis MM, Triche TJ, Jürgens H, Pollak MN, Aparicio SA, Sorensen PH
Synthetic lethality screens reveal RPS6 and MST1R as modifiers of insulin-like growth factor-1 receptor inhibitor activity in childhood sarcomas.
Cancer Res 70: 8770-81 (2010)
PM ID: 20959493
214: Raffaghello L, Safdie F, Bianchi G, Dorff T, Fontana L, Longo VD
Fasting and differential chemotherapy protection in patients.
Cell Cycle 9: 4474-6 (2010)
PM ID: 21088487 PMC3048045
215: Longo VD, Nislow C, Fabrizio P
Endosomal protein sorting and autophagy genes contribute to the regulation of yeast life span.
Autophagy 6: 1227-8 (2010)
PM ID: 20953148
216: Ahmad A, Groshong JS, Matta H, Schamus S, Punj V, Robinson LJ, Gill PS, Chaudhary PM
Kaposi sarcoma-associated herpesvirus-encoded viral FLICE inhibitory protein (vFLIP) K13 cooperates with Myc to promote lymphoma in mice.
Cancer Biol Ther 10: 1033-40 (2010)
PM ID: 20818173 PMC3047095
217: Lai CK, Jeng KS, Machida K, Lai MM
Hepatitis C virus egress and release depend on endosomal trafficking of core protein.
J Virol 84: 11590-8 (2010)
PM ID: 20739534 PMC2953145
218: Machida K, McNamara G, Cheng KT, Huang J, Wang CH, Comai L, Ou JH, Lai MM
Hepatitis C virus inhibits DNA damage repair through reactive oxygen and nitrogen species and by interfering with the ATM-NBS1/Mre11/Rad50 DNA repair pathway in monocytes and hepatocytes.
J Immunol 185: 6985-98 (2010)
PM ID: 20974981 PMC3101474 NIHMS293685
219: Pepper ED, Farrell MJ, Nord G, Finkel SE
Antiglycation effects of carnosine and other compounds on the long-term survival of Escherichia coli.
Appl Environ Microbiol 76: 7925-30 (2010)
PM ID: 20952637 PMC3008226
220: Gai D, Chang YP, Chen XS
Origin DNA melting and unwinding in DNA replication.
Curr Opin Struct Biol 20: 756-62 (2010)
PM ID: 20870402 PMC2997676 NIHMS235546
221: Kim HJ, Lee S, Jung JU
When autophagy meets viruses: a double-edged sword with functions in defense and offense.
Semin Immunopathol 32: 323-41 (2010)
PM ID: 20865416 PMC3169181 NIHMS306151
222: Zhang X, Lee SW, Zhao L, Xia T, Qin PZ
Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.
RNA 16: 2474-83 (2010)
PM ID: 20980674 PMC2995408
223: Hunninghake GM, Soto-Quirós ME, Avila L, Kim HP, Lasky-Su J, Rafaels N, Ruczinski I, Beaty TH, Mathias RA, Barnes KC, Wilk JB, O'Connor GT, Gauderman WJ, Vora H, Baurley JW, Gilliland F, Liang C, Sylvia JS, Klanderman BJ, Sharma SS, Himes BE, Bossley CJ, Israel E, Raby BA, Bush A, Choi AM, Weiss ST, Celedón JC
TSLP polymorphisms are associated with asthma in a sex-specific fashion.
Allergy 65: 1566-75 (2010)
PM ID: 20560908 PMC2970693 NIHMS233299
224: Joo CH, Lee U, Nam YR, Jung JU, Lee H, Cho YK, Kim YK
Gene therapeutic approach for inhibiting hepatitis C virus replication using a recombinant protein that controls interferon expression.
Antimicrob Agents Chemother 54: 5048-56 (2010)
PM ID: 20855734 PMC2981247
225: Gandara DR, Grimminger P, Mack PC, Lara PN, Li T, Danenberg PV, Danenberg KD
Association of epidermal growth factor receptor activating mutations with low ERCC1 gene expression in non-small cell lung cancer.
J Thorac Oncol 5: 1933-8 (2010)
PM ID: 20975603
226: Jeong JH, Bhatia A, Toth Z, Oh S, Inn KS, Liao CP, Roy-Burman P, Melamed J, Coetzee GA, Jung JU
TPL2/COT/MAP3K8 (TPL2) activation promotes androgen depletion-independent (ADI) prostate cancer growth.
PLoS One 6: e16205 (2011)
PM ID: 21267413 PMC3022761
227: Moser AB, Steinberg SJ, Watkins PA, Moser HW, Ramaswamy K, Siegmund KD, Lee DR, Ely JJ, Ryder OA, Hacia JG
Human and great ape red blood cells differ in plasmalogen levels and composition.
Lipids Health Dis 10: 101 (2011)
PM ID: 21679470 PMC3129581
228: Siegmund KD, Marjoram P, Tavaré S, Shibata D
High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.
PLoS One 6: e21657 (2011)
PM ID: 21738754 PMC3125304
229: Kamerlin SC, Vicatos S, Dryga A, Warshel A
Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems.
Annu Rev Phys Chem 62: 41-64 (2011)
PM ID: 21034218
230: Na B, Huang Z, Wang Q, Qi Z, Tian Y, Lu CC, Yu J, Hanes MA, Kakar S, Huang EJ, Ou JH, Liu L, Yen TS
Transgenic expression of entire hepatitis B virus in mice induces hepatocarcinogenesis independent of chronic liver injury.
PLoS One 6: e26240 (2011)
PM ID: 22022578 PMC3192172
231: Kido T, Ou JH, Lau YF
The X-linked tumor suppressor TSPX interacts and promotes degradation of the hepatitis B viral protein HBx via the proteasome pathway.
PLoS One 6: e22979 (2011)
PM ID: 21829568 PMC3146538
232: Wang X, Kang GH, Campan M, Weisenberger DJ, Long TI, Cozen W, Bernstein L, Wu AH, Siegmund KD, Shibata D, Laird PW
Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors.
PLoS One 6: e25985 (2011)
PM ID: 22028801 PMC3197593
233: Yang SJ, Lopez LA, Exline CM, Haworth KG, Cannon PM
Lack of adaptation to human tetherin in HIV-1 group O and P.
Retrovirology 8: 78 (2011)
PM ID: 21955466 PMC3192746
234: Wei M, Madia F, Longo VD
Studying age-dependent genomic instability using the S. cerevisiae chronological lifespan model.
J Vis Exp : (2011)
PM ID: 21989366 PMC3230202
235: Campan M, Moffitt M, Houshdaran S, Shen H, Widschwendter M, Daxenbichler G, Long T, Marth C, Laird-Offringa IA, Press MF, Dubeau L, Siegmund KD, Wu AH, Groshen S, Chandavarkar U, Roman LD, Berchuck A, Pearce CL, Laird PW
Genome-scale screen for DNA methylation-based detection markers for ovarian cancer.
PLoS One 6: e28141 (2011)
PM ID: 22163280 PMC3233546
236: Pirooz SD, Lee JH, Zhao Z, Ni D, Oh S, Liang C
Measurement of γHV68 infection in mice.
J Vis Exp : (2011)
PM ID: 22127138 PMC3308616
237: Li Z, Jin Q, Huang C, Dasa S, Chen L, Yap LP, Liu S, Cai H, Park R, Conti PS
Trackable and Targeted Phage as Positron Emission Tomography (PET) Agent for Cancer Imaging.
Theranostics 1: 371-80 (2011)
PM ID: 22211143 PMC3248641
238: Cooper A, van Doorninck J, Ji L, Russell D, Ladanyi M, Shimada H, Krailo M, Womer RB, Hsu JH, Thomas D, Triche TJ, Sposto R, Lawlor ER
Ewing tumors that do not overexpress BMI-1 are a distinct molecular subclass with variant biology: a report from the Children's Oncology Group.
Clin Cancer Res 17: 56-66 (2011)
PM ID: 21047978 PMC3711406 NIHMS246539
239: Dasgupta J, Bienkowska-Haba M, Ortega ME, Patel HD, Bodevin S, Spillmann D, Bishop B, Sapp M, Chen XS
Structural basis of oligosaccharide receptor recognition by human papillomavirus.
J Biol Chem 286: 2617-24 (2011)
PM ID: 21115492 PMC3024757
240: Grimminger CM, Danenberg PV
Update of prognostic and predictive biomarkers in oropharyngeal squamous cell carcinoma: a review.
Eur Arch Otorhinolaryngol 268: 5-16 (2011)
PM ID: 20827554
241: Muggia F, Safra T, Dubeau L
BRCA genes: lessons learned from experimental and clinical cancer.
Ann Oncol 22 Suppl 1: i7-10 (2011)
PM ID: 21285156
242: Biffinger JC, Fitzgerald LA, Ray R, Little BJ, Lizewski SE, Petersen ER, Ringeisen BR, Sanders WC, Sheehan PE, Pietron JJ, Baldwin JW, Nadeau LJ, Johnson GR, Ribbens M, Finkel SE, Nealson KH
The utility of Shewanella japonica for microbial fuel cells.
Bioresour Technol 102: 290-7 (2011)
PM ID: 20663660
243: Li PC, Chretien L, Côté J, Kelly TJ, Forsburg SL
S. pombe replication protein Cdc18 (Cdc6) interacts with Swi6 (HP1) heterochromatin protein: region specific effects and replication timing in the centromere.
Cell Cycle 10: 323-36 (2011)
PM ID: 21239883 PMC3025051 NIHMS260190
244: Choi SH, Heo K, Byun HM, An W, Lu W, Yang AS
Identification of preferential target sites for human DNA methyltransferases.
Nucleic Acids Res 39: 104-18 (2011)
PM ID: 20841325 PMC3017615
245: Shibata D
Mutation and epigenetic molecular clocks in cancer.
Carcinogenesis 32: 123-8 (2011)
PM ID: 21076057 PMC3026845
246: Candelario J, Borrego S, Reddy S, Comai L
Accumulation of distinct prelamin A variants in human diploid fibroblasts differentially affects cell homeostasis.
Exp Cell Res 317: 319-29 (2011)
PM ID: 20974128
247: Nambiar M, Goldsmith G, Moorthy BT, Lieber MR, Joshi MV, Choudhary B, Hosur RV, Raghavan SC
Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma.
Nucleic Acids Res 39: 936-48 (2011)
PM ID: 20880994 PMC3035451
248: Dellisanti CD, Hanson SM, Chen L, Czajkowski C
Packing of the extracellular domain hydrophobic core has evolved to facilitate pentameric ligand-gated ion channel function.
J Biol Chem 286: 3658-70 (2011)
PM ID: 21098036 PMC3030369
249: Inn KS, Gack MU, Tokunaga F, Shi M, Wong LY, Iwai K, Jung JU
Linear ubiquitin assembly complex negatively regulates RIG-I- and TRIM25-mediated type I interferon induction.
Mol Cell 41: 354-65 (2011)
PM ID: 21292167 PMC3070481 NIHMS263182
250: Guevara-Aguirre J, Balasubramanian P, Guevara-Aguirre M, Wei M, Madia F, Cheng CW, Hwang D, Martin-Montalvo A, Saavedra J, Ingles S, de Cabo R, Cohen P, Longo VD
Growth hormone receptor deficiency is associated with a major reduction in pro-aging signaling, cancer, and diabetes in humans.
Sci Transl Med 3: 70ra13 (2011)
PM ID: 21325617 PMC3357623 NIHMS367592
251: Oh S, Pirooz SD, Ni D, Zhao Z, Liang C
Anti-autophagic Bcl-2: Not just an innocent bystander.
Autophagy 7: 231-2 (2011)
PM ID: 21099349 PMC3679092
252: Honig B, Rohs R
Biophysics: Flipping Watson and Crick.
Nature 470: 472-3 (2011)
PM ID: 21350476
253: Zhu D, Deng X, Spee C, Sonoda S, Hsieh CL, Barron E, Pera M, Hinton DR
Polarized secretion of PEDF from human embryonic stem cell-derived RPE promotes retinal progenitor cell survival.
Invest Ophthalmol Vis Sci 52: 1573-85 (2011)
PM ID: 21087957
254: Oh S, Xiaofei E, Ni D, Pirooz SD, Lee JY, Lee D, Zhao Z, Lee S, Lee H, Ku B, Kowalik T, Martin SE, Oh BH, Jung JU, Liang C
Downregulation of autophagy by Bcl-2 promotes MCF7 breast cancer cell growth independent of its inhibition of apoptosis.
Cell Death Differ 18: 452-64 (2011)
PM ID: 20885445 PMC3017654 NIHMS229584
255: Ku B, Liang C, Jung JU, Oh BH
Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX.
Cell Res 21: 627-41 (2011)
PM ID: 21060336 PMC3343310
256: Chakrabarty S, Namslauer I, Brzezinski P, Warshel A
Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects.
Biochim Biophys Acta 1807: 413-26 (2011)
PM ID: 21232525 PMC3055932 NIHMS264852
257: Rodeberg DA, Garcia-Henriquez N, Lyden ER, Davicioni E, Parham DM, Skapek SX, Hayes-Jordan AA, Donaldson SS, Brown KL, Triche TJ, Meyer WH, Hawkins DS
Prognostic significance and tumor biology of regional lymph node disease in patients with rhabdomyosarcoma: a report from the Children's Oncology Group.
J Clin Oncol 29: 1304-11 (2011)
PM ID: 21357792 PMC3083998
258: Dey R, Chen L
In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening.
J Biomol Struct Dyn 28: 695-715 (2011)
PM ID: 21294583
259: Frushicheva MP, Cao J, Warshel A
Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.
Biochemistry 50: 3849-58 (2011)
PM ID: 21443179 PMC3086991 NIHMS285392
260: He J, Ye J, Cai Y, Riquelme C, Liu JO, Liu X, Han A, Chen L
Structure of p300 bound to MEF2 on DNA reveals a mechanism of enhanceosome assembly.
Nucleic Acids Res 39: 4464-74 (2011)
PM ID: 21278418 PMC3105382
261: Grimminger PP, Danenberg P, Dellas K, Arnold D, Rödel C, Machiels JP, Haustermans K, Debucquoy A, Velenik V, Sempoux C, Bracko M, Hölscher AH, Semrau R, Yang D, Danenberg K, Lenz HJ, Vallböhmer D
Biomarkers for cetuximab-based neoadjuvant radiochemotherapy in locally advanced rectal cancer.
Clin Cancer Res 17: 3469-77 (2011)
PM ID: 21558395
262: Dranchak PK, Di Pietro E, Snowden A, Oesch N, Braverman NE, Steinberg SJ, Hacia JG
Nonsense suppressor therapies rescue peroxisome lipid metabolism and assembly in cells from patients with specific PEX gene mutations.
J Cell Biochem 112: 1250-8 (2011)
PM ID: 21465523 PMC3136445 NIHMS289429
263: Oghamian S, Sodir NM, Bashir MU, Shen H, Cullins AE, Carroll CA, Kundu P, Shibata D, Laird PW
Reduction of pancreatic acinar cell tumor multiplicity in Dnmt1 hypomorphic mice.
Carcinogenesis 32: 829-35 (2011)
PM ID: 21362628 PMC3106433
264: Sehati S, Clement MH, Martins J, Xu L, Longo VD, Valentine JS, Gralla EB
Metabolic alterations in yeast lacking copper-zinc superoxide dismutase.
Free Radic Biol Med 50: 1591-8 (2011)
PM ID: 21397007 PMC3090513 NIHMS281014
265: Jog SP, Reddy S, Comai L
Cell cycle-regulated association between the Werner syndrome protein and its molecular partners.
Cell Cycle 10: 2038-40 (2011)
PM ID: 21558813 PMC3154421
266: Plotnikov NV, Kamerlin SC, Warshel A
Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.
J Phys Chem B 115: 7950-62 (2011)
PM ID: 21618985 PMC3124314 NIHMS300724
267: Adamczyk AJ, Warshel A
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome.
Proc Natl Acad Sci U S A 108: 9827-32 (2011)
PM ID: 21617092 PMC3116401
268: Kamerlin SC, Warshel A
Multiscale modeling of biological functions.
Phys Chem Chem Phys 13: 10401-11 (2011)
PM ID: 21526232 PMC3102780 NIHMS291135
269: Matta H, Gopalakrishnan R, Punj V, Yi H, Suo Y, Chaudhary PM
A20 is induced by Kaposi sarcoma-associated herpesvirus-encoded viral FLICE inhibitory protein (vFLIP) K13 and blocks K13-induced nuclear factor-kappaB in a negative feedback manner.
J Biol Chem 286: 21555-64 (2011)
PM ID: 21531730 PMC3122214
270: Parekh C, Jubran R, Erdreich-Epstein A, Panigrahy A, Bluml S, Finlay J, Dhall G
Treatment of children with recurrent high grade gliomas with a bevacizumab containing regimen.
J Neurooncol 103: 673-80 (2011)
PM ID: 21038110
271: Lee C, Longo VD
Fasting vs dietary restriction in cellular protection and cancer treatment: from model organisms to patients.
Oncogene 30: 3305-16 (2011)
PM ID: 21516129
272: Pham P, Calabrese P, Park SJ, Goodman MF
Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity.
J Biol Chem 286: 24931-42 (2011)
PM ID: 21572036 PMC3137067
273: Tian Y, Chen WL, Ou JH
Effects of interferon-α/β on HBV replication determined by viral load.
PLoS Pathog 7: e1002159 (2011)
PM ID: 21829354 PMC3145790
274: Zhou J, Tan T, Tian Y, Zheng B, Ou JH, Huang EJ, Yen TS
Krüppel-like factor 15 activates hepatitis B virus gene expression and replication.
Hepatology 54: 109-21 (2011)
PM ID: 21503941 PMC3125411 NIHMS288236
275: Dansithong W, Jog SP, Paul S, Mohammadzadeh R, Tring S, Kwok Y, Fry RC, Marjoram P, Comai L, Reddy S
RNA steady-state defects in myotonic dystrophy are linked to nuclear exclusion of SHARP.
EMBO Rep 12: 735-42 (2011)
PM ID: 21637295 PMC3128970
276: Yamanaka K, Minko IG, Finkel SE, Goodman MF, Lloyd RS
Role of high-fidelity Escherichia coli DNA polymerase I in replication bypass of a deoxyadenosine DNA-peptide cross-link.
J Bacteriol 193: 3815-21 (2011)
PM ID: 21622737 PMC3147505
277: Yang Y, Groshong JS, Matta H, Gopalakrishnan R, Yi H, Chaudhary PM
Constitutive NF-kappaB activation confers interleukin 6 (IL6) independence and resistance to dexamethasone and Janus kinase inhibitor INCB018424 in murine plasmacytoma cells.
J Biol Chem 286: 27988-97 (2011)
PM ID: 21705340 PMC3151044
278: Adamczyk AJ, Cao J, Kamerlin SC, Warshel A
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions.
Proc Natl Acad Sci U S A 108: 14115-20 (2011)
PM ID: 21831831 PMC3161549
279: Lee G, Liang C, Park G, Jang C, Jung JU, Chung J
UVRAG is required for organ rotation by regulating Notch endocytosis in Drosophila.
Dev Biol 356: 588-97 (2011)
PM ID: 21729695
280: Klvaňa M, Jeřábek P, Goodman MF, Florián J
An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity.
Biochemistry 50: 7023-32 (2011)
PM ID: 21739967 PMC3477174 NIHMS314289
281: Johansson AL, Chakrabarty S, Berthold CL, Högbom M, Warshel A, Brzezinski P
Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects.
Biochim Biophys Acta 1807: 1083-94 (2011)
PM ID: 21463601 PMC3139697 NIHMS291130
282: Ding L, Forsburg SL
Schizosaccharomyces pombe minichromosome maintenance-binding protein (MCM-BP) antagonizes MCM helicase.
J Biol Chem 286: 32918-30 (2011)
PM ID: 21813639 PMC3190919
283: Masly JP, Dalton JE, Srivastava S, Chen L, Arbeitman MN
The genetic basis of rapidly evolving male genital morphology in Drosophila.
Genetics 189: 357-74 (2011)
PM ID: 21750260 PMC3176115
284: Kim H, Heo K, Choi J, Kim K, An W
Histone variant H3.3 stimulates HSP70 transcription through cooperation with HP1γ.
Nucleic Acids Res 39: 8329-41 (2011)
PM ID: 21742762 PMC3201866
285: Inn KS, Lee SH, Rathbun JY, Wong LY, Toth Z, Machida K, Ou JH, Jung JU
Inhibition of RIG-I-mediated signaling by Kaposi's sarcoma-associated herpesvirus-encoded deubiquitinase ORF64.
J Virol 85: 10899-904 (2011)
PM ID: 21835791 PMC3187500
286: Lim M, Chuong CM, Roy-Burman P
PI3K, Erk signaling in BMP7-induced epithelial-mesenchymal transition (EMT) of PC-3 prostate cancer cells in 2- and 3-dimensional cultures.
Horm Cancer 2: 298-309 (2011)
PM ID: 21948155
287: Li S, Kanno S, Watanabe R, Ogiwara H, Kohno T, Watanabe G, Yasui A, Lieber MR
Polynucleotide kinase and aprataxin-like forkhead-associated protein (PALF) acts as both a single-stranded DNA endonuclease and a single-stranded DNA 3' exonuclease and can participate in DNA end joining in a biochemical system.
J Biol Chem 286: 36368-77 (2011)
PM ID: 21885877 PMC3196146
288: Ram Prasad B, Warshel A
Prechemistry versus preorganization in DNA replication fidelity.
Proteins 79: 2900-19 (2011)
PM ID: 21905114 PMC3172682 NIHMS314034
289: Li SX, Huang S, Bren N, Noridomi K, Dellisanti CD, Sine SM, Chen L
Ligand-binding domain of an α7-nicotinic receptor chimera and its complex with agonist.
Nat Neurosci 14: 1253-9 (2011)
PM ID: 21909087 PMC3489043 NIHMS410628
290: Kingston D, Chang H, Ensser A, Lee HR, Lee J, Lee SH, Jung JU, Cho NH
Inhibition of retromer activity by herpesvirus saimiri tip leads to CD4 downregulation and efficient T cell transformation.
J Virol 85: 10627-38 (2011)
PM ID: 21849449 PMC3187508
291: Ye F, Gao SJ
A novel role of hydrogen peroxide in Kaposi sarcoma-associated herpesvirus reactivation.
Cell Cycle 10: 3237-8 (2011)
PM ID: 21941083 PMC3233619
292: Lagos-Jaramillo VI, Press MF, Ricker CN, Dubeau L, Mai PL, Weitzel JN
Pathological characteristics of BRCA-associated breast cancers in Hispanics.
Breast Cancer Res Treat 130: 281-9 (2011)
PM ID: 21604016 PMC3526343 NIHMS366513
293: Sun J, Desai MM, Soong L, Ou JH
IFN-α/β and autophagy: tug-of-war between HCV and the host.
Autophagy 7: 1394-6 (2011)
PM ID: 21997372 PMC3359484
294: Choi J, Kim H, Kim K, Lee B, Lu W, An W
Selective requirement of H2B N-Terminal tail for p14ARF-induced chromatin silencing.
Nucleic Acids Res 39: 9167-80 (2011)
PM ID: 21846774 PMC3241654
295: Paul S, Dansithong W, Jog SP, Holt I, Mittal S, Brook JD, Morris GE, Comai L, Reddy S
Expanded CUG repeats Dysregulate RNA splicing by altering the stoichiometry of the muscleblind 1 complex.
J Biol Chem 286: 38427-38 (2011)
PM ID: 21900255 PMC3207417
296: Longo VD, Fontana L
Intermittent supplementation with rapamycin as a dietary restriction mimetic.
Aging (Albany NY) 3: 1039-40 (2011)
PM ID: 22147496 PMC3249447
297: Shibata D
Molecular tumor clocks to study the evolution of drug resistance.
Mol Pharm 8: 2050-4 (2011)
PM ID: 21732670
298: Tian Y, Sir D, Kuo CF, Ann DK, Ou JH
Autophagy required for hepatitis B virus replication in transgenic mice.
J Virol 85: 13453-6 (2011)
PM ID: 21957292 PMC3233133
299: Warshel A, Dryga A
Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties.
Proteins 79: 3469-84 (2011)
PM ID: 21910139
300: Droniou-Bonzom ME, Reignier T, Oldenburg JE, Cox AU, Exline CM, Rathbun JY, Cannon PM
Substitutions in the glycoprotein (GP) of the Candid#1 vaccine strain of Junin virus increase dependence on human transferrin receptor 1 for entry and destabilize the metastable conformation of GP.
J Virol 85: 13457-62 (2011)
PM ID: 21976641 PMC3233171
301: Jeong KW, Kim K, Situ AJ, Ulmer TS, An W, Stallcup MR
Recognition of enhancer element-specific histone methylation by TIP60 in transcriptional activation.
Nat Struct Mol Biol 18: 1358-65 (2011)
PM ID: 22081016 PMC3230772 NIHMS321138
302: Lacruz RS, Smith CE, Chen YB, Hubbard MJ, Hacia JG, Paine ML
Gene-expression analysis of early- and late-maturation-stage rat enamel organ.
Eur J Oral Sci 119 Suppl 1: 149-57 (2011)
PM ID: 22243241 PMC3286129 NIHMS323965
303: Mukherjee S, Warshel A
Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase.
Proc Natl Acad Sci U S A 108: 20550-5 (2011)
PM ID: 22143769 PMC3251122
304: Lee HR, Choi WC, Lee S, Hwang J, Hwang E, Guchhait K, Haas J, Toth Z, Jeon YH, Oh TK, Kim MH, Jung JU
Bilateral inhibition of HAUSP deubiquitinase by a viral interferon regulatory factor protein.
Nat Struct Mol Biol 18: 1336-44 (2011)
PM ID: 22056774 PMC3589550 NIHMS365785
305: Jiang XX, Nguyen Q, Chou Y, Wang T, Nandakumar V, Yates P, Jones L, Wang L, Won H, Lee HR, Jung JU, Müschen M, Huang XF, Chen SY
Control of B cell development by the histone H2A deubiquitinase MYSM1.
Immunity 35: 883-96 (2011)
PM ID: 22169041
306: Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Cell 147: 1270-82 (2011)
PM ID: 22153072 PMC3319069 NIHMS339365
307: Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD
A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.
ACS Chem Biol 6: 1314-20 (2011)
PM ID: 21967305 PMC3241897 NIHMS330529
308: Choi SK, Yoon SR, Calabrese P, Arnheim N
Positive selection for new disease mutations in the human germline: evidence from the heritable cancer syndrome multiple endocrine neoplasia type 2B.
PLoS Genet 8: e1002420 (2012)
PM ID: 22359510 PMC3280958
309: Vergara IA, Erho N, Triche TJ, Ghadessi M, Crisan A, Sierocinski T, Black PC, Buerki C, Davicioni E
Genomic "Dark Matter" in Prostate Cancer: Exploring the Clinical Utility of ncRNA as Biomarkers.
Front Genet 3: 23 (2012)
PM ID: 22371711 PMC3284255
310: Murphree AL, Triche TJ
An epigenomic mechanism in retinoblastoma: the end of the story?
Genome Med 4: 15 (2012)
PM ID: 22364211 PMC3392761
311: Mitra SA, Mitra AP, Triche TJ
A central role for long non-coding RNA in cancer.
Front Genet 3: 17 (2012)
PM ID: 22363342 PMC3279698
312: Greene W, Zhang W, He M, Witt C, Ye F, Gao SJ
The ubiquitin/proteasome system mediates entry and endosomal trafficking of Kaposi's sarcoma-associated herpesvirus in endothelial cells.
PLoS Pathog 8: e1002703 (2012)
PM ID: 22615563 PMC3355089
313: Garlick DS, Li J, Sansoucy B, Wang T, Griffith L, Fitzgerald T, Butterfield J, Charbonneau B, Violette SM, Weinreb PH, Ratliff TL, Liao CP, Roy-Burman P, Vietri M, Lian JB, Stein GS, Altieri DC, Languino LR
α(V)β(6) integrin expression is induced in the POET and Pten(pc-/-) mouse models of prostatic inflammation and prostatic adenocarcinoma.
Am J Transl Res 4: 165-74 (2012)
PM ID: 22611469 PMC3353537
314: Wang Q, Na B, Ou JH, Pulliam L, Yen TS
Hepatitis B virus alters the antioxidant system in transgenic mice and sensitizes hepatocytes to Fas signaling.
PLoS One 7: e36818 (2012)
PM ID: 22606292 PMC3350475
315: Punj V, Matta H, Chaudhary PM
A computational profiling of changes in gene expression and transcription factors induced by vFLIP K13 in primary effusion lymphoma.
PLoS One 7: e37498 (2012)
PM ID: 22624040 PMC3356309
316: Matta H, Gopalakrishnan R, Graham C, Tolani B, Khanna A, Yi H, Suo Y, Chaudhary PM
Kaposi's sarcoma associated herpesvirus encoded viral FLICE inhibitory protein K13 activates NF-κB pathway independent of TRAF6, TAK1 and LUBAC.
PLoS One 7: e36601 (2012)
PM ID: 22590573 PMC3348130
317: Bullock S, Hope Q, Edwards S, Bryant S, Mulholland S, Jugurnauth S, Garcia N, Guy M, O'Brien L, Gehr-Swain B, Hall A, Wilkinson R, Ardern-Jones A, Dearnaley D, Eeles R, Evans C, Teare M, Easton D, Hopper J, Giles G, English D, Severi G, Foulkes WD, Hamel N, Narod S, Simard J, Badzioch M, Amos C, Heimdal K, Maehle L, Møller P, Wessel N, Andersen T, Bishop T, Balise RN, Gallagher R, Halpern J, Hsieh CL, Kolonel L, Oakley I, West D, Whittemore AS, Wu A, Cancel-Tassin G, Valéri A, Mangin P, Cussenot O, Wiley KE, Isaacs SD, Gielzak M, Ewing CM, Walsh PC, Isaacs WB, Schaid DJ, McDonnell SK, Christensen GB, Cunningham JM, Hebbring S, Guenther JC, Thibodeau SN, Lange EM, Davis CC, Brown W, Bock CH, Cooney KA, Deutsch K, Friedrichsen DM, Kolb S, Ostrander EA, Hood L, Stanford JL, Wahlfors T, Mattila H, Laitinen V, Nurminen R, Fischer D, Tammela TL, George A, Bailey-Wilson J, Schleutker J, Bochum S, Paiss T, Hoegel J, Kurtz F, Luedeke M, Rinckleb A, Herkommer K, Vogel W, Schrader M, Maier C, Wiklund F, Bergh A, Emanuelsson M, Göransson I, Jonsson BA, Lindmark F, Stenman E, Grönberg H, Cannon-Albright LA, Camp NJ, Farnham JM, Xu J, Meyers DA, Chang BL, Turner AR, Dimitrov L, Adams TS, Seminara D, Bailey-Wilson JE, Childs EJ, Cropp CD, Schaid DJ, Xu J, Camp NJ, Cannon-Albright LA, Farnham JM, George A, Powell I, Carpten JD, Giles GG, Hopper JL, Severi G, English DR, Foulkes WD, Maehle L, Møller P, Eeles R, Easton D, Guy M, Edwards S, Badzioch MD, Whittemore AS, Oakley-Girvan I, Hsieh CL, Dimitrov L, Stanford JL, Karyadi DM, Deutsch K, McIntosh L, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Thibodeau SN, McDonnell SK, Hebbring S, Lange EM, Cooney KA, Tammela TL, Schleutker J, Maier C, Bochum S, Hoegel J, Grönberg H, Wiklund F, Emanuelsson M, Cancel-Tassin G, Valeri A, Cussenot O, Isaacs WB, International Consortium for Prostate Cancer Genetics
Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families.
BMC Med Genet 13: 46 (2012)
PM ID: 22712434 PMC3495053
318: Longo VD, Fabrizio P
Chronological Aging in Saccharomyces cerevisiae.
Subcell Biochem 57: 101-21 (2012)
PM ID: 22094419 PMC4048025 NIHMS585021
319: Liu HM, Aizaki H, Machida K, Ou JH, Lai MM
Hepatitis C virus translation preferentially depends on active RNA replication.
PLoS One 7: e43600 (2012)
PM ID: 22937067 PMC3427374
320: Erho N, Buerki C, Triche TJ, Davicioni E, Vergara IA
Transcriptome-wide detection of differentially expressed coding and non-coding transcripts and their clinical significance in prostate cancer.
J Oncol 2012: 541353 (2012)
PM ID: 22956952 PMC3431106
321: Wu CC, D'Argenio D, Asgharzadeh S, Triche T
TARGETgene: a tool for identification of potential therapeutic targets in cancer.
PLoS One 7: e43305 (2012)
PM ID: 22952662 PMC3432038
322: Federman N, Chan J, Nagy JO, Landaw EM, McCabe K, Wu AM, Triche T, Kang H, Liu B, Marks JD, Denny CT
Enhanced growth inhibition of osteosarcoma by cytotoxic polymerized liposomal nanoparticles targeting the alcam cell surface receptor.
Sarcoma 2012: 126906 (2012)
PM ID: 23024593 PMC3447386
323: Safdie F, Brandhorst S, Wei M, Wang W, Lee C, Hwang S, Conti PS, Chen TC, Longo VD
Fasting enhances the response of glioma to chemo- and radiotherapy.
PLoS One 7: e44603 (2012)
PM ID: 22984531 PMC3439413
324: Lee SH, Toth Z, Wong LY, Brulois K, Nguyen J, Lee JY, Zandi E, Jung JU
Novel Phosphorylations of IKKγ/NEMO.
MBio 3: e00411-12 (2012)
PM ID: 23131831 PMC3487776
325: McDonald JP, Vaisman A, Kuban W, Goodman MF, Woodgate R
Mechanisms employed by Escherichia coli to prevent ribonucleotide incorporation into genomic DNA by Pol V.
PLoS Genet 8: e1003030 (2012)
PM ID: 23144626 PMC3493448
326: Liu H, Liu S, Wang H, Xie X, Chen X, Zhang X, Zhang Y
Genomic amplification of the human telomerase gene (hTERC) associated with human papillomavirus is related to the progression of uterine cervical dysplasia to invasive cancer.
Diagn Pathol 7: 147 (2012)
PM ID: 23107094 PMC3488518
327: Nguyen P, Qin PZ
RNA dynamics: perspectives from spin labels.
Wiley Interdiscip Rev RNA 3: 62-72 (2012)
PM ID: 21882345 PMC3235270 NIHMS314855
328: Zhang W, Greene W, Gao SJ
Microtubule- and dynein-dependent nuclear trafficking of rhesus rhadinovirus in rhesus fibroblasts.
J Virol 86: 599-604 (2012)
PM ID: 22031929 PMC3255885
329: Iwata J, Tung L, Urata M, Hacia JG, Pelikan R, Suzuki A, Ramenzoni L, Chaudhry O, Parada C, Sanchez-Lara PA, Chai Y
Fibroblast growth factor 9 (FGF9)-pituitary homeobox 2 (PITX2) pathway mediates transforming growth factor β (TGFβ) signaling to regulate cell proliferation in palatal mesenchyme during mouse palatogenesis.
J Biol Chem 287: 2353-63 (2012)
PM ID: 22123828 PMC3268397
330: Frushicheva MP, Warshel A
Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A.
Chembiochem 13: 215-23 (2012)
PM ID: 22190449 PMC3414264 NIHMS379144
331: Kaddis JS, Wai DH, Bowers J, Hartmann N, Baeriswyl L, Bajaj S, Anderson MJ, Getts RC, Triche TJ
Influence of RNA labeling on expression profiling of microRNAs.
J Mol Diagn 14: 12-21 (2012)
PM ID: 22074760 PMC3338349
332: Knott SR, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM
Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae.
Cell 148: 99-111 (2012)
PM ID: 22265405 PMC3266545 NIHMS345626
333: Peters U, Hutter CM, Hsu L, Schumacher FR, Conti DV, Carlson CS, Edlund CK, Haile RW, Gallinger S, Zanke BW, Lemire M, Rangrej J, Vijayaraghavan R, Chan AT, Hazra A, Hunter DJ, Ma J, Fuchs CS, Giovannucci EL, Kraft P, Liu Y, Chen L, Jiao S, Makar KW, Taverna D, Gruber SB, Rennert G, Moreno V, Ulrich CM, Woods MO, Green RC, Parfrey PS, Prentice RL, Kooperberg C, Jackson RD, Lacroix AZ, Caan BJ, Hayes RB, Berndt SI, Chanock SJ, Schoen RE, Chang-Claude J, Hoffmeister M, Brenner H, Frank B, Bézieau S, Küry S, Slattery ML, Hopper JL, Jenkins MA, Le Marchand L, Lindor NM, Newcomb PA, Seminara D, Hudson TJ, Duggan DJ, Potter JD, Casey G
Meta-analysis of new genome-wide association studies of colorectal cancer risk.
Hum Genet 131: 217-34 (2012)
PM ID: 21761138 PMC3257356 NIHMS324653
334: Dryga A, Chakrabarty S, Vicatos S, Warshel A
Coarse grained model for exploring voltage dependent ion channels.
Biochim Biophys Acta 1818: 303-17 (2012)
PM ID: 21843502 PMC3232338 NIHMS317569
335: Kim Y, Kwon EK, Jeon JH, So I, Kim IG, Choi MS, Kim IS, Choi JK, Jung JU, Cho NH
Activation of the STAT6 transcription factor in Jurkat T-cells by the herpesvirus saimiri Tip protein.
J Gen Virol 93: 330-40 (2012)
PM ID: 22012462 PMC3352339
336: Tian Y, Kuo CF, Chen WL, Ou JH
Enhancement of hepatitis B virus replication by androgen and its receptor in mice.
J Virol 86: 1904-10 (2012)
PM ID: 22156518 PMC3302417
337: Kim K, Heo K, Choi J, Jackson S, Kim H, Xiong Y, An W
Vpr-binding protein antagonizes p53-mediated transcription via direct interaction with H3 tail.
Mol Cell Biol 32: 783-96 (2012)
PM ID: 22184063 PMC3272969
338: Kim H, Kim K, Choi J, Heo K, Baek HJ, Roeder RG, An W
p53 requires an intact C-terminal domain for DNA binding and transactivation.
J Mol Biol 415: 843-54 (2012)
PM ID: 22178617 PMC3267882 NIHMS343347
339: Zhang X, Tung CS, Sowa GZ, Hatmal MM, Haworth IS, Qin PZ
Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling.
J Am Chem Soc 134: 2644-52 (2012)
PM ID: 22229766 PMC3279945 NIHMS353713
340: Dryga A, Chakrabarty S, Vicatos S, Warshel A
Realistic simulation of the activation of voltage-gated ion channels.
Proc Natl Acad Sci U S A 109: 3335-40 (2012)
PM ID: 22331900 PMC3295319
341: Campbell M, Chang PC, Huerta S, Izumiya C, Davis R, Tepper CG, Kim KY, Shevchenko B, Wang DH, Jung JU, Luciw PA, Kung HJ, Izumiya Y
Protein arginine methyltransferase 1-directed methylation of Kaposi sarcoma-associated herpesvirus latency-associated nuclear antigen.
J Biol Chem 287: 5806-18 (2012)
PM ID: 22179613 PMC3285351
342: Liang C
Viral FLIPping autophagy for longevity.
Cell Host Microbe 11: 101-3 (2012)
PM ID: 22341458
343: Lee C, Raffaghello L, Longo VD
Starvation, detoxification, and multidrug resistance in cancer therapy.
Drug Resist Updat 15: 114-22 (2012)
PM ID: 22391012 PMC3573885 NIHMS438727
344: Seal S, Hall A, Staples M, McCudden B, Connal J, Thorowgood R, Costa C, Kevan M, Palmer S, Karpowicz J, Gerrard W, Duhon M, Chalsty Ja, Jaffe PK, Bullock S, Hope Q, Bryant S, Mulholland S, Jugurnauth S, Garcia N, O'Brien L, Gehr-Swain B, Hall A, Ardern-Jones A, Dearnaley D, Evans C, Teare MD, Southey M, Hamel N, Narod S, Simard J, Amos C, Heimdal K, Mahle L, Moller P, Wessel N, Andersen T, Bishop T, Lu L, Cancel-Tassin G, Valeri A, Cussenot O, Lange EM, Cooney KA, Farnham JM, Camp NJ, Cannon-Albright LA, Tammela TL, Schleutker J, Hoegel J, Herkommer K, Maier C, Vogel W, Wiklund F, Emanuelsson M, Grönberg H, Wiley KE, Isaacs SD, Walsh PC, Helfand BT, Kan D, Catalona WJ, Stanford JL, FitzGerald LM, Johanneson B, Deutsch K, McIntosh L, Ostrander EA, Thibodeau SN, McDonnell SK, Hebbring S, Schaid DJ, Whittemore AS, Oakley-Girvan I, Hsieh CL, Powell I, Bailey-Wilson JE, Cropp CD, Simpson C, Carpten JD, Seminara D, Zheng SL, Xu J, Giles GG, Severi G, Hopper JL, English DR, Foulkes WD, Maehle L, Moller P, Badzioch MD, Edwards S, Guy M, Eeles R, Easton D, Isaacs WB, International Consortium for Prostate Cancer Genetics
Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG.
Prostate 72: 410-26 (2012)
PM ID: 21748754 PMC3568777 NIHMS301718
345: Ng TL, Leprivier G, Robertson MD, Chow C, Martin MJ, Laderoute KR, Davicioni E, Triche TJ, Sorensen PH
The AMPK stress response pathway mediates anoikis resistance through inhibition of mTOR and suppression of protein synthesis.
Cell Death Differ 19: 501-10 (2012)
PM ID: 21941369 PMC3278733
346: Jones T, Ye F, Bedolla R, Huang Y, Meng J, Qian L, Pan H, Zhou F, Moody R, Wagner B, Arar M, Gao SJ
Direct and efficient cellular transformation of primary rat mesenchymal precursor cells by KSHV.
J Clin Invest 122: 1076-81 (2012)
PM ID: 22293176 PMC3287217
347: Iwata J, Hacia JG, Suzuki A, Sanchez-Lara PA, Urata M, Chai Y
Modulation of noncanonical TGF-β signaling prevents cleft palate in Tgfbr2 mutant mice.
J Clin Invest 122: 873-85 (2012)
PM ID: 22326956 PMC3287237
348: Yang CS, Lee JS, Rodgers M, Min CK, Lee JY, Kim HJ, Lee KH, Kim CJ, Oh B, Zandi E, Yue Z, Kramnik I, Liang C, Jung JU
Autophagy protein Rubicon mediates phagocytic NADPH oxidase activation in response to microbial infection or TLR stimulation.
Cell Host Microbe 11: 264-76 (2012)
PM ID: 22423966 PMC3616771 NIHMS361158
349: Yang CS, Rodgers M, Min CK, Lee JS, Kingeter L, Lee JY, Jong A, Kramnik I, Lin X, Jung JU
The autophagy regulator Rubicon is a feedback inhibitor of CARD9-mediated host innate immunity.
Cell Host Microbe 11: 277-89 (2012)
PM ID: 22423967 PMC3615900 NIHMS361159
350: Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH
Stereospecific formation of a ternary complex of (S)-α,β-fluoromethylene-dATP with DNA pol β.
Chembiochem 13: 528-30 (2012)
PM ID: 22315190 PMC3788113 NIHMS493590
351: Lee C, Raffaghello L, Brandhorst S, Safdie FM, Bianchi G, Martin-Montalvo A, Pistoia V, Wei M, Hwang S, Merlino A, Emionite L, de Cabo R, Longo VD
Fasting cycles retard growth of tumors and sensitize a range of cancer cell types to chemotherapy.
Sci Transl Med 4: 124ra27 (2012)
PM ID: 22323820 PMC3608686 NIHMS438726
352: Fischer JM, Miller AJ, Shibata D, Liskay RM
Different phenotypic consequences of simultaneous versus stepwise Apc loss.
Oncogene 31: 2028-38 (2012)
PM ID: 21892206 PMC3235266 NIHMS315854
353: Singh N, Frushicheva MP, Warshel A
Validating the vitality strategy for fighting drug resistance.
Proteins 80: 1110-22 (2012)
PM ID: 22275047 PMC3299486 NIHMS358866
354: Bai Z, Zhou F, Lei X, Ma X, Lu C, Gao SJ
A cluster of transcripts encoded by KSHV ORF30-33 gene locus.
Virus Genes 44: 225-36 (2012)
PM ID: 22180077 PMC3290719 NIHMS353196
355: Moon HJ, Lee JS, Choi YK, Park JY, Talactac MR, Chowdhury MY, Poo H, Sung MH, Lee JH, Jung JU, Kim CJ
Induction of type I interferon by high-molecular poly-γ-glutamate protects B6.A2G-Mx1 mice against influenza A virus.
Antiviral Res 94: 98-102 (2012)
PM ID: 22401806
356: Shibata D
Cancer. Heterogeneity and tumor history.
Science 336: 304-5 (2012)
PM ID: 22517848
357: Karata K, Vaisman A, Goodman MF, Woodgate R
Simple and efficient purification of Escherichia coli DNA polymerase V: cofactor requirements for optimal activity and processivity in vitro.
DNA Repair (Amst) 11: 431-40 (2012)
PM ID: 22341652 PMC3471214 NIHMS353792
358: Fontana L, Vinciguerra M, Longo VD
Growth factors, nutrient signaling, and cardiovascular aging.
Circ Res 110: 1139-50 (2012)
PM ID: 22499903 PMC3376758 NIHMS369171
359: Parekh C, Sahaghian A, Kim W, Scholes J, Ge S, Zhu Y, Asgharzadeh S, Hollis R, Kohn D, Ji L, Malvar J, Wang X, Crooks G
Novel pathways to erythropoiesis induced by dimerization of intracellular C-Mpl in human hematopoietic progenitors.
Stem Cells 30: 697-708 (2012)
PM ID: 22290824 PMC3973153 NIHMS565950
360: Mo RH, Zaro JL, Ou JH, Shen WC
Effects of Lipofectamine 2000/siRNA complexes on autophagy in hepatoma cells.
Mol Biotechnol 51: 1-8 (2012)
PM ID: 21660602
361: Lacruz RS, Smith CE, Bringas P, Chen YB, Smith SM, Snead ML, Kurtz I, Hacia JG, Hubbard MJ, Paine ML
Identification of novel candidate genes involved in mineralization of dental enamel by genome-wide transcript profiling.
J Cell Physiol 227: 2264-75 (2012)
PM ID: 21809343 PMC3243804 NIHMS314583
362: Ting MC, Liao CP, Yan C, Jia L, Groshen S, Frenkel B, Roy-Burman P, Coetzee GA, Maxson R
An enhancer from the 8q24 prostate cancer risk region is sufficient to direct reporter gene expression to a subset of prostate stem-like epithelial cells in transgenic mice.
Dis Model Mech 5: 366-74 (2012)
PM ID: 22279083 PMC3339830
363: Han D, Zhao H, Parada C, Hacia JG, Bringas P, Chai Y
A TGFβ-Smad4-Fgf6 signaling cascade controls myogenic differentiation and myoblast fusion during tongue development.
Development 139: 1640-50 (2012)
PM ID: 22438570 PMC3317969
364: Lopez LA, Yang SJ, Exline CM, Rengarajan S, Haworth KG, Cannon PM
Anti-tetherin activities of HIV-1 Vpu and Ebola virus glycoprotein do not involve removal of tetherin from lipid rafts.
J Virol 86: 5467-80 (2012)
PM ID: 22398279 PMC3347301
365: Sir D, Kuo CF, Tian Y, Liu HM, Huang EJ, Jung JU, Machida K, Ou JH
Replication of hepatitis C virus RNA on autophagosomal membranes.
J Biol Chem 287: 18036-43 (2012)
PM ID: 22496373 PMC3365724
366: Zhao Z, Oh S, Li D, Ni D, Pirooz SD, Lee JH, Yang S, Lee JY, Ghozalli I, Costanzo V, Stark JM, Liang C
A dual role for UVRAG in maintaining chromosomal stability independent of autophagy.
Dev Cell 22: 1001-16 (2012)
PM ID: 22542840 PMC3356442 NIHMS367824
367: Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE
β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases.
J Am Chem Soc 134: 8734-7 (2012)
PM ID: 22397499 PMC3595068 NIHMS363879
368: Senavirathne G, Jaszczur M, Auerbach PA, Upton TG, Chelico L, Goodman MF, Rueda D
Single-stranded DNA scanning and deamination by APOBEC3G cytidine deaminase at single molecule resolution.
J Biol Chem 287: 15826-35 (2012)
PM ID: 22362763 PMC3346118
369: Yu VM, Marion CM, Austria TM, Yeh J, Schönthal AH, Dubeau L
Role of BRCA1 in controlling mitotic arrest in ovarian cystadenoma cells.
Int J Cancer 130: 2495-504 (2012)
PM ID: 21792894 PMC3299830 NIHMS338868
370: Tsai AG, Chen DM, Lin M, Hsieh JC, Okitsu CY, Taghva A, Shibata D, Hsieh CL
Heterogeneity and randomness of DNA methylation patterns in human embryonic stem cells.
DNA Cell Biol 31: 893-907 (2012)
PM ID: 22277069
371: Yen HY, Gabet Y, Liu Y, Martin A, Wu NL, Pike MC, Frenkel B, Maxson R, Dubeau L
Alterations in Brca1 expression in mouse ovarian granulosa cells have short-term and long-term consequences on estrogen-responsive organs.
Lab Invest 92: 802-11 (2012)
PM ID: 22488153
372: Popova AM, Hatmal MM, Frushicheva MP, Price EA, Qin PZ, Haworth IS
Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.
J Phys Chem B 116: 6387-96 (2012)
PM ID: 22574834 PMC3382087 NIHMS377685
373: Goodman MF
An accidental biochemist.
DNA Repair (Amst) 11: 527-36 (2012)
PM ID: 22808529
374: Lacruz RS, Hacia JG, Bromage TG, Boyde A, Lei Y, Xu Y, Miller JD, Paine ML, Snead ML
The circadian clock modulates enamel development.
J Biol Rhythms 27: 237-45 (2012)
PM ID: 22653892 PMC3511783 NIHMS422630
375: Cooney KA, Ray AM, Zuhlke KA, Lange EM, FitzGerald LM, Stanford JL, Foulkes WD, Giles GG, Hopper JL, Severi G, Eeles R, Easton D, Kote-Jarai Z, Guy M, Rinckleb A, Maier C, Vogel W, Thibodeau SN, McDonnell SK, Schaid DJ, Wiklund F, Grönberg H, Emanuelsson M, Whittemore AS, Oakley-Girvan I, Hsieh C-, Wahlfors T, Tammela T, Schleutker J, Jin G, Lu L, Cooney KA, Ray AM, Zuhlke KA, Lange EM, Cannon-Albright LA, Camp NJ, Teerlink CC, FitzGerald LM, Stanford JL, Wiley KE, Isaacs SD, Walsh PC, Foulkes WD, Giles GG, Hopper JL, Severi G, Eeles R, Easton D, Kote-Jarai Z, Guy M, Rinckleb A, Maier C, Vogel W, Cancel-Tassin G, Egrot C, Cussenot O, Thibodeau SN, McDonnell SK, Schaid DJ, Wiklund F, Grönberg H, Emanuelsson M, Whittemore AS, Oakley-Girvan I, Hsieh CL, Wahlfors T, Tammela T, Schleutker J, Catalona WJ, Zheng SL, Ostrander EA, Isaacs WB, Xu J, International Consortium for Prostate Cancer Genetics
Validation of prostate cancer risk-related loci identified from genome-wide association studies using family-based association analysis: evidence from the International Consortium for Prostate Cancer Genetics (ICPCG).
Hum Genet 131: 1095-103 (2012)
PM ID: 22198737 PMC3535428 NIHMS403275
376: Mao GE, Harris DM, Moro A, Heber D, Roy-Burman P, Zhang ZF, Rao J
A joint effect of new Western diet and retinoid X receptor α prostate-specific knockout with development of high-grade prostatic intraepithelial neoplasia in mice--a preliminary study.
Prostate 72: 1052-9 (2012)
PM ID: 22314496
377: Jayathilaka N, Han A, Gaffney KJ, Dey R, Jarusiewicz JA, Noridomi K, Philips MA, Lei X, He J, Ye J, Gao T, Petasis NA, Chen L
Inhibition of the function of class IIa HDACs by blocking their interaction with MEF2.
Nucleic Acids Res 40: 5378-88 (2012)
PM ID: 22396528 PMC3384312
378: He M, Zhang W, Bakken T, Schutten M, Toth Z, Jung JU, Gill P, Cannon M, Gao SJ
Cancer angiogenesis induced by Kaposi sarcoma-associated herpesvirus is mediated by EZH2.
Cancer Res 72: 3582-92 (2012)
PM ID: 22593192 PMC4034471 NIHMS582836
379: Tjong H, Gong K, Chen L, Alber F
Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.
Genome Res 22: 1295-305 (2012)
PM ID: 22619363 PMC3396370
380: Vaisman A, Kuban W, McDonald JP, Karata K, Yang W, Goodman MF, Woodgate R
Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity.
Nucleic Acids Res 40: 6144-57 (2012)
PM ID: 22422840 PMC3401427
381: Longo VD, Shadel GS, Kaeberlein M, Kennedy B
Replicative and chronological aging in Saccharomyces cerevisiae.
Cell Metab 16: 18-31 (2012)
PM ID: 22768836 PMC3392685 NIHMS385505
382: Fu B, Yang R, Xia F, Li B, Ouyang X, Gao SJ, Wang L
Gender differences in Kaposi's sarcoma-associated herpesvirus infection in a population with schistosomiasis in rural China.
Jpn J Infect Dis 65: 350-3 (2012)
PM ID: 22814163 PMC3513380 NIHMS419306
383: Hong B, Peng G, Berry L, Gottschalk S, Jung JU, Chen SY, Huang XF
Generating CTLs against the subdominant EBV LMP antigens by transient expression of an A20 inhibitor with EBV LMP proteins in human DCs.
Gene Ther 19: 818-27 (2012)
PM ID: 22052242 PMC3288357 NIHMS324802
384: Mu Y, Prochnow C, Pham P, Chen XS, Goodman MF
A structural basis for the biochemical behavior of activation-induced deoxycytidine deaminase class-switch recombination-defective hyper-IgM-2 mutants.
J Biol Chem 287: 28007-16 (2012)
PM ID: 22715099 PMC3431652
385: Zhou B, Arnett DR, Yu X, Brewster A, Sowd GA, Xie CL, Vila S, Gai D, Fanning E, Chen XS
Structural basis for the interaction of a hexameric replicative helicase with the regulatory subunit of human DNA polymerase α-primase.
J Biol Chem 287: 26854-66 (2012)
PM ID: 22700977 PMC3411022
386: Candelario J, Chen LY, Marjoram P, Reddy S, Comai L
A filtering strategy identifies FOXQ1 as a potential effector of lamin A dysfunction.
Aging (Albany NY) 4: 567-77 (2012)
PM ID: 22948034 PMC3461344
387: Plotnikov NV, Warshel A
Exploring, refining, and validating the paradynamics QM/MM sampling.
J Phys Chem B 116: 10342-56 (2012)
PM ID: 22853800
388: Wang ET, Cody NA, Jog S, Biancolella M, Wang TT, Treacy DJ, Luo S, Schroth GP, Housman DE, Reddy S, Lécuyer E, Burge CB
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins.
Cell 150: 710-24 (2012)
PM ID: 22901804 PMC3428802 NIHMS398461
389: Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Becksfort J, Gupta P, Ma J, Easton J, Vadodaria B, Onar-Thomas A, Lin T, Li S, Pounds S, Paugh S, Zhao D, Kawauchi D, Roussel MF, Finkelstein D, Ellison DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Gajjar A, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ
Novel mutations target distinct subgroups of medulloblastoma.
Nature 488: 43-8 (2012)
PM ID: 22722829 PMC3412905 NIHMS374717
390: Kim K, Jeong KW, Kim H, Choi J, Lu W, Stallcup MR, An W
Functional interplay between p53 acetylation and H1.2 phosphorylation in p53-regulated transcription.
Oncogene 31: 4290-301 (2012)
PM ID: 22249259 PMC3330162 NIHMS341053
391: Gadd S, Beezhold P, Jennings L, George D, Leuer K, Huang CC, Huff V, Tognon C, Sorensen PH, Triche T, Coffin CM, Perlman EJ
Mediators of receptor tyrosine kinase activation in infantile fibrosarcoma: a Children's Oncology Group study.
J Pathol 228: 119-30 (2012)
PM ID: 22374738
392: Toth Z, Brulois KF, Wong LY, Lee HR, Chung B, Jung JU
Negative elongation factor-mediated suppression of RNA polymerase II elongation of Kaposi's sarcoma-associated herpesvirus lytic gene expression.
J Virol 86: 9696-707 (2012)
PM ID: 22740393 PMC3446579
393: Brulois KF, Chang H, Lee AS, Ensser A, Wong LY, Toth Z, Lee SH, Lee HR, Myoung J, Ganem D, Oh TK, Kim JF, Gao SJ, Jung JU
Construction and manipulation of a new Kaposi's sarcoma-associated herpesvirus bacterial artificial chromosome clone.
J Virol 86: 9708-20 (2012)
PM ID: 22740391 PMC3446615
394: Tian Y, Chen WL, Kuo CF, Ou JH
Viral-load-dependent effects of liver injury and regeneration on hepatitis B virus replication in mice.
J Virol 86: 9599-605 (2012)
PM ID: 22718822 PMC3446606
395: Kuban W, Vaisman A, McDonald JP, Karata K, Yang W, Goodman MF, Woodgate R
Escherichia coli UmuC active site mutants: effects on translesion DNA synthesis, mutagenesis and cell survival.
DNA Repair (Amst) 11: 726-32 (2012)
PM ID: 22784977 PMC3419331 NIHMS393901
396: Mukherjee S, Warshel A
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase.
Proc Natl Acad Sci U S A 109: 14876-81 (2012)
PM ID: 22927379 PMC3443130
397: Cox SG, Kim H, Garnett AT, Medeiros DM, An W, Crump JG
An essential role of variant histone H3.3 for ectomesenchyme potential of the cranial neural crest.
PLoS Genet 8: e1002938 (2012)
PM ID: 23028350 PMC3447937
398: Chen X, Cui D, Papusha A, Zhang X, Chu CD, Tang J, Chen K, Pan X, Ira G
The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends.
Nature 489: 576-80 (2012)
PM ID: 22960743 PMC3640768 NIHMS389653
399: Grimminger PP, Shi M, Barrett C, Lebwohl D, Danenberg KD, Brabender J, Vigen CL, Danenberg PV, Winder T, Lenz HJ
TS and ERCC-1 mRNA expressions and clinical outcome in patients with metastatic colon cancer in CONFIRM-1 and -2 clinical trials.
Pharmacogenomics J 12: 404-11 (2012)
PM ID: 21788964
400: Goel HL, Chang C, Pursell B, Leav I, Lyle S, Xi HS, Hsieh CC, Adisetiyo H, Roy-Burman P, Coleman IM, Nelson PS, Vessella RL, Davis RJ, Plymate SR, Mercurio AM
VEGF/neuropilin-2 regulation of Bmi-1 and consequent repression of IGF-IR define a novel mechanism of aggressive prostate cancer.
Cancer Discov 2: 906-21 (2012)
PM ID: 22777769
401: Greisman HA, Lu Z, Tsai AG, Greiner TC, Yi HS, Lieber MR
IgH partner breakpoint sequences provide evidence that AID initiates t(11;14) and t(8;14) chromosomal breaks in mantle cell and Burkitt lymphomas.
Blood 120: 2864-7 (2012)
PM ID: 22915650 PMC3466967
402: Grimminger PP, Maus MK, Schneider PM, Metzger R, Hölscher AH, Sugita H, Danenberg PV, Alakus H, Brabender J
Glutathione S-transferase PI (GST-PI) mRNA expression and DNA methylation is involved in the pathogenesis and prognosis of NSCLC.
Lung Cancer 78: 87-91 (2012)
PM ID: 22884253
403: Wang XM, Yik WY, Zhang P, Lu W, Dranchak PK, Shibata D, Steinberg SJ, Hacia JG
The gene expression profiles of induced pluripotent stem cells from individuals with childhood cerebral adrenoleukodystrophy are consistent with proposed mechanisms of pathogenesis.
Stem Cell Res Ther 3: 39 (2012)
PM ID: 23036268 PMC3580430
404: Oertell K, Wu Y, Zakharova VM, Kashemirov BA, Shock DD, Beard WA, Wilson SH, McKenna CE, Goodman MF
Effect of β,γ-CHF- and β,γ-CHCl-dGTP halogen atom stereochemistry on the transition state of DNA polymerase β.
Biochemistry 51: 8491-501 (2012)
PM ID: 23043620 PMC3548995 NIHMS417577
405: Mirisola MG, Longo VD
Acetic acid and acidification accelerate chronological and replicative aging in yeast.
Cell Cycle 11: 3532-3 (2012)
PM ID: 22951542 PMC3478300
406: Lei X, Zhu Y, Jones T, Bai Z, Huang Y, Gao SJ
A Kaposi's sarcoma-associated herpesvirus microRNA and its variants target the transforming growth factor β pathway to promote cell survival.
J Virol 86: 11698-711 (2012)
PM ID: 22915806 PMC3486299
407: Aguilar B, Choi I, Choi D, Chung HK, Lee S, Yoo J, Lee YS, Maeng YS, Lee HN, Park E, Kim KE, Kim NY, Baik JM, Jung JU, Koh CJ, Hong YK
Lymphatic reprogramming by Kaposi sarcoma herpes virus promotes the oncogenic activity of the virus-encoded G-protein-coupled receptor.
Cancer Res 72: 5833-42 (2012)
PM ID: 22942256 PMC3500425 NIHMS404933
408: Machado AC, Saleebyan SB, Holmes BT, Karelina M, Tam J, Kim SY, Kim KH, Dror I, Hodis E, Martz E, Compeau PA, Rohs R
Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes.
Biochem Mol Biol Educ 40: 400-1 (2012)
PM ID: 23166030
409: Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L
DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation.
Cell Rep 2: 1197-206 (2012)
PM ID: 23142663 PMC3978094 NIHMS417448
410: Klvaňa M, Murphy DL, Jeřábek P, Goodman MF, Warshel A, Sweasy JB, Florián J
Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment.
Biochemistry 51: 8829-43 (2012)
PM ID: 23013478 PMC3982232 NIHMS418196
411: Frushicheva MP, Mukherjee S, Warshel A
Electrostatic origin of the catalytic effect of a supramolecular host catalyst.
J Phys Chem B 116: 13353-60 (2012)
PM ID: 23088306 PMC3536831 NIHMS418455
412: Pfaffenbach KT, Pong M, Morgan TE, Wang H, Ott K, Zhou B, Longo VD, Lee AS
GRP78/BiP is a novel downstream target of IGF-1 receptor mediated signaling.
J Cell Physiol 227: 3803-11 (2012)
PM ID: 22422508 PMC3421054 NIHMS364068
413: Liu Z, Tian Y, Machida K, Lai MM, Luo G, Foung SK, Ou JH
Transient activation of the PI3K-AKT pathway by hepatitis C virus to enhance viral entry.
J Biol Chem 287: 41922-30 (2012)
PM ID: 23095753 PMC3516739
414: Sabatinos SA, Green MD, Forsburg SL
Continued DNA synthesis in replication checkpoint mutants leads to fork collapse.
Mol Cell Biol 32: 4986-97 (2012)
PM ID: 23045396 PMC3510540
415: Droniou-Bonzom ME, Cannon PM
A systems biology starter kit for arenaviruses.
Viruses 4: 3625-46 (2012)
PM ID: 23342371 PMC3528283
416: Zhang W, Gao SJ
Exploitation of Cellular Cytoskeletons and Signaling Pathways for Cell Entry by Kaposi's Sarcoma-Associated Herpesvirus and the Closely Related Rhesus Rhadinovirus.
Pathogens 1: 102-127 (2012)
PM ID: 23420076 PMC3571711 NIHMS419304
417: Christensen L, Joo J, Lee S, Wai D, Triche TJ, May WA
FOXM1 is an oncogenic mediator in Ewing Sarcoma.
PLoS One 8: e54556 (2013)
PM ID: 23365673 PMC3554707
418: Wu H, Chen L, Zhang X, Zhou Q, Li JM, Berger S, Borok Z, Zhou B, Xiao Z, Yin H, Liu M, Wang Y, Jin J, Blackburn MR, Xia Y, Zhang W
Aqp5 is a new transcriptional target of Dot1a and a regulator of Aqp2.
PLoS One 8: e53342 (2013)
PM ID: 23326416 PMC3542343
419: Hu J, Wei M, Mirisola MG, Longo VD
Assessing chronological aging in Saccharomyces cerevisiae.
Methods Mol Biol 965: 463-72 (2013)
PM ID: 23296677 PMC4041521 NIHMS585020
420: Gonidakis S, Longo VD
Assessing chronological aging in bacteria.
Methods Mol Biol 965: 421-37 (2013)
PM ID: 23296675 PMC4077615 NIHMS584874
421: Gao F, Wei Z, An W, Wang K, Lu W
The interactomes of POU5F1 and SOX2 enhancers in human embryonic stem cells.
Sci Rep 3: 1588 (2013)
PM ID: 23549118 PMC4070749
422: Li PC, Green MD, Forsburg SL
Mutations disrupting histone methylation have different effects on replication timing in S. pombe centromere.
PLoS One 8: e61464 (2013)
PM ID: 23658693 PMC3641051
423: McCaffrey TA, Tziros C, Lewis J, Katz R, Siegel R, Weglicki W, Kramer J, Mak IT, Toma I, Chen L, Benas E, Lowitt A, Rao S, Witkin L, Lian Y, Lai Y, Yang Z, Fu SW
Genomic profiling reveals the potential role of TCL1A and MDR1 deficiency in chemotherapy-induced cardiotoxicity.
Int J Biol Sci 9: 350-60 (2013)
PM ID: 23630447 PMC3638290
424: Erho N, Crisan A, Vergara IA, Mitra AP, Ghadessi M, Buerki C, Bergstralh EJ, Kollmeyer T, Fink S, Haddad Z, Zimmermann B, Sierocinski T, Ballman KV, Triche TJ, Black PC, Karnes RJ, Klee G, Davicioni E, Jenkins RB
Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy.
PLoS One 8: e66855 (2013)
PM ID: 23826159 PMC3691249
425: Kim K, Punj V, Choi J, Heo K, Kim JM, Laird PW, An W
Gene dysregulation by histone variant H2A.Z in bladder cancer.
Epigenetics Chromatin 6: 34 (2013)
PM ID: 24279307 PMC3853418
426: Kim JM, Heo K, Choi J, Kim K, An W
The histone variant MacroH2A regulates Ca(2+) influx through TRPC3 and TRPC6 channels.
Oncogenesis 2: e77 (2013)
PM ID: 24165580 PMC3816217
427: Okitsu CY, Van Den Berg DJ, Lieber MR, Hsieh CL
Reproducibility and reliability of SNP analysis using human cellular DNA at or near nanogram levels.
BMC Res Notes 6: 515 (2013)
PM ID: 24314330 PMC4029319
428: Klussmann JP, Schädlich PK, Chen X, Rémy V
Annual cost of hospitalization, inpatient rehabilitation, and sick leave for head and neck cancers in Germany.
Clinicoecon Outcomes Res 5: 203-13 (2013)
PM ID: 23717047 PMC3662462
429: Gao W, Weng J, Gao Y, Chen X
Comparison of the vaginal microbiota diversity of women with and without human papillomavirus infection: a cross-sectional study.
BMC Infect Dis 13: 271 (2013)
PM ID: 23758857 PMC3684509
430: Asokan R, Banda NK, Szakonyi G, Chen XS, Holers VM
Human complement receptor 2 (CR2/CD21) as a receptor for DNA: implications for its roles in the immune response and the pathogenesis of systemic lupus erythematosus (SLE).
Mol Immunol 53: 99-110 (2013)
PM ID: 22885687 PMC3439536 NIHMS396375
431: Chakrabarty S, Warshel A
Capturing the energetics of water insertion in biological systems: the water flooding approach.
Proteins 81: 93-106 (2013)
PM ID: 22911614
432: Sottoriva A, Spiteri I, Shibata D, Curtis C, Tavaré S
Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization.
Cancer Res 73: 41-9 (2013)
PM ID: 23090114 PMC3544316
433: Xu J, Lange EM, Lu L, Zheng SL, Wang Z, Thibodeau SN, Cannon-Albright LA, Teerlink CC, Camp NJ, Johnson AM, Zuhlke KA, Stanford JL, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Maier C, Luedeke M, Vogel W, Schleutker J, Wahlfors T, Tammela T, Schaid D, McDonnell SK, Derycke MS, Cancel-Tassin G, Cussenot O, Wiklund F, Grönberg H, Eeles R, Easton D, Kote-Jarai Z, Whittemore AS, Hsieh CL, Giles GG, Hopper JL, Severi G, Catalona WJ, Mandal D, Ledet E, Foulkes WD, Hamel N, Mahle L, Moller P, Powell I, Bailey-Wilson JE, Carpten JD, Seminara D, Cooney KA, Isaacs WB, International Consortium for Prostate Cancer Genetics
HOXB13 is a susceptibility gene for prostate cancer: results from the International Consortium for Prostate Cancer Genetics (ICPCG).
Hum Genet 132: 5-14 (2013)
PM ID: 23064873 PMC3535370
434: Sabatinos SA, Mastro TL, Green MD, Forsburg SL
A mammalian-like DNA damage response of fission yeast to nucleoside analogs.
Genetics 193: 143-57 (2013)
PM ID: 23150603 PMC3527242
435: Rychkova A, Warshel A
Exploring the nature of the translocon-assisted protein insertion.
Proc Natl Acad Sci U S A 110: 495-500 (2013)
PM ID: 23269832 PMC3545795
436: Prasad BR, Plotnikov NV, Warshel A
Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping.
J Phys Chem B 117: 153-63 (2013)
PM ID: 23198768 PMC3542406 NIHMS427102
437: Aparicio OM
Location, location, location: it's all in the timing for replication origins.
Genes Dev 27: 117-28 (2013)
PM ID: 23348837 PMC3566304
438: Kreso A, O'Brien CA, van Galen P, Gan OI, Notta F, Brown AM, Ng K, Ma J, Wienholds E, Dunant C, Pollett A, Gallinger S, McPherson J, Mullighan CG, Shibata D, Dick JE
Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer.
Science 339: 543-8 (2013)
PM ID: 23239622
439: Graham C, Matta H, Yang Y, Yi H, Suo Y, Tolani B, Chaudhary PM
Kaposi's sarcoma-associated herpesvirus oncoprotein K13 protects against B cell receptor-induced growth arrest and apoptosis through NF-κB activation.
J Virol 87: 2242-52 (2013)
PM ID: 23236068 PMC3571451
440: Kamerlin SC, Sharma PK, Prasad RB, Warshel A
Why nature really chose phosphate.
Q Rev Biophys 46: 1-132 (2013)
PM ID: 23318152
441: Matsuo K, Gray MJ, Yang DY, Srivastava SA, Tripathi PB, Sonoda LA, Yoo EJ, Dubeau L, Lee AS, Lin YG
The endoplasmic reticulum stress marker, glucose-regulated protein-78 (GRP78) in visceral adipocytes predicts endometrial cancer progression and patient survival.
Gynecol Oncol 128: 552-9 (2013)
PM ID: 23200913
442: Cui X, Lu Z, Kurosawa A, Klemm L, Bagshaw AT, Tsai AG, Gemmell N, Müschen M, Adachi N, Hsieh CL, Lieber MR
Both CpG methylation and activation-induced deaminase are required for the fragility of the human bcl-2 major breakpoint region: implications for the timing of the breaks in the t(14;18) translocation.
Mol Cell Biol 33: 947-57 (2013)
PM ID: 23263985 PMC3623081
443: Slaymaker IM, Fu Y, Toso DB, Ranatunga N, Brewster A, Forsburg SL, Zhou ZH, Chen XS
Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology.
Nucleic Acids Res 41: 3446-56 (2013)
PM ID: 23361460 PMC3597688
444: Pope BD, Aparicio OM, Gilbert DM
SnapShot: Replication timing.
Cell 152: 1390-1390.e1 (2013)
PM ID: 23498945
445: Li PC, Petreaca RC, Jensen A, Yuan JP, Green MD, Forsburg SL
Replication fork stability is essential for the maintenance of centromere integrity in the absence of heterochromatin.
Cell Rep 3: 638-45 (2013)
PM ID: 23478021 PMC3652564 NIHMS445375
446: Trisciuoglio D, De Luca T, Desideri M, Passeri D, Gabellini C, Scarpino S, Liang C, Orlandi A, Del Bufalo D
Removal of the BH4 domain from Bcl-2 protein triggers an autophagic process that impairs tumor growth.
Neoplasia 15: 315-27 (2013)
PM ID: 23479509 PMC3593154
447: Ramsingh G, Westervelt P, Cashen AF, Uy GL, Stockerl-Goldstein K, Abboud CN, Bernabe N, Monahan R, DiPersio JF, Vij R
A phase 1 study of concomitant high-dose lenalidomide and 5-azacitidine induction in the treatment of AML.
Leukemia 27: 725-8 (2013)
PM ID: 22828444
448: Pelikan RC, Iwata J, Suzuki A, Chai Y, Hacia JG
Identification of candidate downstream targets of TGFβ signaling during palate development by genome-wide transcript profiling.
J Cell Biochem 114: 796-807 (2013)
PM ID: 23060211 PMC3777336 NIHMS470529
449: Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD
Low-level processing of Illumina Infinium DNA Methylation BeadArrays.
Nucleic Acids Res 41: e90 (2013)
PM ID: 23476028 PMC3627582
450: Hsieh JC, Van Den Berg D, Kang H, Hsieh CL, Lieber MR
Large chromosome deletions, duplications, and gene conversion events accumulate with age in normal human colon crypts.
Aging Cell 12: 269-79 (2013)
PM ID: 23425690
451: Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ
Probing DNA shape and methylation state on a genomic scale with DNase I.
Proc Natl Acad Sci U S A 110: 6376-81 (2013)
PM ID: 23576721 PMC3631675
452: Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.
Cell Rep 3: 1093-104 (2013)
PM ID: 23562153 PMC3640701 NIHMS459092
453: Chang YP, Xu M, Machado AC, Yu XJ, Rohs R, Chen XS
Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen.
Cell Rep 3: 1117-27 (2013)
PM ID: 23545501 PMC3748285 NIHMS453299
454: Indiani C, Patel M, Goodman MF, O'Donnell ME
RecA acts as a switch to regulate polymerase occupancy in a moving replication fork.
Proc Natl Acad Sci U S A 110: 5410-5 (2013)
PM ID: 23509251 PMC3619308
455: Amini-Bavil-Olyaee S, Choi YJ, Lee JH, Shi M, Huang IC, Farzan M, Jung JU
The antiviral effector IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry.
Cell Host Microbe 13: 452-64 (2013)
PM ID: 23601107 PMC3646482 NIHMS460345
456: Parrella E, Maxim T, Maialetti F, Zhang L, Wan J, Wei M, Cohen P, Fontana L, Longo VD
Protein restriction cycles reduce IGF-1 and phosphorylated Tau, and improve behavioral performance in an Alzheimer's disease mouse model.
Aging Cell 12: 257-68 (2013)
PM ID: 23362919 PMC3982836 NIHMS566268
457: Zhong Y, Nellimoottil T, Peace JM, Knott SR, Villwock SK, Yee JM, Jancuska JM, Rege S, Tecklenburg M, Sclafani RA, Tavaré S, Aparicio OM
The level of origin firing inversely affects the rate of replication fork progression.
J Cell Biol 201: 373-83 (2013)
PM ID: 23629964 PMC3639389
458: Heo K, Kim JS, Kim K, Kim H, Choi J, Yang K, An W
Cell-penetrating H4 tail peptides potentiate p53-mediated transactivation via inhibition of G9a and HDAC1.
Oncogene 32: 2510-20 (2013)
PM ID: 22751130
459: Parekh C, Crooks GM
Critical differences in hematopoiesis and lymphoid development between humans and mice.
J Clin Immunol 33: 711-5 (2013)
PM ID: 23274800 PMC3633618 NIHMS432026
460: Getz G, Gabriel SB, Cibulskis K, Lander E, Sivachenko A, Sougnez C, Lawrence M, Kandoth C, Dooling D, Fulton R, Fulton L, Kalicki-Veizer J, McLellan MD, O'Laughlin M, Schmidt H, Wilson RK, Ye K, Ding L, Mardis ER, Ally A, Balasundaram M, Birol I, Butterfield YS, Carlsen R, Carter C, Chu A, Chuah E, Chuah HJ, Dhalla N, Guin R, Hirst C, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Plettner P, Schein JE, Sipahimalani P, Tam A, Varhol RJ, Robertson A, Cherniack AD, Pashtan I, Saksena G, Onofrio RC, Schumacher SE, Tabak B, Carter SL, Hernandez B, Gentry J, Salvesen HB, Ardlie K, Getz G, Winckler W, Beroukhim R, Gabriel SB, Meyerson M, Hadjipanayis A, Lee S, Mahadeshwar HS, Park P, Protopopov A, Ren X, Seth S, Song X, Tang J, Xi R, Yang L, Zeng D, Kucherlapati R, Chin L, Zhang J, Auman T, Balu S, Bodenheimer T, Buda E, Hayes D, Hoyle AP, Jefferys SR, Jones CD, Meng S, Mieczkowski PA, Mose LE, Parker JS, Perou CM, Roach J, Shi Y, Simons JV, Soloway MG, Tan D, Topal MD, Waring S, Wu J, Hoadley KA, Baylin SB, Bootwalla MS, Lai PH, Triche TJ, Van Den Berg DJ, Weisenberger DJ, Laird PW, Shen H, Chin L, Zhang J, Getz G, Cho J, DiCara D, Frazer S, Heiman D, Jing R, Lin P, Mallard W, Stojanov P, Voet D, Zhang H, Zou L, Noble M, Lawrence M, Reynolds SM, Shmulevich I, Aksoy B, Antipin Y, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Ladanyi M, Reva B, Sander C, Sinha R, Sumer S, Taylor BS, Cerami E, Weinhold N, Schultz N, Shen R, Benz S, Goldstein T, Haussler D, Ng S, Szeto C, Stuart J, Benz CC, Yau C, Zhang W, Annala M, Broom BM, Casasent TD, Ju Z, Liang H, Liu G, Lu Y, Unruh AK, Wakefield C, Weinstein JN, Zhang N, Liu Y, Broaddus R, Akbani R, Mills GB, Adams C, Barr T, Black AD, Bowen J, Deardurff J, Frick J, Gastier-Foster JM, Grossman T, Harper HA, Hart-Kothari M, Helsel C, Hobensack A, Kuck H, Kneile K, Leraas KM, Lichtenberg TM, McAllister C, Pyatt RE, Ramirez NC, Tabler TR, Vanhoose N, White P, Wise L, Zmuda E, Barnabas N, Berry-Green C, Blanc V, Boice L, Button M, Farkas A, Green A, MacKenzie J, Nicholson D, Kalloger SE, Gilks CB, Karlan BY, Lester J, Orsulic S, Borowsky M, Cadungog M, Czerwinski C, Huelsenbeck-Dill L, Iacocca M, Petrelli N, Rabeno B, Witkin G, Nemirovich-Danchenko E, Potapova O, Rotin D, Berchuck A, Birrer M, DiSaia P, Monovich L, Curley E, Gardner J, Mallery D, Penny R, Dowdy SC, Winterhoff B, Dao L, Gostout B, Meuter A, Teoman A, Dao F, Olvera N, Bogomolniy F, Garg K, Soslow RA, Levine DA, Abramov M, Bartlett JM, Kodeeswaran S, Parfitt J, Moiseenko F, Clarke BA, Goodman MT, Carney ME, Matsuno RK, Fisher J, Huang M, Rathmell W, Thorne L, Van Le L, Dhir R, Edwards R, Elishaev E, Zorn K, Broaddus R, Goodfellow PJ, Mutch D, Schultz N, Liu Y, Akbani R, Cherniack AD, Cerami E, Weinhold N, Shen H, Hoadley KA, Kahn AB, Bell DW, Pollock PM, Wang C, Wheeler DA, Shinbrot E, Karlan BY, Berchuck A, Dowdy SC, Winterhoff B, Goodman MT, Robertson A, Beroukhim R, Pashtan I, Salvesen HB, Laird PW, Noble M, Stuart J, Ding L, Kandoth C, Gilks C, Soslow RA, Goodfellow PJ, Mutch D, Broaddus R, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA, Ayala B, Chu AL, Jensen MA, Kothiyal P, Pihl TD, Pontius J, Pot DA, Snyder EE, Srinivasan D, Kahn AB, Shaw KR, Sheth M, Davidsen T, Eley G, Ferguson ML, Demchok JA, Yang L, Guyer MS, Ozenberger BA, Sofia HJ, Cancer Genome Atlas Research Network , Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA
Integrated genomic characterization of endometrial carcinoma.
Nature 497: 67-73 (2013)
PM ID: 23636398 PMC3704730 NIHMS458933
461: Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G, Alonso S, Ayala B, Baboud J, Backus M, Barletta SP, Berton DL, Chu AL, Girshik S, Jensen MA, Kahn A, Kothiyal P, Nicholls MC, Pihl TD, Pot DA, Raman R, Sanbhadti RN, Snyder EE, Srinivasan D, Walton J, Wan Y, Wang Z, Issa JP, Le Beau M, Carroll M, Kantarjian H, Kornblau S, Bootwalla MS, Lai PH, Shen H, Van Den Berg DJ, Weisenberger DJ, Link DC, Walter MJ, Ozenberger BA, Mardis ER, Westervelt P, Graubert TA, Dipersio JF, Wilson RK, Cancer Genome Atlas Research Network
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.
N Engl J Med 368: 2059-74 (2013)
PM ID: 23634996 PMC3767041 NIHMS491910
462: Lu Z, Tsai AG, Akasaka T, Ohno H, Jiang Y, Melnick AM, Greisman HA, Lieber MR
BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements.
Blood 121: 4551-4 (2013)
PM ID: 23476051 PMC3668488
463: Toth Z, Brulois K, Jung JU
The chromatin landscape of Kaposi's sarcoma-associated herpesvirus.
Viruses 5: 1346-73 (2013)
PM ID: 23698402 PMC3712311
464: Kao YP, Hsieh WC, Hung ST, Huang CW, Lieber MR, Huang FT
Detection and characterization of R-loops at the murine immunoglobulin Sα region.
Mol Immunol 54: 208-16 (2013)
PM ID: 23287599
465: Ye FC, Zhou FC, Nithianantham S, Chandran B, Yu XL, Weinberg A, Gao SJ
Kaposi's sarcoma-associated herpesvirus induces rapid release of angiopoietin-2 from endothelial cells.
J Virol 87: 6326-35 (2013)
PM ID: 23536671 PMC3648120
466: Li L, Krymskaya L, Wang J, Henley J, Rao A, Cao LF, Tran CA, Torres-Coronado M, Gardner A, Gonzalez N, Kim K, Liu PQ, Hofer U, Lopez E, Gregory PD, Liu Q, Holmes MC, Cannon PM, Zaia JA, Digiusto DL
Genomic editing of the HIV-1 coreceptor CCR5 in adult hematopoietic stem and progenitor cells using zinc finger nucleases.
Mol Ther 21: 1259-69 (2013)
PM ID: 23587921 PMC3677314
467: Yoon SR, Choi SK, Eboreime J, Gelb BD, Calabrese P, Arnheim N
Age-dependent germline mosaicism of the most common noonan syndrome mutation shows the signature of germline selection.
Am J Hum Genet 92: 917-26 (2013)
PM ID: 23726368 PMC3682763
468: Corzett CH, Goodman MF, Finkel SE
Competitive fitness during feast and famine: how SOS DNA polymerases influence physiology and evolution in Escherichia coli.
Genetics 194: 409-20 (2013)
PM ID: 23589461 PMC3664851
469: Pomerantz RT, Kurth I, Goodman MF, O'Donnell ME
Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination.
Nat Struct Mol Biol 20: 748-55 (2013)
PM ID: 23686288 PMC3685420 NIHMS467652
470: Rychkova A, Mukherjee S, Bora RP, Warshel A
Simulating the pulling of stalled elongated peptide from the ribosome by the translocon.
Proc Natl Acad Sci U S A 110: 10195-200 (2013)
PM ID: 23729811 PMC3690858
471: Hong EE, Okitsu CY, Smith AD, Hsieh CL
Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA.
Mol Cell Biol 33: 2683-90 (2013)
PM ID: 23671186 PMC3700126 [Available on 01/01/14]
472: Zhou T, Yang L, Lu Y, Dror I, Dantas Machado AC, Ghane T, Di Felice R, Rohs R
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.
Nucleic Acids Res 41: W56-62 (2013)
PM ID: 23703209 PMC3692085
473: Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC
Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
Nucleic Acids Res 41: 6750-60 (2013)
PM ID: 23661683 PMC3711457
474: Mendoza-Naranjo A, El-Naggar A, Wai DH, Mistry P, Lazic N, Ayala FR, da Cunha IW, Rodriguez-Viciana P, Cheng H, Tavares Guerreiro Fregnani JH, Reynolds P, Arceci RJ, Nicholson A, Triche TJ, Soares FA, Flanagan AM, Wang YZ, Strauss SJ, Sorensen PH
ERBB4 confers metastatic capacity in Ewing sarcoma.
EMBO Mol Med 5: 1019-34 (2013)
PM ID: 23681745 PMC3721475
475: Wei Z, Gao F, Kim S, Yang H, Lyu J, An W, Wang K, Lu W
Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency.
Cell Stem Cell 13: 36-47 (2013)
PM ID: 23747203
476: Le AH, Mastro TL, Forsburg SL
The C-terminus of S. pombe DDK subunit Dfp1 is required for meiosis-specific transcription and cohesin cleavage.
Biol Open 2: 728-38 (2013)
PM ID: 23862021 PMC3711041
477: St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.
Genome Biol 14: R73 (2013)
PM ID: 23876380 PMC4053963
478: Wang Y, Lu X, Zhu L, Shen Y, Chengedza S, Feng H, Wang L, Jung JU, Gutkind JS, Gutkind JS, Feng P
IKK epsilon kinase is crucial for viral G protein-coupled receptor tumorigenesis.
Proc Natl Acad Sci U S A 110: 11139-44 (2013)
PM ID: 23771900 PMC3703966
479: Chen X, Liu G, Leffak M
Activation of a human chromosomal replication origin by protein tethering.
Nucleic Acids Res 41: 6460-74 (2013)
PM ID: 23658226 PMC3711443
480: Gu Y, Wang J, Li S, Kamiya K, Chen X, Zhou P
Determination of the biochemical properties of full-length human PIF1 ATPase.
Prion 7: 341-7 (2013)
PM ID: 23924759 PMC3904321
481: Wu X, Gong S, Roy-Burman P, Lee P, Culig Z
Current mouse and cell models in prostate cancer research.
Endocr Relat Cancer 20: R155-70 (2013)
PM ID: 23580590 PMC3855867 NIHMS497209
482: Czaja MJ, Ding WX, Donohue TM, Friedman SL, Kim JS, Komatsu M, Lemasters JJ, Lemoine A, Lin JD, Ou JH, Perlmutter DH, Randall G, Ray RB, Tsung A, Yin XM
Functions of autophagy in normal and diseased liver.
Autophagy 9: 1131-58 (2013)
PM ID: 23774882 PMC3748187
483: Law MJ, Lee DS, Lee CS, Anglim PP, Haworth IS, Laird-Offringa IA
The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA.
Nucleic Acids Res 41: 7092-100 (2013)
PM ID: 23703211 PMC3737524
484: Wei Z, Huang D, Gao F, Chang WH, An W, Coetzee GA, Wang K, Lu W
Biological implications and regulatory mechanisms of long-range chromosomal interactions.
J Biol Chem 288: 22369-77 (2013)
PM ID: 23779110 PMC3829327
485: Riedel TE, Berelson WM, Nealson KH, Finkel SE
Oxygen consumption rates of bacteria under nutrient-limited conditions.
Appl Environ Microbiol 79: 4921-31 (2013)
PM ID: 23770901 PMC3754705
486: Pomerantz RT, Goodman MF, O'Donnell ME
DNA polymerases are error-prone at RecA-mediated recombination intermediates.
Cell Cycle 12: 2558-63 (2013)
PM ID: 23907132 PMC3865045
487: Jaszczur M, Bertram JG, Pham P, Scharff MD, Goodman MF
AID and Apobec3G haphazard deamination and mutational diversity.
Cell Mol Life Sci 70: 3089-108 (2013)
PM ID: 23178850 PMC3600397 NIHMS424222
488: Skapek SX, Anderson J, Barr FG, Bridge JA, Gastier-Foster JM, Parham DM, Rudzinski ER, Triche T, Hawkins DS
PAX-FOXO1 fusion status drives unfavorable outcome for children with rhabdomyosarcoma: a children's oncology group report.
Pediatr Blood Cancer 60: 1411-7 (2013)
PM ID: 23526739
489: Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L
Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.
Nucleic Acids Res 41: 8368-76 (2013)
PM ID: 23836939 PMC3783167
490: Awad S, Kunhi M, Little GH, Bai Y, An W, Bers D, Kedes L, Poizat C
Nuclear CaMKII enhances histone H3 phosphorylation and remodels chromatin during cardiac hypertrophy.
Nucleic Acids Res 41: 7656-72 (2013)
PM ID: 23804765 PMC3763528
491: Gopalakrishnan R, Matta H, Chaudhary PM
A purine scaffold HSP90 inhibitor BIIB021 has selective activity against KSHV-associated primary effusion lymphoma and blocks vFLIP K13-induced NF-κB.
Clin Cancer Res 19: 5016-26 (2013)
PM ID: 23881928 PMC3804723 NIHMS510002
492: Nguyen P, Shi X, Sigurdsson ST, Herschlag D, Qin PZ
A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme.
Chembiochem 14: 1720-3 (2013)
PM ID: 23900919 PMC3817310 NIHMS512386
493: Wilson RA, Teng L, Bachmeyer KM, Bissonnette ML, Husain AN, Parham DM, Triche TJ, Wing MR, Gastier-Foster JM, Barr FG, Hawkins DS, Anderson JR, Skapek SX, Volchenboum SL
A novel algorithm for simplification of complex gene classifiers in cancer.
Cancer Res 73: 5625-32 (2013)
PM ID: 23913937
494: Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A
Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces.
J Phys Chem B 117: 12807-19 (2013)
PM ID: 23601038 PMC3797183 NIHMS471698
495: Brandhorst S, Wei M, Hwang S, Morgan TE, Longo VD
Short-term calorie and protein restriction provide partial protection from chemotoxicity but do not delay glioma progression.
Exp Gerontol 48: 1120-8 (2013)
PM ID: 23454633 PMC3762887 NIHMS462462
496: Shinde DN, Elmer DP, Calabrese P, Boulanger J, Arnheim N, Tiemann-Boege I
New evidence for positive selection helps explain the paternal age effect observed in achondroplasia.
Hum Mol Genet 22: 4117-26 (2013)
PM ID: 23740942 PMC3781639
497: Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z
Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
Nucleic Acids Res 41: 8748-59 (2013)
PM ID: 23863845 PMC3794590
498: Reiff A, Weinberg KI, Triche T, Masinsin B, Mahadeo KM, Lin CH, Brown D, Parkman R
T lymphocyte abnormalities in juvenile systemic sclerosis patients.
Clin Immunol 149: 146-55 (2013)
PM ID: 23994768
499: Wiseman SM, Haddad Z, Walker B, Vergara IA, Sierocinski T, Crisan A, Ghadessi M, Dao P, Zimmermann B, Triche TJ, Erho N, Davicioni E
Whole-transcriptome profiling of thyroid nodules identifies expression-based signatures for accurate thyroid cancer diagnosis.
J Clin Endocrinol Metab 98: 4072-9 (2013)
PM ID: 23928671
500: Fam HK, Walton C, Mitra SA, Chowdhury M, Osborne N, Choi K, Sun G, Wong PC, O'Sullivan MJ, Turashvili G, Aparicio S, Triche TJ, Bond M, Pallen CJ, Boerkoel CF
TDP1 and PARP1 deficiency are cytotoxic to rhabdomyosarcoma cells.
Mol Cancer Res 11: 1179-92 (2013)
PM ID: 23913164
501: Goodman MF, Woodgate R
Translesion DNA polymerases.
Cold Spring Harb Perspect Biol 5: a010363 (2013)
PM ID: 23838442
502: Mak CH, Pham P, Afif SA, Goodman MF
A mathematical model for scanning and catalysis on single-stranded DNA, illustrated with activation-induced deoxycytidine deaminase.
J Biol Chem 288: 29786-95 (2013)
PM ID: 23979486 PMC3795277
503: Pham P, Landolph A, Mendez C, Li N, Goodman MF
A biochemical analysis linking APOBEC3A to disparate HIV-1 restriction and skin cancer.
J Biol Chem 288: 29294-304 (2013)
PM ID: 23979356 PMC3795231
504: Ramsingh G, Jacoby MA, Shao J, De Jesus Pizzaro RE, Shen D, Trissal M, Getz AH, Ley TJ, Walter MJ, Link DC
Acquired copy number alterations of miRNA genes in acute myeloid leukemia are uncommon.
Blood 122: e44-51 (2013)
PM ID: 24009227 PMC3795465
505: Shen J, Tower J
Aging, MnSOD, and hormesis mechanisms converge on liver mUPR.
Cell Cycle 12: 3237-8 (2013)
PM ID: 24036542 PMC3885629
506: Wei L, Nakajima S, Hsieh CL, Kanno S, Masutani M, Levine AS, Yasui A, Lan L
Damage response of XRCC1 at sites of DNA single strand breaks is regulated by phosphorylation and ubiquitylation after degradation of poly(ADP-ribose).
J Cell Sci 126: 4414-23 (2013)
PM ID: 23868975 PMC3784821
507: Silva LM, Jung JU
Modulation of the autophagy pathway by human tumor viruses.
Semin Cancer Biol 23: 323-8 (2013)
PM ID: 23727156 PMC3791178 NIHMS486348
508: Mukherjee S, Warshel A
Electrostatic origin of the unidirectionality of walking myosin V motors.
Proc Natl Acad Sci U S A 110: 17326-31 (2013)
PM ID: 24106304 PMC3808596
509: He S, Ni D, Ma B, Lee JH, Zhang T, Ghozalli I, Pirooz SD, Zhao Z, Bharatham N, Li B, Oh S, Lee WH, Takahashi Y, Wang HG, Minassian A, Feng P, Deretic V, Pepperkok R, Tagaya M, Yoon HS, Liang C
PtdIns(3)P-bound UVRAG coordinates Golgi-ER retrograde and Atg9 transport by differential interactions with the ER tether and the beclin 1 complex.
Nat Cell Biol 15: 1206-19 (2013)
PM ID: 24056303 PMC3805255 NIHMS517928
510: Wilson MA, Kwon Y, Xu Y, Chung WH, Chi P, Niu H, Mayle R, Chen X, Malkova A, Sung P, Ira G
Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration.
Nature 502: 393-6 (2013)
PM ID: 24025768 PMC3915060 NIHMS518346
511: Dubeau L, Drapkin R
Coming into focus: the nonovarian origins of ovarian cancer.
Ann Oncol 24 Suppl 8: viii28-viii35 (2013)
PM ID: 24131966 PMC3805308
512: Widschwendter M, Rosenthal AN, Philpott S, Rizzuto I, Fraser L, Hayward J, Intermaggio MP, Edlund CK, Ramus SJ, Gayther SA, Dubeau L, Fourkala EO, Zaikin A, Menon U, Jacobs IJ
The sex hormone system in carriers of BRCA1/2 mutations: a case-control study.
Lancet Oncol 14: 1226-32 (2013)
PM ID: 24140203
513: Kim K, Kim JM, Kim JS, Choi J, Lee YS, Neamati N, Song JS, Heo K, An W
VprBP has intrinsic kinase activity targeting histone H2A and represses gene transcription.
Mol Cell 52: 459-67 (2013)
PM ID: 24140421 PMC3851289 NIHMS531474
514: Wong LY, Brulois K, Toth Z, Inn KS, Lee SH, O'Brien K, Lee H, Gao SJ, Cesarman E, Ensser A, Jung JU
The product of Kaposi's sarcoma-associated herpesvirus immediate early gene K4.2 regulates immunoglobulin secretion and calcium homeostasis by interacting with and inhibiting pERP1.
J Virol 87: 12069-79 (2013)
PM ID: 23986581 PMC3807884
515: Liang Q, Chang B, Brulois KF, Castro K, Min CK, Rodgers MA, Shi M, Ge J, Feng P, Oh BH, Jung JU
Kaposi's sarcoma-associated herpesvirus K7 modulates Rubicon-mediated inhibition of autophagosome maturation.
J Virol 87: 12499-503 (2013)
PM ID: 24027317 PMC3807930
516: Rychkova A, Warshel A
On the nature of the apparent free energy of inserting amino acids into membrane through the translocon.
J Phys Chem B 117: 13748-54 (2013)
PM ID: 24087983 PMC3931232 NIHMS530756
517: Hofer U, Henley JE, Exline CM, Mulhern O, Lopez E, Cannon PM
Pre-clinical modeling of CCR5 knockout in human hematopoietic stem cells by zinc finger nucleases using humanized mice.
J Infect Dis 208 Suppl 2: S160-4 (2013)
PM ID: 24151324 PMC3807977
518: Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex.
Nat Genet 45: 1392-8 (2013)
PM ID: 24076601 PMC3812362 NIHMS521199
519: Karnes RJ, Bergstralh EJ, Davicioni E, Ghadessi M, Buerki C, Mitra AP, Crisan A, Erho N, Vergara IA, Lam LL, Carlson R, Thompson DJ, Haddad Z, Zimmermann B, Sierocinski T, Triche TJ, Kollmeyer T, Ballman KV, Black PC, Klee GG, Jenkins RB
Validation of a genomic classifier that predicts metastasis following radical prostatectomy in an at risk patient population.
J Urol 190: 2047-53 (2013)
PM ID: 23770138
520: Kim K, Lee B, Kim J, Choi J, Kim JM, Xiong Y, Roeder RG, An W
Linker Histone H1.2 cooperates with Cul4A and PAF1 to drive H4K31 ubiquitylation-mediated transactivation.
Cell Rep 5: 1690-703 (2013)
PM ID: 24360965 PMC3901356 NIHMS545033
521: Maeda K, Almofty SA, Singh SK, Eid MM, Shimoda M, Ikeda T, Koito A, Pham P, Goodman MF, Sakaguchi N
GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity.
J Immunol 191: 6030-9 (2013)
PM ID: 24198285 PMC4086635 NIHMS531550
522: B RP, Plotnikov NV, Lameira J, Warshel A
Quantitative exploration of the molecular origin of the activation of GTPase.
Proc Natl Acad Sci U S A 110: 20509-14 (2013)
PM ID: 24282301 PMC3870692
523: Pham LK, Liang M, Adisetiyo HA, Liao CP, Cohen MB, Tahara SM, Frenkel B, Kasahara N, Roy-Burman P
Contextual effect of repression of bone morphogenetic protein activity in prostate cancer.
Endocr Relat Cancer 20: 861-74 (2013)
PM ID: 24042462 PMC3885249 NIHMS537855
524: Raji CA, Tarzwell R, Pavel D, Schneider H, Uszler M, Thornton J, van Lierop M, Cohen P, Amen DG, Henderson T
Clinical utility of SPECT neuroimaging in the diagnosis and treatment of traumatic brain injury: a systematic review.
PLoS One 9: e91088 (2014)
PM ID: 24646878 PMC3960124
525: Ostrow AZ, Nellimoottil T, Knott SR, Fox CA, Tavaré S, Aparicio OM
Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics.
PLoS One 9: e87647 (2014)
PM ID: 24504085 PMC3913637
526: Fischer JM, Schepers AG, Clevers H, Shibata D, Liskay RM
Occult progression by Apc-deficient intestinal crypts as a target for chemoprevention.
Carcinogenesis 35: 237-46 (2014)
PM ID: 23996931 PMC3871938
527: Dror I, Zhou T, Mandel-Gutfreund Y, Rohs R
Covariation between homeodomain transcription factors and the shape of their DNA binding sites.
Nucleic Acids Res 42: 430-41 (2014)
PM ID: 24078250 PMC3874178
528: Rodgers MA, Bowman JW, Liang Q, Jung JU
Regulation where autophagy intersects the inflammasome.
Antioxid Redox Signal 20: 495-506 (2014)
PM ID: 23642014 PMC3894701
529: Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R
TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Nucleic Acids Res 42: D148-55 (2014)
PM ID: 24214955 PMC3964943
530: He S, O'Connell D, Zhang X, Yang Y, Liang C
The intersection of Golgi-ER retrograde and autophagic trafficking.
Autophagy 10: 180-1 (2014)
PM ID: 24246972
531: Bai Z, Huang Y, Li W, Zhu Y, Jung JU, Lu C, Gao SJ
Genomewide mapping and screening of Kaposi's sarcoma-associated herpesvirus (KSHV) 3' untranslated regions identify bicistronic and polycistronic viral transcripts as frequent targets of KSHV microRNAs.
J Virol 88: 377-92 (2014)
PM ID: 24155407 PMC3911756
532: Cohen P, Levy JD, Zhang Y, Frontini A, Kolodin DP, Svensson KJ, Lo JC, Zeng X, Ye L, Khandekar MJ, Wu J, Gunawardana SC, Banks AS, Camporez JP, Jurczak MJ, Kajimura S, Piston DW, Mathis D, Cinti S, Shulman GI, Seale P, Spiegelman BM
Ablation of PRDM16 and beige adipose causes metabolic dysfunction and a subcutaneous to visceral fat switch.
Cell 156: 304-16 (2014)
PM ID: 24439384 PMC3922400 NIHMS552456
533: Lin KM, Hu W, Troutman TD, Jennings M, Brewer T, Li X, Nanda S, Cohen P, Thomas JA, Pasare C
IRAK-1 bypasses priming and directly links TLRs to rapid NLRP3 inflammasome activation.
Proc Natl Acad Sci U S A 111: 775-80 (2014)
PM ID: 24379360 PMC3896167
534: Galet C, Gollapudi K, Stepanian S, Byrd JB, Henning SM, Grogan T, Elashoff D, Heber D, Said J, Cohen P, Aronson WJ
Effect of a low-fat fish oil diet on proinflammatory eicosanoids and cell-cycle progression score in men undergoing radical prostatectomy.
Cancer Prev Res (Phila) 7: 97-104 (2014)
PM ID: 24169960 PMC3947245 NIHMS536914
535: Qi M, Zhang J, Zeng W, Chen X
DNAJB1 stabilizes MDM2 and contributes to cancer cell proliferation in a p53-dependent manner.
Biochim Biophys Acta 1839: 62-9 (2014)
PM ID: 24361594
536: Finch CE, Tower J
Sex-specific aging in flies, worms, and missing great-granddads.
Cell 156: 398-9 (2014)
PM ID: 24485449 PMC3988832 NIHMS559707
537: Lan L, Nakajima S, Wei L, Sun L, Hsieh CL, Sobol RW, Bruchez M, Van Houten B, Yasui A, Levine AS
Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin.
Nucleic Acids Res 42: 2330-45 (2014)
PM ID: 24293652 PMC3936713
538: Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.
Nucleic Acids Res 42: 2789-97 (2014)
PM ID: 24293651 PMC3936745
539: Pirooz SD, He S, Zhang T, Zhang X, Zhao Z, Oh S, O'Connell D, Khalilzadeh P, Amini-Bavil-Olyaee S, Farzan M, Liang C
UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs.
Proc Natl Acad Sci U S A 111: 2716-21 (2014)
PM ID: 24550300 PMC3932887
540: Coleman CB, McGraw JE, Feldman ER, Roth AN, Keyes LR, Grau KR, Cochran SL, Waldschmidt TJ, Liang C, Forrest JC, Tibbetts SA
A gammaherpesvirus Bcl-2 ortholog blocks B cell receptor-mediated apoptosis and promotes the survival of developing B cells in vivo.
PLoS Pathog 10: e1003916 (2014)
PM ID: 24516386 PMC3916410
541: Kim I, Warshel A
Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel.
Proc Natl Acad Sci U S A 111: 2128-33 (2014)
PM ID: 24464485 PMC3926088
542: Lee HR, Doğanay S, Chung B, Toth Z, Brulois K, Lee S, Kanketayeva Z, Feng P, Ha T, Jung JU
Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 4 (vIRF4) targets expression of cellular IRF4 and the Myc gene to facilitate lytic replication.
J Virol 88: 2183-94 (2014)
PM ID: 24335298 PMC3911525
543: Kram KE, Finkel SE
Culture volume and vessel affect long-term survival, mutation frequency, and oxidative stress of Escherichia coli.
Appl Environ Microbiol 80: 1732-8 (2014)
PM ID: 24375138 PMC3957596
544: Chen L, Charrier A, Zhou Y, Chen R, Yu B, Agarwal K, Tsukamoto H, Lee LJ, Paulaitis ME, Brigstock DR
Epigenetic regulation of connective tissue growth factor by MicroRNA-214 delivery in exosomes from mouse or human hepatic stellate cells.
Hepatology 59: 1118-29 (2014)
PM ID: 24122827 PMC3943742 NIHMS531561
545: Li S, Chang HH, Niewolik D, Hedrick MP, Pinkerton AB, Hassig CA, Schwarz K, Lieber MR
Evidence that the DNA endonuclease ARTEMIS also has intrinsic 5'-exonuclease activity.
J Biol Chem 289: 7825-34 (2014)
PM ID: 24500713 PMC3953294
546: Jones T, Ramos da Silva S, Bedolla R, Ye F, Zhou F, Gao SJ
Viral cyclin promotes KSHV-induced cellular transformation and tumorigenesis by overriding contact inhibition.
Cell Cycle 13: 845-58 (2014)
PM ID: 24419204 PMC3979920
547: Levine ME, Suarez JA, Brandhorst S, Balasubramanian P, Cheng CW, Madia F, Fontana L, Mirisola MG, Guevara-Aguirre J, Wan J, Passarino G, Kennedy BK, Wei M, Cohen P, Crimmins EM, Longo VD
Low protein intake is associated with a major reduction in IGF-1, cancer, and overall mortality in the 65 and younger but not older population.
Cell Metab 19: 407-17 (2014)
PM ID: 24606898 PMC3988204 NIHMS569447
548: Cohen P
New role for the mitochondrial peptide humanin: protective agent against chemotherapy-induced side effects.
J Natl Cancer Inst 106: dju006 (2014)
PM ID: 24586106 PMC3982780
549: André F, Bachelot T, Commo F, Campone M, Arnedos M, Dieras V, Lacroix-Triki M, Lacroix L, Cohen P, Gentien D, Adélaide J, Dalenc F, Goncalves A, Levy C, Ferrero JM, Bonneterre J, Lefeuvre C, Jimenez M, Filleron T, Bonnefoi H
Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER).
Lancet Oncol 15: 267-74 (2014)
PM ID: 24508104
550: Teerlink CC, Thibodeau SN, McDonnell SK, Schaid DJ, Rinckleb A, Maier C, Vogel W, Cancel-Tassin G, Egrot C, Cussenot O, Foulkes WD, Giles GG, Hopper JL, Severi G, Eeles R, Easton D, Kote-Jarai Z, Guy M, Cooney KA, Ray AM, Zuhlke KA, Lange EM, FitzGerald LM, Stanford JL, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Isaacs WB, Wahlfors T, Tammela T, Schleutker J, Wiklund F, Grönberg H, Emanuelsson M, Carpten J, Bailey-Wilson J, Whittemore AS, Oakley-Girvan I, Hsieh CL, Catalona WJ, Zheng SL, Jin G, Lu L, Xu J, International Consortium for Prostate Cancer Genetics , Camp NJ, Cannon-Albright LA
Association analysis of 9,560 prostate cancer cases from the International Consortium of Prostate Cancer Genetics confirms the role of reported prostate cancer associated SNPs for familial disease.
Hum Genet 133: 347-56 (2014)
PM ID: 24162621 PMC3945961 NIHMS535278
551: Ross AE, Feng FY, Ghadessi M, Erho N, Crisan A, Buerki C, Sundi D, Mitra AP, Vergara IA, Thompson DJ, Triche TJ, Davicioni E, Bergstralh EJ, Jenkins RB, Karnes RJ, Schaeffer EM
A genomic classifier predicting metastatic disease progression in men with biochemical recurrence after prostatectomy.
Prostate Cancer Prostatic Dis 17: 64-9 (2014)
PM ID: 24145624
552: Tower J, Landis G, Gao R, Luan A, Lee J, Sun Y
Variegated expression of Hsp22 transgenic reporters indicates cell-specific patterns of aging in Drosophila oenocytes.
J Gerontol A Biol Sci Med Sci 69: 253-9 (2014)
PM ID: 23723429 PMC3976136
553: Oertell K, Chamberlain BT, Wu Y, Ferri E, Kashemirov BA, Beard WA, Wilson SH, McKenna CE, Goodman MF
Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration.
Biochemistry 53: 1842-8 (2014)
PM ID: 24580380 PMC3985788
554: Donigan KA, McLenigan MP, Yang W, Goodman MF, Woodgate R
The steric gate of DNA polymerase ι regulates ribonucleotide incorporation and deoxyribonucleotide fidelity.
J Biol Chem 289: 9136-45 (2014)
PM ID: 24532793 PMC3979402
555: Ramsingh G, Westervelt P, McBride A, Stockerl-Goldstein K, Vij R, Fiala M, Uy G, Cashen A, Dipersio JF, Abboud CN
Phase I study of cladribine, cytarabine, granulocyte colony stimulating factor (CLAG regimen) and midostaurin and all-trans retinoic acid in relapsed/refractory AML.
Int J Hematol 99: 272-8 (2014)
PM ID: 24488798
556: Lay FD, Triche TJ, Tsai YC, Su SF, Martin SE, Daneshmand S, Skinner EC, Liang G, Chihara Y, Jones PA
Reprogramming of the human intestinal epigenome by surgical tissue transposition.
Genome Res 24: 545-53 (2014)
PM ID: 24515120 PMC3975055
557: Tognarelli S, Gayet J, Lambert M, Dupuy S, Karras A, Cohen P, Guillevin L, de Menthon M, Caillat-Zucman S
Tissue-specific microvascular endothelial cells show distinct capacity to activate NK cells: implications for the pathophysiology of granulomatosis with polyangiitis.
J Immunol 192: 3399-408 (2014)
PM ID: 24600034
558: Terrier B, Chironi G, Pagnoux C, Cohen P, Puéchal X, Simon A, Mouthon L, Guillevin L, French Vasculitis Study Group
Factors associated with major cardiovascular events in patients with systemic necrotizing vasculitides: results of a longterm followup study.
J Rheumatol 41: 723-9 (2014)
PM ID: 24584925
559: Moody G, Beltran PJ, Mitchell P, Cajulis E, Chung YA, Hwang D, Kendall R, Radinsky R, Cohen P, Calzone FJ
IGF1R blockade with ganitumab results in systemic effects on the GH-IGF axis in mice.
J Endocrinol 221: 145-55 (2014)
PM ID: 24492468 PMC4160154 NIHMS623545
560: Hiebler S, Masuda T, Hacia JG, Moser AB, Faust PL, Liu A, Chowdhury N, Huang N, Lauer A, Bennett J, Watkins PA, Zack DJ, Braverman NE, Raymond GV, Steinberg SJ
The Pex1-G844D mouse: a model for mild human Zellweger spectrum disorder.
Mol Genet Metab 111: 522-32 (2014)
PM ID: 24503136
561: Li B, Iglesias-Pedraz JM, Chen LY, Yin F, Cadenas E, Reddy S, Comai L
Downregulation of the Werner syndrome protein induces a metabolic shift that compromises redox homeostasis and limits proliferation of cancer cells.
Aging Cell 13: 367-78 (2014)
PM ID: 24757718 PMC3999508 NIHMS538077
562: Tolani B, Gopalakrishnan R, Punj V, Matta H, Chaudhary PM
Targeting Myc in KSHV-associated primary effusion lymphoma with BET bromodomain inhibitors.
Oncogene 33: 2928-37 (2014)
PM ID: 23792448
563: Pannunzio NR, Li S, Watanabe G, Lieber MR
Non-homologous end joining often uses microhomology: implications for alternative end joining.
DNA Repair (Amst) 17: 74-80 (2014)
PM ID: 24613510
564: Yan Q, Ma X, Shen C, Cao X, Feng N, Qin D, Zeng Y, Zhu J, Gao SJ, Lu C
Inhibition of Kaposi's sarcoma-associated herpesvirus lytic replication by HIV-1 Nef and cellular microRNA hsa-miR-1258.
J Virol 88: 4987-5000 (2014)
PM ID: 24554664 PMC3993842
565: Shah ED, Fisch BM, Arceci RJ, Buckley JD, Reaman GH, Sorensen PH, Triche TJ, Reynolds CP
DrugPath: a database for academic investigators to match oncology molecular targets with drugs in development.
Cancer Chemother Pharmacol 73: 1089-93 (2014)
PM ID: 24663501
566: Mukherjee S, Warshel A
Response to Vilfan: Constructing structure-based free energy surfaces is the key to understand myosin V unidirectionality.
Proc Natl Acad Sci U S A 111: E2077 (2014)
PM ID: 24967456 PMC4034243
567: Li Q, He M, Zhou F, Ye F, Gao SJ
Activation of Kaposi's sarcoma-associated herpesvirus (KSHV) by inhibitors of class III histone deacetylases: identification of sirtuin 1 as a regulator of the KSHV life cycle.
J Virol 88: 6355-67 (2014)
PM ID: 24672028 PMC4093851
568: Tolani B, Matta H, Gopalakrishnan R, Punj V, Chaudhary PM
NEMO is essential for Kaposi's sarcoma-associated herpesvirus-encoded vFLIP K13-induced gene expression and protection against death receptor-induced cell death, and its N-terminal 251 residues are sufficient for this process.
J Virol 88: 6345-54 (2014)
PM ID: 24672029 PMC4093867
569: Cheng CW, Adams GB, Perin L, Wei M, Zhou X, Lam BS, Da Sacco S, Mirisola M, Quinn DI, Dorff TB, Kopchick JJ, Longo VD
Prolonged fasting reduces IGF-1/PKA to promote hematopoietic-stem-cell-based regeneration and reverse immunosuppression.
Cell Stem Cell 14: 810-23 (2014)
PM ID: 24905167 PMC4102383 NIHMS601547
570: Cohen P, Weng W, Rogol AD, Rosenfeld RG, Kappelgaard AM, Germak J
Dose-sparing and safety-enhancing effects of an IGF-I-based dosing regimen in short children treated with growth hormone in a 2-year randomized controlled trial: therapeutic and pharmacoeconomic considerations.
Clin Endocrinol (Oxf) 81: 71-6 (2014)
PM ID: 24428305 PMC4160145 NIHMS623543
571: Schopf P, Warshel A
Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B.
Proteins 82: 1387-99 (2014)
PM ID: 24403025 PMC4057354 NIHMS558175
572: Vicatos S, Rychkova A, Mukherjee S, Warshel A
An effective coarse-grained model for biological simulations: recent refinements and validations.
Proteins 82: 1168-85 (2014)
PM ID: 25050439 PMC4109661 NIHMS544914
573: Pirooz S, He S, O'Connell D, Khalilzadeh P, Yang Y, Liang C
Viruses customize autophagy protein for efficient viral entry.
Autophagy 10: 1355-6 (2014)
PM ID: 24905575
574: Liang D, Hu H, Li S, Dong J, Wang X, Wang Y, He L, He Z, Gao Y, Gao SJ, Lan K
Oncogenic herpesvirus KSHV Hijacks BMP-Smad1-Id signaling to promote tumorigenesis.
PLoS Pathog 10: e1004253 (2014)
PM ID: 25010525 PMC4092152
575: Agarwal JR, Wang Q, Tanno T, Rasheed Z, Merchant A, Ghosh N, Borrello I, Huff CA, Parhami F, Matsui W
Activation of liver X receptors inhibits hedgehog signaling, clonogenic growth, and self-renewal in multiple myeloma.
Mol Cancer Ther 13: 1873-81 (2014)
PM ID: 24807964 PMC4182725 NIHMS595601
576: Milman S, Atzmon G, Huffman DM, Wan J, Crandall JP, Cohen P, Barzilai N
Low insulin-like growth factor-1 level predicts survival in humans with exceptional longevity.
Aging Cell 13: 769-71 (2014)
PM ID: 24618355 PMC4116456 NIHMS565991
577: Slagle BL, Andrisani OM, Bouchard MJ, Lee CG, Ou JH, Siddiqui A
Technical standards for hepatitis B virus X protein (HBx) research.
Hepatology : (2014)
PM ID: 25099228
578: Kim I, Chakrabarty S, Brzezinski P, Warshel A
Modeling gating charge and voltage changes in response to charge separation in membrane proteins.
Proc Natl Acad Sci U S A 111: 11353-8 (2014)
PM ID: 25049404 PMC4128161
579: Frushicheva MP, Mills MJ, Schopf P, Singh MK, Prasad RB, Warshel A
Computer aided enzyme design and catalytic concepts.
Curr Opin Chem Biol 21: 56-62 (2014)
PM ID: 24814389 PMC4149935 NIHMS582832
580: Brulois K, Toth Z, Wong LY, Feng P, Gao SJ, Ensser A, Jung JU
Kaposi's sarcoma-associated herpesvirus K3 and K5 ubiquitin E3 ligases have stage-specific immune evasion roles during lytic replication.
J Virol 88: 9335-49 (2014)
PM ID: 24899205 PMC4136276
581: Zhu Y, Huang Y, Jung JU, Lu C, Gao SJ
Viral miRNA targeting of bicistronic and polycistronic transcripts.
Curr Opin Virol 7: 66-72 (2014)
PM ID: 24821460 PMC4149931 NIHMS588493
582: Warshel A
Multiscale modeling of biological functions: from enzymes to molecular machines (nobel lecture).
Angew Chem Int Ed Engl 53: 10020-31 (2014)
PM ID: 25060243
583: Zhao J, Siegmund KD, Shibata D, Marjoram P
Ancestral inference in tumors: how much can we know?
J Theor Biol 359: 136-45 (2014)
PM ID: 24907673 PMC4138290 NIHMS603488
584: Xue M, Yao S, Hu M, Li W, Hao T, Zhou F, Zhu X, Lu H, Qin D, Yan Q, Zhu J, Gao SJ, Lu C
HIV-1 Nef and KSHV oncogene K1 synergistically promote angiogenesis by inducing cellular miR-718 to regulate the PTEN/AKT/mTOR signaling pathway.
Nucleic Acids Res 42: 9862-79 (2014)
PM ID: 25104021