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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: 536
Inter Programmatic Publications: 109
Intra Programmatic Publications: 54

1: Banki F, Mason RJ, Hagen JA, DeMeester SR, Lipham JC, Danenberg K, Danenberg P, DeMeester TR
Plasma DNA: a molecular marker of surgical insult and postoperative recovery in esophageal cancer.
Eur Surg Res 40: 273-8 (2008)
PM ID: 18219202
2: Ishikita H, Warshel A
Predicting drug-resistant mutations of HIV protease.
Angew Chem Int Ed Engl 47: 697-700 (2008)
PM ID: 18058968
3: Theisen J, Danenberg K, Ott K, Becker K, Danenberg P, Stein HJ, Siewert JR
Predictors of response and survival for neoadjuvant treated patients with esophageal adenocarcinoma.
Dis Esophagus 21: 601-6 (2008)
PM ID: 18430179
4: Gutschow CA, Vallböhmer D, Stolte M, Oh D, Danenberg K, Danenberg P, Schneider PM, Hölscher AH
Adenocarcinoma developing in de novo Barrett's mucosa in the remnant esophagus after esophagectomy: clinical and molecular assessment.
Dis Esophagus 21: E6-8 (2008)
PM ID: 18430096
5: Chen YH, Ishii M, Sucov HM, Maxson RE
Msx1 and Msx2 are required for endothelial-mesenchymal transformation of the atrioventricular cushions and patterning of the atrioventricular myocardium.
BMC Dev Biol 8: 75 (2008)
PM ID: 18667074 PMC2518925
6: Siegmund KD, Marjoram P, Shibata D
Modeling DNA methylation in a population of cancer cells.
Stat Appl Genet Mol Biol 7: Article 18 (2008)
PM ID: 18597664
7: Basile LA, Gallaher TK, Shibata D, Miller JD, Douer D
Multilineage hematopoietic recovery with concomitant antitumor effects using low dose Interleukin-12 in myelosuppressed tumor-bearing mice.
J Transl Med 6: 26 (2008)
PM ID: 18489769 PMC2424034
8: Makino H, Uetake H, Danenberg K, Danenberg PV, Sugihara K
Efficacy of laser capture microdissection plus RT-PCR technique in analyzing gene expression levels in human gastric cancer and colon cancer.
BMC Cancer 8: 210 (2008)
PM ID: 18652704 PMC2533342
9: Magda D, Lecane PS, Prescott J, Thiemann P, Ma X, Dranchak PK, Toleno DM, Ramaswamy K, Siegmund KD, Hacia JG
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.
BMC Genomics 9: 521 (2008)
PM ID: 18980691 PMC2612029
10: Dansithong W, Wolf CM, Sarkar P, Paul S, Chiang AN, Holt I, Morris GE, Branco D, Sherwood MC, Comai L, Berul CI, Reddy S
Cytoplasmic CUG RNA foci are insufficient to elicit key DM1 features.
PLoS One 3: e3968 (2008)
PM ID: 19092997 PMC2597774
11: Lieber MR, Raghavan SC, Yu KJ
Mechanistic aspects of lymphoid chromosomal translocations.
J Natl Cancer Inst Monogr : 8-11 (2008)
PM ID: 18647994
12: Uchida K, Danenberg PV, Danenberg KD, Grem JL
Thymidylate synthase, dihydropyrimidine dehydrogenase, ERCC1, and thymidine phosphorylase gene expression in primary and metastatic gastrointestinal adenocarcinoma tissue in patients treated on a phase I trial of oxaliplatin and capecitabine.
BMC Cancer 8: 386 (2008)
PM ID: 19105824 PMC2637882
13: Lieber MR
The mechanism of human nonhomologous DNA end joining.
J Biol Chem 283: 1-5 (2008)
PM ID: 17999957
14: Roy D, Yu KJ, Lieber MR
Mechanism of R-loop formation at immunoglobulin class switch sequences.
Mol Cell Biol 28: 50-60 (2008)
PM ID: 17954560 PMC2223306
15: Yang S, Pham LK, Liao CP, Frenkel B, Reddi AH, Roy-Burman P
A novel bone morphogenetic protein signaling in heterotypic cell interactions in prostate cancer.
Cancer Res 68: 198-205 (2008)
PM ID: 18172312
16: Mori R, Wang Q, Quek ML, Tarabolous C, Cheung E, Ye W, Groshen S, Hawes D, Togo S, Shimada H, Danenberg KD, Danenberg PV, Pinski JK
Prognostic value of the androgen receptor and its coactivators in patients with D1 prostate cancer.
Anticancer Res 28: 425-30 (2008)
PM ID: 18383880
17: Dong D, Ni M, Li J, Xiong S, Ye W, Virrey JJ, Mao C, Ye R, Wang M, Pen L, Dubeau L, Groshen S, Hofman FM, Lee AS
Critical role of the stress chaperone GRP78/BiP in tumor proliferation, survival, and tumor angiogenesis in transgene-induced mammary tumor development.
Cancer Res 68: 498-505 (2008)
PM ID: 18199545
18: Shibata D
Stem cells as common ancestors in a colorectal cancer ancestral tree.
Curr Opin Gastroenterol 24: 59-63 (2008)
PM ID: 18043234
19: Madia F, Gattazzo C, Wei M, Fabrizio P, Burhans WC, Weinberger M, Galbani A, Smith JR, Nguyen C, Huey S, Comai L, Longo VD
Longevity mutation in SCH9 prevents recombination errors and premature genomic instability in a Werner/Bloom model system.
J Cell Biol 180: 67-81 (2008)
PM ID: 18195102 PMC2213615
20: Lieber MR, Lu H, Gu J, Schwarz K
Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining: relevance to cancer, aging, and the immune system.
Cell Res 18: 125-33 (2008)
PM ID: 18087292
21: Xiang YB, Warshel A
Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
J Phys Chem B 112: 1007-15 (2008)
PM ID: 18166038
22: Sucato CA, Upton TG, Kashemirov BA, Osuna J, Oertell K, Beard WA, Wilson SH, Florián J, Warshel A, McKenna CE, Goodman MF
DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state.
Biochemistry 47: 870-9 (2008)
PM ID: 18161950
23: Xiang YB, Goodman MF, Beard WA, Wilson SH, Warshel A
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta.
Proteins 70: 231-47 (2008)
PM ID: 17671961 PMC2365506 NIHMS44484
24: Wei M, Fabrizio P, Hu J, Ge H, Cheng CY, Li L, Longo VD
Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9.
PLoS Genet 4: e13 (2008)
PM ID: 18225956 PMC2213705
25: Kuramochi H, Tanaka K, Oh D, Lehman BJ, Dunst CM, Yang DY, De Meester SR, Hagen JA, Danenberg KD, De Meester TR, Danenberg PV
Thymidylate synthase polymorphisms and mRNA expression are independent chemotherapy predictive markers in esophageal adenocarcinoma patients.
Int J Oncol 32: 201-8 (2008)
PM ID: 18097560
26: Lai CK, Jeng KS, Machida K, Cheng YS, Lai MM
Hepatitis C virus NS3/4A protein interacts with ATM, impairs DNA repair and enhances sensitivity to ionizing radiation.
Virology 370: 295-309 (2008)
PM ID: 17931678
27: Wang G, Klein MG, Tokonzaba E, Zhang Y, Holden LG, Chen XS
The structure of a DnaB-family replicative helicase and its interactions with primase.
Nat Struct Mol Biol 15: 94-100 (2008)
PM ID: 18157148
28: Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S
Sparse representation and Bayesian detection of genome copy number alterations from microarray data.
Bioinformatics 24: 309-18 (2008)
PM ID: 18203770 PMC2704547
29: Dowd CL, Sutch BT, Haworth IS, Eritja R, Marquez VE, Yang AS
Incorporation of zebularine from its 2'-deoxyribonucleoside triphosphate derivative and activity as a template-coding nucleobase.
Nucleosides Nucleotides Nucleic Acids 27: 131-45 (2008)
PM ID: 18205068
30: Shibata D
Mistakes make history: visualizing intestinal tectonics.
Gastroenterology 134: 628-31 (2008)
PM ID: 18242228
31: Gu J, Lieber MR
Mechanistic flexibility as a conserved theme across 3 billion years of nonhomologous DNA end-joining.
Genes Dev 22: 411-5 (2008)
PM ID: 18281457 PMC2731650
32: Forsburg SL
The MCM helicase: linking checkpoints to the replication fork.
Biochem Soc Trans 36: 114-9 (2008)
PM ID: 18208397
33: Tsai AG, Lieber MR
RAGs found "not guilty": cleared by DNA evidence.
Blood 111: 1750 (2008)
PM ID: 19048671
34: Hacia JG, Lee CC, Jimenez DF, Karaman MW, Ho VV, Siegmund KD, Tarantal AF
Age-related gene expression profiles of rhesus monkey bone marrow-derived mesenchymal stem cells.
J Cell Biochem 103: 1198-210 (2008)
PM ID: 17685434
35: Miller AJ, Dudley SD, Tsao JL, Shibata D, Liskay RM
Tractable Cre-lox system for stochastic alteration of genes in mice.
Nat Methods 5: 227-9 (2008)
PM ID: 18264106 PMC2394730 NIHMS49371
36: Li B, Jog SP, Reddy S, Comai L
WRN controls formation of extrachromosomal telomeric circles and is required for TRF2DeltaB-mediated telomere shortening.
Mol Cell Biol 28: 1892-904 (2008)
PM ID: 18212065 PMC2268394
37: Kang JC, Gu Y, Li P, Johnson BL, Sucov HM, Thomas PS
PDGF-A as an epicardial mitogen during heart development.
Dev Dyn 237: 692-701 (2008)
PM ID: 18297729
38: Shimazaki N, Lieber MR
DNA-PKcs at 7 angstrom: insights for DNA repair.
Structure 16: 334-6 (2008)
PM ID: 18334206
39: Rosta E, Kamerlin SC, Warshel A
On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution.
Biochemistry 47: 3725-35 (2008)
PM ID: 18307312
40: Bailis JM, Luche DD, Hunter T, Forsburg SL
Minichromosome maintenance proteins interact with checkpoint and recombination proteins to promote s-phase genome stability.
Mol Cell Biol 28: 1724-38 (2008)
PM ID: 18180284 PMC2258774
41: Kobayashi H, Sugihara K, Uetake H, Higuchi T, Yasuno M, Enomoto M, Kuramochi H, Lenz HJ, Danenberg KD, Danenberg PV
Messenger RNA expression of vascular endothelial growth factor and its receptors in primary colorectal cancer and corresponding liver metastasis.
Ann Surg Oncol 15: 1232-8 (2008)
PM ID: 18239970
42: Makita T, Sucov HM, Gariepy CE, Yanagisawa M, Ginty DD
Endothelins are vascular-derived axonal guidance cues for developing sympathetic neurons.
Nature 452: 759-63 (2008)
PM ID: 18401410 PMC2713667 NIHMS106478
43: Kim KJ, Choi J, Heo K, Kim HJ, Levens D, Kohno K, Johnson EM, Brock HW, An W
Isolation and characterization of a novel H1.2 complex that acts as a repressor of p53-mediated transcription.
J Biol Chem 283: 9113-26 (2008)
PM ID: 18258596 PMC2431041
44: Heo K, Kim HJ, Choi SH, Choi J, Kim KJ, Gu J, Lieber MR, Yang AS, An W
FACT-mediated exchange of histone variant H2AX regulated by phosphorylation of H2AX and ADP-ribosylation of Spt16.
Mol Cell 30: 86-97 (2008)
PM ID: 18406329
45: Furukohri A, Goodman MF, Maki H
A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp.
J Biol Chem 283: 11260-9 (2008)
PM ID: 18308729 PMC2431065
46: Li K, Xu L, Kulkarni AA, Perkins DI, Haworth IS, Davies DL
Ethanol inhibits functional activity of the human intestinal dipeptide transporter hPepT1 expressed in Xenopus oocytes.
Alcohol Clin Exp Res 32: 777-84 (2008)
PM ID: 18336632
47: Pike BL, Greiner TC, Wang X, Weisenburger DD, Hsu YH, Renaud G, Wolfsberg TG, Kim M, Weisenberger DJ, Siegmund KD, Ye W, Groshen S, Mehrian-Shai R, Delabie J, Chan WC, Laird PW, Hacia JG
DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status.
Leukemia 22: 1035-43 (2008)
PM ID: 18288132 PMC2654231 NIHMS97202
48: Braun-Sand S, Sharma PK, Chu ZT, Pisliakov AV, Warshel A
The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all.
Biochim Biophys Acta 1777: 441-52 (2008)
PM ID: 18387356 PMC2443747 NIHMS51300
49: Chelico L, Sacho EJ, Erie DA, Goodman MF
A model for oligomeric regulation of APOBEC3G cytosine deaminase-dependent restriction of HIV.
J Biol Chem 283: 13780-91 (2008)
PM ID: 18362149 PMC2376223
50: Wang LC, Okitsu CY, Kochounian HH, Rodriguez A, Hsieh CL, Zandi E
A simple and inexpensive on-column frit fabrication method for fused-silica capillaries for increased capacity and versatility in LC-MS/MS applications.
Proteomics 8: 1758-61 (2008)
PM ID: 18384106
51: Rosta E, Haranczyk M, Chu ZT, Warshel A
Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.
J Phys Chem B 112: 5680-92 (2008)
PM ID: 18412414 PMC2651397 NIHMS96684
52: Mavri J, Liu HM, Olsson MH, Warshel A
Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase.
J Phys Chem B 112: 5950-4 (2008)
PM ID: 18069813
53: Zwerner JP, Joo J, Warner KL, Christensen L, Hu-Lieskovan S, Triche TJ, May WA
The EWS/FLI1 oncogenic transcription factor deregulates GLI1.
Oncogene 27: 3282-91 (2008)
PM ID: 18084326
54: Bates DL, Barthel KK, Wu Y, Kalhor R, Stroud JC, Giffin MJ, Chen L
Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element.
Structure 16: 684-94 (2008)
PM ID: 18462673 PMC2697820 NIHMS118754
55: Candelario J, Sudhakar S, Navarro S, Reddy S, Comai L
Perturbation of wild-type lamin A metabolism results in a progeroid phenotype.
Aging Cell 7: 355-67 (2008)
PM ID: 18363904 PMC2527236 NIHMS56478
56: Chu MW, Siegmund KD, Hao QL, Crooks GM, Tavaré S, Shibata D
Inferring relative numbers of human leucocyte genome replications.
Br J Haematol 141: 862-71 (2008)
PM ID: 18410448
57: Raffaghello L, Lee CT, Safdie FM, Wei M, Madia F, Bianchi G, Longo VD
Starvation-dependent differential stress resistance protects normal but not cancer cells against high-dose chemotherapy.
Proc Natl Acad Sci U S A 105: 8215-20 (2008)
PM ID: 18378900 PMC2448817
58: Hu F, Gan Y, Aparicio OM
Identification of Clb2 residues required for Swe1 regulation of Clb2-Cdc28 in Saccharomyces cerevisiae.
Genetics 179: 863-74 (2008)
PM ID: 18558651 PMC2429880
59: Pisliakov AV, Sharma PK, Chu ZT, Haranczyk M, Warshel A
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.
Proc Natl Acad Sci U S A 105: 7726-31 (2008)
PM ID: 18509049 PMC2409407
60: Gómez EB, Nugent RL, Laria S, Forsburg SL
Schizosaccharomyces pombe histone acetyltransferase Mst1 (KAT5) is an essential protein required for damage response and chromosome segregation.
Genetics 179: 757-71 (2008)
PM ID: 18505873 PMC2429872
61: Pham P, Smolka MB, Calabrese P, Landolph A, Zhang K, Zhou H, Goodman MF
Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase.
J Biol Chem 283: 17428-39 (2008)
PM ID: 18417471 PMC2427360
62: Greenleaf WB, Shen J, Gai D, Chen XS
Systematic study of the functions for the residues around the nucleotide pocket in simian virus 40 AAA+ hexameric helicase.
J Virol 82: 6017-23 (2008)
PM ID: 18400864 PMC2395154
63: Johnson SA, Dubeau L, Johnson DL
Enhanced RNA polymerase III-dependent transcription is required for oncogenic transformation.
J Biol Chem 283: 19184-91 (2008)
PM ID: 18456653 PMC2443659
64: Neale G, Su X, Morton CL, Phelps D, Gorlick R, Lock RB, Reynolds CP, Maris JM, Friedman HS, Dome J, Khoury J, Triche TJ, Seeger RC, Gilbertson R, Khan J, Smith MA, Houghton PJ
Molecular characterization of the pediatric preclinical testing panel.
Clin Cancer Res 14: 4572-83 (2008)
PM ID: 18628472
65: Ma HC, Lin TW, Li HY, Iguchi-Ariga SM, Ariga H, Chuang YL, Ou JH, Lo SY
Hepatitis C virus ARFP/F protein interacts with cellular MM-1 protein and enhances the gene trans-activation activity of c-Myc.
J Biomed Sci 15: 417-25 (2008)
PM ID: 18398700
66: Banki F, Yacoub WN, Hagen JA, Mason RJ, Ayazi S, DeMeester SR, Lipham JC, Danenberg K, Danenberg P, DeMeester TR
Plasma DNA is more reliable than carcinoembryonic antigen for diagnosis of recurrent esophageal cancer.
J Am Coll Surg 207: 30-5 (2008)
PM ID: 18589358
67: Szyjka SJ, Aparicio JG, Viggiani CJ, Knott S, Xu W, Tavaré S, Aparicio OM
Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae.
Genes Dev 22: 1906-20 (2008)
PM ID: 18628397 PMC2492737
68: Magda D, Lecane PS, Wang ZZ, Hu W, Thiemann P, Ma X, Dranchak PK, Wang XD, Lynch V, Wei W, Csokai V, Hacia JG, Sessler JL
Synthesis and anticancer properties of water-soluble zinc ionophores.
Cancer Res 68: 5318-25 (2008)
PM ID: 18593933
69: Li YT, Xu W, McBurney MW, Longo VD
SirT1 inhibition reduces IGF-I/IRS-2/Ras/ERK1/2 signaling and protects neurons.
Cell Metab 8: 38-48 (2008)
PM ID: 18590691
70: Fabrizio P, Longo VD
Chronological aging-induced apoptosis in yeast.
Biochim Biophys Acta 1783: 1280-5 (2008)
PM ID: 18445486 PMC2536486 NIHMS56388
71: Choi SK, Yoon SR, Calabrese P, Arnheim N
A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations.
Proc Natl Acad Sci U S A 105: 10143-8 (2008)
PM ID: 18632557 PMC2474563
72: Hoffmann AC, Mori R, Vallbohmer D, Brabender J, Klein E, Drebber U, Baldus SE, Cooc J, Azuma M, Metzger R, Hoelscher AH, Danenberg KD, Prenzel KL, Danenberg PV
High expression of HIF1a is a predictor of clinical outcome in patients with pancreatic ductal adenocarcinomas and correlated to PDGFA, VEGF, and bFGF.
Neoplasia 10: 674-9 (2008)
PM ID: 18592007 PMC2435004
73: Machida K, Kondo Y, Huang JY, Chen YC, Cheng KT, Keck Z, Foung S, Dubuisson J, Sung VM, Lai MM
Hepatitis C virus (HCV)-induced immunoglobulin hypermutation reduces the affinity and neutralizing activities of antibodies against HCV envelope protein.
J Virol 82: 6711-20 (2008)
PM ID: 18417597 PMC2447061
74: Sir D, Liang C, Chen WL, Jung JU, Ou JH
Perturbation of autophagic pathway by hepatitis C virus.
Autophagy 4: 830-1 (2008)
PM ID: 18635950 PMC2574555 NIHMS60148
75: Liang C, Sir D, Lee SY, Ou JH, Jung JU
Beyond autophagy: the role of UVRAG in membrane trafficking.
Autophagy 4: 817-20 (2008)
PM ID: 18612260
76: Haranczyk M, Gutowski M, Warshel A
Solvation free energies of molecules. The most stable anionic tautomers of uracil.
Phys Chem Chem Phys 10: 4442-8 (2008)
PM ID: 18654684 PMC2562795 NIHMS50105
77: Douglas D, Hsu JH, Hung L, Cooper A, Abdueva D, van Doorninck J, Peng G, Shimada H, Triche TJ, Lawlor ER
BMI-1 promotes ewing sarcoma tumorigenicity independent of CDKN2A repression.
Cancer Res 68: 6507-15 (2008)
PM ID: 18701473 PMC2570201 NIHMS56191
78: Kim JH, Yang CK, Heo K, Roeder RG, An W, Stallcup MR
CCAR1, a key regulator of mediator complex recruitment to nuclear receptor transcription complexes.
Mol Cell 31: 510-9 (2008)
PM ID: 18722177 PMC2562329 NIHMS64408
79: Lu H, Shimazaki N, Raval P, Gu J, Watanabe G, Schwarz K, Swanson PC, Lieber MR
A biochemically defined system for coding joint formation in V(D)J recombination.
Mol Cell 31: 485-97 (2008)
PM ID: 18722175 PMC2564285 NIHMS67395
80: Ren YX, Finckenstein FG, Abdueva DA, Shahbazian V, Chung B, Weinberg KI, Triche TJ, Shimada H, Anderson MJ
Mouse mesenchymal stem cells expressing PAX-FKHR form alveolar rhabdomyosarcomas by cooperating with secondary mutations.
Cancer Res 68: 6587-97 (2008)
PM ID: 18701482
81: Yoo CB, Chuang JC, Byun HM, Egger G, Yang AS, Dubeau L, Long TI, Laird PW, Marquez VE, Jones PA
Long-term epigenetic therapy with oral zebularine has minimal side effects and prevents intestinal tumors in mice.
Cancer Prev Res (Phila Pa) 1: 233-40 (2008)
PM ID: 19138966
82: Roca M, Messer B, Hilvert D, Warshel A
On the relationship between folding and chemical landscapes in enzyme catalysis.
Proc Natl Acad Sci U S A 105: 13877-82 (2008)
PM ID: 18779576 PMC2544547
83: Kamerlin SC, Williams NH, Warshel A
Dineopentyl phosphate hydrolysis: evidence for stepwise water attack.
J Org Chem 73: 6960-9 (2008)
PM ID: 18729515
84: Robinson PJ, An W, Routh A, Martino F, Chapman L, Roeder RG, Rhodes D
30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction.
J Mol Biol 381: 816-25 (2008)
PM ID: 18653199
85: Zagar TM, Triche TJ, Kinsella TJ
Extraosseous Ewing's sarcoma: 25 years later.
J Clin Oncol 26: 4230-2 (2008)
PM ID: 18779607
86: Bates DL, Chen Y, Kim G, Guo L, Chen L
Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA.
J Mol Biol 381: 1292-306 (2008)
PM ID: 18621058
87: Lai CK, Jeng KS, Machida K, Lai MM
Association of hepatitis C virus replication complexes with microtubules and actin filaments is dependent on the interaction of NS3 and NS5A.
J Virol 82: 8838-48 (2008)
PM ID: 18562541 PMC2519648
88: Jiang X, Castelao JE, Groshen S, Cortessis VK, Shibata DK, Conti DV, Gago-Dominguez M
Water intake and bladder cancer risk in Los Angeles County.
Int J Cancer 123: 1649-56 (2008)
PM ID: 18623082
89: Sir D, Chen WL, Choi J, Wakita T, Yen TS, Ou JH
Induction of incomplete autophagic response by hepatitis C virus via the unfolded protein response.
Hepatology 48: 1054-61 (2008)
PM ID: 18688877 PMC2562598 NIHMS57806
90: Kumari A, Minko IG, Harbut MB, Finkel SE, Goodman MF, Lloyd RS
Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV.
J Biol Chem 283: 27433-7 (2008)
PM ID: 18697749 PMC2562078
91: Mori R, Wang Q, Danenberg KD, Pinski JK, Danenberg PV
Both beta-actin and GAPDH are useful reference genes for normalization of quantitative RT-PCR in human FFPE tissue samples of prostate cancer.
Prostate 68: 1555-60 (2008)
PM ID: 18651557
92: Minko IG, Yamanaka K, Kozekov ID, Kozekova A, Indiani C, O'Donnell ME, Jiang Q, Goodman MF, Rizzo CJ, Lloyd RS
Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family.
Chem Res Toxicol 21: 1983-90 (2008)
PM ID: 18788757 PMC2673917 NIHMS86382
93: Hoffmann AC, Mori R, Vallbohmer D, Brabender J, Drebber U, Baldus SE, Klein E, Azuma M, Metzger R, Hoffmann C, Hoelscher AH, Danenberg KD, Prenzel KL, Danenberg PV
High expression of heparanase is significantly associated with dedifferentiation and lymph node metastasis in patients with pancreatic ductal adenocarcinomas and correlated to PDGFA and via HIF1a to HB-EGF and bFGF.
J Gastrointest Surg 12: 1674-81; discussion 1681-2 (2008)
PM ID: 18704599
94: Somlo G, Chu P, Frankel P, Ye W, Groshen S, Doroshow JH, Danenberg K, Danenberg P
Molecular profiling including epidermal growth factor receptor and p21 expression in high-risk breast cancer patients as indicators of outcome.
Ann Oncol 19: 1853-9 (2008)
PM ID: 18641005 PMC2733077
95: Longo VD, Lieber MR, Vijg J
Turning anti-ageing genes against cancer.
Nat Rev Mol Cell Biol 9: 903-10 (2008)
PM ID: 18946478
96: Gajecka M, Gentles AJ, Tsai AG, Chitayat D, Mackay KL, Glotzbach CD, Lieber MR, Shaffer LG
Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13).
Genome Res 18: 1733-42 (2008)
PM ID: 18765821 PMC2577863
97: Pham P, Zhang K, Goodman MF
Hypermutation at A/T sites during G.U mismatch repair in vitro by human B-cell lysates.
J Biol Chem 283: 31754-62 (2008)
PM ID: 18786917 PMC2581569 [Available on 11/14/09]
98: Holden LG, Prochnow C, Chang YP, Bransteitter R, Chelico L, Sen U, Stevens RC, Goodman MF, Chen XS
Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications.
Nature 456: 121-4 (2008)
PM ID: 18849968 PMC2714533 NIHMS115824
99: Kuramochi H, Hayashi K, Uchida K, Nakajima G, Hatori T, Danenberg KD, Danenberg PV, Yamamoto M
High intratumoral dihydropyrimidine dehydrogenase mRNA levels in pancreatic cancer associated with a high rate of response to S-1.
Cancer Chemother Pharmacol 63: 85-9 (2008)
PM ID: 18309485
100: Fukui Y, Oka T, Nagayama S, Danenberg PV, Danenberg KD, Fukushima M
Thymidylate synthase, dihydropyrimidine dehydrogenase, orotate phosphoribosyltransferase mRNA and protein expression levels in solid tumors in large scale population analysis.
Int J Mol Med 22: 709-16 (2008)
PM ID: 19020767
101: Kobayashi H, Sugihara K, Uetake H, Higuchi T, Yasuno M, Enomoto M, Iida S, Azuma M, Mori R, Omori A, Lenz HJ, Danenberg KD, Danenberg PV
Messenger RNA expression of TS and ERCC1 in colorectal cancer and matched liver metastasis.
Int J Oncol 33: 1257-62 (2008)
PM ID: 19020759
102: Fu Y, Wey S, Wang M, Ye R, Liao CP, Roy-Burman P, Lee AS
Pten null prostate tumorigenesis and AKT activation are blocked by targeted knockout of ER chaperone GRP78/BiP in prostate epithelium.
Proc Natl Acad Sci U S A 105: 19444-9 (2008)
PM ID: 19033462 PMC2614780
103: Dubeau L
The cell of origin of ovarian epithelial tumours.
Lancet Oncol 9: 1191-7 (2008)
PM ID: 19038766
104: Tsai AG, Lu H, Raghavan SC, Muschen M, Hsieh CL, Lieber MR
Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity.
Cell 135: 1130-42 (2008)
PM ID: 19070581 PMC2642632 [Available on 12/12/09] NIHMS84558 [Available on 12/12/09]
105: Li P, Tong C, Mehrian-Shai R, Jia L, Wu N, Yan Y, Maxson RE, Schulze EN, Song H, Hsieh CL, Pera MF, Ying QL
Germline competent embryonic stem cells derived from rat blastocysts.
Cell 135: 1299-310 (2008)
PM ID: 19109898 PMC2735113 NIHMS131481
106: Parrella E, Longo VD
The chronological life span of Saccharomyces cerevisiae to study mitochondrial dysfunction and disease.
Methods 46: 256-62 (2008)
PM ID: 18930829
107: Jao CC, Hegde BG, Chen J, Haworth IS, Langen R
Structure of membrane-bound alpha-synuclein from site-directed spin labeling and computational refinement.
Proc Natl Acad Sci U S A 105: 19666-71 (2008)
PM ID: 19066219 PMC2605001
108: Brewster AS, Wang G, Yu X, Greenleaf WB, Carazo JM, Tjajadia M, Klein MG, Chen XS
Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase.
Proc Natl Acad Sci U S A 105: 20191-6 (2008)
PM ID: 19073923 PMC2629282
109: 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
110: 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
111: 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
112: Sabatinos SA, Forsburg SL
Measuring DNA content by flow cytometry in fission yeast.
Methods Mol Biol 521: 449-61 (2009)
PM ID: 19563122
113: Luche DD, Forsburg SL
Cell-cycle synchrony for analysis of S. pombe DNA replication.
Methods Mol Biol 521: 437-48 (2009)
PM ID: 19563121
114: 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
115: 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
116: 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
117: 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
118: 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
119: Longo VD
Linking sirtuins, IGF-I signaling, and starvation.
Exp Gerontol 44: 70-4 (2009)
PM ID: 18638538
120: 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
121: 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
122: Haga K, Tomioka A, Liao CP, Kimura T, Matsumoto H, Ohno I, Hermann K, Logg CR, Jiao J, Tanaka MS, 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
123: 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
124: 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
125: Chen JL, Lin HH, Kim KJ, Lin AH, 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
126: Choudhary B, Zhou JY, Li P, Thomas SN, 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
127: Kraigsley AM, Finkel SE
Adaptive evolution in single species bacterial biofilms.
FEMS Microbiol Lett 293: 135-40 (2009)
PM ID: 19239496
128: 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
129: Gasparyan HJ, Xu LY, 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
130: 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
131: Yu XJ, 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
132: 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 [Available on 03/01/10] NIHMS98872 [Available on 03/01/10]
133: 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 [Available on 03/13/10]
134: 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 [Available on 03/01/10] NIHMS99063 [Available on 03/01/10]
135: 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
136: 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
137: 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 [Available on 03/10/10]
138: 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
139: 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 [Available on 02/05/10] NIHMS86597 [Available on 02/05/10]
140: 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 [Available on 03/13/10]
141: 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 [Available on 03/12/10]
142: 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
143: 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
144: 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
145: Shao CH, Lacey M, Dubeau L, Ehrlich M
Hemimethylation footprints of DNA demethylation in cancer.
Epigenetics 4: 165-75 (2009)
PM ID: 19287214
146: 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
147: Roca M, Vardi-Kilshtain A, Warshel A
Toward accurate screening in computer-aided enzyme design.
Biochemistry 48: 3046-56 (2009)
PM ID: 19161327
148: 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
149: Indiani C, Langston LD, Yurieva O, Goodman MF, O'Donnell ME
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
150: 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
151: 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
152: 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
153: 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 [Available on 05/21/10] NIHMS114340 [Available on 05/21/10]
154: 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
155: 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
156: Willmann M, Wacheck V, Buckley JD, Nagy K, Thalhammer J, Paschke R, Triche TJ, Jansen B, Selzer E
Characterization of NVX-207, a novel betulinic acid-derived anti-cancer compound.
Eur J Clin Invest 39: 384-94 (2009)
PM ID: 19309323
157: 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
158: 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
159: 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 [Available on 05/07/10] NIHMS108641 [Available on 05/07/10]
160: 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
161: 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
162: Oh DS, DeMeester SR, Dunst CM, Mori R, Lehman BJ, Kuramochi H, Danenberg K, Danenberg P, Hagen JA, Chandrasoma PT, 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
163: 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
164: 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 [Available on 12/01/09]
165: 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 [Available on 12/01/09]
166: 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
167: 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
168: Sucov HM, Gu Y, Thomas SN, Li P, Pashmforoush M
Epicardial control of myocardial proliferation and morphogenesis.
Pediatr Cardiol 30: 617-25 (2009)
PM ID: 19277768
169: Siegmund KD, Marjoram P, Tavaré S, Shibata D
Many colorectal cancers are "flat" clonal expansions.
Cell Cycle 8: 2187-93 (2009)
PM ID: 19556889
170: Kim HJ, Heo K, Kim JH, Kim KJ, 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 [Available on 07/24/10]
171: 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 [Available on 07/15/10] NIHMS124813 [Available on 07/15/10]
172: Yoon SR, Qin J, Glaser RL, Wang Jabs E, Wexler NS, Sokol RZ, 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
173: 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 [Available on 01/01/10] NIHMS135635 [Available on 01/01/10]
174: 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
175: 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
176: 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 [Available on 08/06/10] NIHMS125551 [Available on 08/06/10]
177: 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 [Available on 02/24/10]
178: 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
179: 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
180: 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
181: 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 [Available on 09/02/10]
182: Lin DY, Hollander Z, Ng RT, Imai C, Ignaszewski A, Balshaw R, Freue GC, Wilson-McManus JE, Qasimi P, Meredith A, Mui A, Triche TJ, McMaster R, Keown PA, McManus BM, Biomarkers in Transplantation Team , NCE CECR Centre of Excellence for the Prevention o
Whole blood genomic biomarkers of acute cardiac allograft rejection.
J Heart Lung Transplant 28: 927-35 (2009)
PM ID: 19716046
183: 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
184: 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 [Available on 04/13/10]
185: 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
186: 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 [Available on 10/16/10] NIHMS139292 [Available on 10/16/10]
187: 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
188: 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
189: 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
190: 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
191: 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
192: 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 [Available on 11/03/10] NIHMS150149 [Available on 11/03/10]
193: Kamerlin SC, Warshel A
On the energetics of ATP hydrolysis in solution.
J Phys Chem B 113: 15692-8 (2009)
PM ID: 19888735
194: 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
195: 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 [Available on 06/01/10]
196: 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
197: 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
198: 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
199: 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
200: Tsai AG, Lieber MR
Mechanisms of chromosomal rearrangement in the human genome.
BMC Genomics 11 Suppl 1: S1 (2010)
PM ID: 20158866 PMC2822523
201: 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
202: 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
203: 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
204: 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
205: 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
206: 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
207: 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
208: 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
209: 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
210: 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
211: 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
212: Sir D, Ou JH
Autophagy in viral replication and pathogenesis.
Mol Cells 29: 1-7 (2010)
PM ID: 20077024 PMC3115743 NIHMS295695
213: 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
214: 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
215: 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
216: 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
217: 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
218: 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
219: Chen L
In pursuit of the high-resolution structure of nicotinic acetylcholine receptors.
J Physiol 588: 557-64 (2010)
PM ID: 19995851 PMC2828130
220: 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
221: 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
222: 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
223: 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
224: 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
225: 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
226: 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
227: 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
228: 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
229: 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
230: 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
231: 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
232: 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
233: 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
234: 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
235: 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
236: 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
237: Lieber MR
NHEJ and its backup pathways in chromosomal translocations.
Nat Struct Mol Biol 17: 393-5 (2010)
PM ID: 20368722 PMC3074614 NIHMS263440
238: 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
239: 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
240: 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
241: 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
242: 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
243: 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
244: 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
245: 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
246: 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
247: 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
248: Sir D, Ann DK, Ou JH
Autophagy by hepatitis B virus and for hepatitis B virus.
Autophagy 6: 548-9 (2010)
PM ID: 20305390
249: 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
250: 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
251: 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
252: 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
253: 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
254: 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
255: 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
256: 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
257: 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
258: 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
259: 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
260: 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
261: 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
262: 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
263: 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
264: 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
265: 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
266: 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
267: Lieber MR, Wilson TE
SnapShot: Nonhomologous DNA end joining (NHEJ).
Cell 142: 496-496.e1 (2010)
PM ID: 20691907
268: 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
269: 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
270: 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
271: 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
272: 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
273: 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
274: 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
275: 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
276: 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
277: 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
278: 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
279: 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
280: 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
281: 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
282: 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
283: Balasubramanian P, Longo VD
Linking Klotho, Nrf2, MAP kinases and aging.
Aging (Albany NY) 2: 632-3 (2010)
PM ID: 21076180 PMC2993790
284: 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
285: 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
286: 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
287: 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
288: 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
289: 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
290: 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
291: 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
292: 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
293: 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
294: 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
295: 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
296: 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
297: 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
298: 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
299: 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
300: 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
301: 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
302: 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
303: 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
304: 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
305: 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
306: 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
307: 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
308: 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
309: 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
310: 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
311: 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
312: Shibata D
Mutation and epigenetic molecular clocks in cancer.
Carcinogenesis 32: 123-8 (2011)
PM ID: 21076057 PMC3026845
313: 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
314: 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
315: 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
316: 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
317: Honig B, Rohs R
Biophysics: Flipping Watson and Crick.
Nature 470: 472-3 (2011)
PM ID: 21350476
318: 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
319: 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
320: 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
321: 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
322: 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
323: 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
324: 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
325: 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
326: 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
327: 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
328: 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
329: 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
330: Kamerlin SC, Warshel A
Multiscale modeling of biological functions.
Phys Chem Chem Phys 13: 10401-11 (2011)
PM ID: 21526232 PMC3102780 NIHMS291135
331: 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
332: 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
333: 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
334: 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
335: 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
336: 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
337: 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
338: 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
339: 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
340: 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
341: 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
342: 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
343: 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
344: 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
345: 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
346: Ram Prasad B, Warshel A
Prechemistry versus preorganization in DNA replication fidelity.
Proteins 79: 2900-19 (2011)
PM ID: 21905114 PMC3172682 NIHMS314034
347: 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
348: 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
349: 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
350: 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
351: 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
352: Longo VD, Fontana L
Intermittent supplementation with rapamycin as a dietary restriction mimetic.
Aging (Albany NY) 3: 1039-40 (2011)
PM ID: 22147496 PMC3249447
353: Shibata D
Molecular tumor clocks to study the evolution of drug resistance.
Mol Pharm 8: 2050-4 (2011)
PM ID: 21732670
354: 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
355: 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
356: 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
357: 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
358: 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
359: 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
360: 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
361: 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
362: 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
363: Murphree AL, Triche TJ
An epigenomic mechanism in retinoblastoma: the end of the story?
Genome Med 4: 15 (2012)
PM ID: 22364211 PMC3392761
364: 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
365: 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
366: 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
367: 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, Borchum S, Hoegel J, Grönberg H, Wiklund F, Emanuelsson M, Cancel-Tassin G, Valeri A, Cussenot O, Isaacs WB
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
368: Slaymaker IM, Chen XS
MCM Structure and Mechanics: What We Have Learned from Archaeal MCM.
Subcell Biochem 62: 89-111 (2012)
PM ID: 22918582
369: Longo VD, Fabrizio P
Chronological Aging in Saccharomyces cerevisiae.
Subcell Biochem 57: 101-21 (2012)
PM ID: 22094419
370: 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
371: 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
372: 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
373: 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
374: 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
375: 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
376: Nguyen P, Qin PZ
RNA dynamics: perspectives from spin labels.
Wiley Interdiscip Rev RNA 3: 62-72 (2012)
PM ID: 21882345 PMC3235270 NIHMS314855
377: 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
378: 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
379: 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
380: 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
381: 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
382: 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
383: 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
384: 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
385: 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
386: 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
387: 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
388: 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
389: 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
390: 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
391: 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
392: 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
393: 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
394: 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
395: Singh N, Frushicheva MP, Warshel A
Validating the vitality strategy for fighting drug resistance.
Proteins 80: 1110-22 (2012)
PM ID: 22275047 PMC3299486 NIHMS358866
396: Shibata D
Cancer. Heterogeneity and tumor history.
Science 336: 304-5 (2012)
PM ID: 22517848
397: 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
398: Fontana L, Vinciguerra M, Longo VD
Growth factors, nutrient signaling, and cardiovascular aging.
Circ Res 110: 1139-50 (2012)
PM ID: 22499903 PMC3376758 NIHMS369171
399: 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
400: 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
401: 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
402: 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
403: 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
404: 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
405: 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
406: 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
407: 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
408: 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
409: 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
410: Goodman MF
An accidental biochemist.
DNA Repair (Amst) 11: 527-36 (2012)
PM ID: 22808529
411: 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
412: 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
413: 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
414: 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
415: 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
416: 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
417: 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
418: 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
419: 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
420: 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
421: Plotnikov NV, Warshel A
Exploring, Refining, and Validating the Paradynamics QM/MM Sampling.
J Phys Chem B : (2012)
PM ID: 22853800
422: 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
423: 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
424: 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
425: 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
426: 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
427: 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
428: 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
429: 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
430: 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
431: 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
432: 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
433: 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
434: 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
435: 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
436: 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
437: 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
438: 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
439: 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
440: 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
441: 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
442: 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
443: 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
444: 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
445: 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
446: Hu J, Wei M, Mirisola MG, Longo VD
Assessing chronological aging in Saccharomyces cerevisiae.
Methods Mol Biol 965: 463-72 (2013)
PM ID: 23296677
447: Gonidakis S, Longo VD
Assessing chronological aging in bacteria.
Methods Mol Biol 965: 421-37 (2013)
PM ID: 23296675
448: 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
449: 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
450: 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
451: 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
452: 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
453: 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
454: 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
455: 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 [Available on 01/01/14] NIHMS396375 [Available on 01/01/14]
456: 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
457: 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
458: 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
459: 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 [Available on 01/01/14]
460: 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
461: 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 [Available on 01/10/14] NIHMS427102 [Available on 01/10/14]
462: Aparicio OM
Location, location, location: it's all in the timing for replication origins.
Genes Dev 27: 117-28 (2013)
PM ID: 23348837 PMC3566304
463: 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
464: Kamerlin SC, Sharma PK, Prasad RB, Warshel A
Why nature really chose phosphate.
Q Rev Biophys 46: 1-132 (2013)
PM ID: 23318152
465: 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
466: 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
467: 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
468: Pope BD, Aparicio OM, Gilbert DM
SnapShot: Replication timing.
Cell 152: 1390-1390.e1 (2013)
PM ID: 23498945
469: 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
470: 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
471: 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
472: 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
473: 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
474: 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
475: 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
476: 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
477: 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 [Available on 10/29/13]
478: 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
479: 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 : (2013)
PM ID: 23726368 PMC3682763
480: 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 [Available on 05/30/14]
481: Toth Z, Brulois K, Jung JU
The chromatin landscape of Kaposi's sarcoma-associated herpesvirus.
Viruses 5: 1346-73 (2013)
PM ID: 23698402 PMC3712311
482: 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
483: 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
484: 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 [Available on 06/01/14]
485: 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 : (2013)
PM ID: 23770138
486: 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 [Available on 12/01/13] NIHMS467652 [Available on 12/01/13]
487: 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
488: 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]
489: 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
490: 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
491: 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
492: 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
493: 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
494: 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
495: 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
496: 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 [Available on 08/01/14]
497: 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
498: 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
499: 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 [Available on 02/01/14]
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
Tyrosyl-DNA phosphodiesterase 1 (TDP1) and Poly (ADP-Ribose) Polymerase-1 (PARP1) deficiency are cytotoxic to rhabdomyosarcoma cells.
Mol Cancer Res : (2013)
PM ID: 23913164
501: 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
502: 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
503: 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
504: 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
505: 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
506: 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
507: 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: 5625-5632 (2013)
PM ID: 23913937
508: Wilson PM, Yang D, Azuma M, Shi MM, Danenberg KD, Lebwohl D, Sherrod A, Ladner RD, Zhang W, Danenberg PV, Trarbach T, Folprecht G, Meinhardt G, Lenz HJ
Intratumoral expression profiling of genes involved in angiogenesis in colorectal cancer patients treated with chemotherapy plus the VEGFR inhibitor PTK787/ZK 222584 (vatalanib).
Pharmacogenomics J 13: 410-6 (2013)
PM ID: 22664478
509: 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
510: 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 [Available on 10/01/14] NIHMS462462 [Available on 10/01/14]
511: 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
512: 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
513: Fischer JM, Schepers AG, Clevers H, Shibata D, Liskay RM
Occult progression by Apc-deficient intestinal crypts as a target for chemoprevention.
Carcinogenesis : (2013)
PM ID: 23996931
514: 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
515: Wiseman S, 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: 4072-4079 (2013)
PM ID: 23928671
516: Goodman MF, Woodgate R
Translesion DNA polymerases.
Cold Spring Harb Perspect Biol 5: a010363 (2013)
PM ID: 23838442
517: 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
518: 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
519: 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
520: Chang K, Creighton CJ, Davis C, Donehower L, Drummond J, Wheeler D, Ally A, Balasundaram M, Birol I, Butterfield SN, Chu A, Chuah E, Chun HJ, Dhalla N, Guin R, Hirst M, Hirst C, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Robertson AG, Schein JE, Sipahimalani P, Tam A, Thiessen N, Varhol RJ, Beroukhim R, Bhatt AS, Brooks AN, Cherniack AD, Freeman SS, Gabriel SB, Helman E, Jung J, Meyerson M, Ojesina AI, Pedamallu CS, Saksena G, Schumacher SE, Tabak B, Zack T, Lander ES, Bristow CA, Hadjipanayis A, Haseley P, Kucherlapati R, Lee S, Lee E, Luquette LJ, Mahadeshwar HS, Pantazi A, Parfenov M, Park PJ, Protopopov A, Ren X, Santoso N, Seidman J, Seth S, Song X, Tang J, Xi R, Xu AW, Yang L, Zeng D, Auman JT, Balu S, Buda E, Fan C, Hoadley KA, Jones CD, Meng S, Mieczkowski PA, Parker JS, Perou CM, Roach J, Shi Y, Silva GO, Tan D, Veluvolu U, Waring S, Wilkerson MD, Wu J, Zhao W, Bodenheimer T, Hayes DN, Hoyle AP, Jeffreys SR, Mose LE, Simons JV, Soloway MG, Baylin SB, Berman BP, Bootwalla MS, Danilova L, Herman JG, Hinoue T, Laird PW, Rhie SK, Shen H, Triche T, Weisenberger DJ, Carter SL, Cibulskis K, Chin L, Zhang J, Getz G, Sougnez C, Wang M, Saksena G, Carter SL, Cibulskis K, Chin L, Zhang J, Getz G, Dinh H, Doddapaneni HV, Gibbs R, Gunaratne P, Han Y, Kalra D, Kovar C, Lewis L, Morgan M, Morton D, Muzny D, Reid J, Xi L, Cho J, DiCara D, Frazer S, Gehlenborg N, Heiman DI, Kim J, Lawrence MS, Lin P, Liu Y, Noble MS, Stojanov P, Voet D, Zhang H, Zou L, Stewart C, Bernard B, Bressler R, Eakin A, Iype L, Knijnenburg T, Kramer R, Kreisberg R, Leinonen K, Lin J, Liu Y, Miller M, Reynolds SM, Rovira H, Shmulevich I, Thorsson V, Yang D, Zhang W, Amin S, Wu CJ, Wu CC, Akbani R, Aldape K, Baggerly KA, Broom B, Casasent TD, Cleland J, Creighton C, Dodda D, Edgerton M, Han L, Herbrich SM, Ju Z, Kim H, Lerner S, Li J, Liang H, Liu W, Lorenzi PL, Lu Y, Melott J, Mills GB, Nguyen L, Su X, Verhaak R, Wang W, Weinstein JN, Wong A, Yang Y, Yao J, Yao R, Yoshihara K, Yuan Y, Yung AK, Zhang N, Zheng S, Ryan M, Kane DW, Aksoy BA, Ciriello G, Dresdner G, Gao J, Gross B, Jacobsen A, Kahles A, Ladanyi M, Lee W, Lehmann KV, Miller ML, Ramirez R, Rätsch G, Reva B, Sander C, Schultz N, Senbabaoglu Y, Shen R, Sinha R, Sumer SO, Sun Y, Taylor BS, Weinhold N, Fei S, Spellman P, Benz C, Carlin D, Cline M, Craft B, Ellrott K, Goldman M, Haussler D, Ma S, Ng S, Paull E, Radenbaugh A, Salama S, Sokolov A, Stuart JM, Swatloski T, Uzunangelov V, Waltman P, Yau C, Zhu J, Hamilton SR, Getz G, Sougnez C, Abbott S, Abbott R, Dees ND, Delehaunty K, Ding L, Dooling DJ, Eldred JM, Fronick CC, Fulton R, Fulton LL, Kalicki-Veizer J, Kanchi KL, Kandoth C, Koboldt DC, Larson DE, Ley TJ, Lin L, Lu C, Magrini VJ, Mardis ER, McLellan MD, McMichael JF, Miller CA, O'Laughlin M, Pohl C, Schmidt H, Smith SM, Walker J, Wallis JW, Wendl MC, Wilson RK, Wylie T, Zhang Q, Burton R, Jensen MA, Kahn A, Pihl T, Pot D, Wan Y, Levine DA, Black AD, Bowen J, Frick J, Gastier-Foster JM, Harper HA, Helsel C, Leraas KM, Lichtenberg TM, McAllister C, Ramirez NC, Sharpe S, Wise L, Zmuda E, Chanock SJ, Davidsen T, Demchok JA, Eley G, Felau I, Ozenberger BA, Sheth M, Sofia H, Staudt L, Tarnuzzer R, Wang Z, Yang L, Zhang J, Omberg L, Margolin A, Raphael BJ, Vandin F, Wu HT, Leiserson MD, Benz SC, Vaske CJ, Noushmehr H, Knijnenburg T, Wolf D, van 't Veer L, Collisson EA, Anastassiou D, Ou Yang TH, Lopez-Bigas N, Gonzalez-Perez A, Tamborero D, Xia Z, Li W, Cho DY, Przytycka T, Hamilton M, McGuire S, Nelander S, Johansson P, Jörnsten R, Kling T, Sanchez J, Cancer Genome Atlas Research Network , Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM
The Cancer Genome Atlas Pan-Cancer analysis project.
Nat Genet 45: 1113-20 (2013)
PM ID: 24071849 PMC3919969 NIHMS549280
521: Shen J, Tower J
Aging, MnSOD, and hormesis mechanisms converge on liver mUPR.
Cell Cycle 12: 3237-8 (2013)
PM ID: 24036542 PMC3885629
522: 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
523: 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
524: 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
525: 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
526: 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
527: 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 : (2013)
PM ID: 24293652
528: 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
529: 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
530: 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
531: 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 : (2013)
PM ID: 24293651
532: 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
533: 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
534: 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
535: 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
536: 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