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Wei Wang - Publications

University of California, San Diego, La Jolla, CA 
Inference of gene regulatory networks and determination of protein specificity

86 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel PS, Ren B. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Reports. 41: 111630. PMID 36351387 DOI: 10.1016/j.celrep.2022.111630  0.526
2021 Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, ... ... Wang W, et al. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science Advances. 7: eabi4360. PMID 34524848 DOI: 10.1126/sciadv.abi4360  0.356
2021 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Wang W, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33398137 DOI: 10.1038/s41586-020-03089-4  0.406
2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Wang W, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33037424 DOI: 10.1038/s41586-020-2841-4  0.392
2020 Li L, Li L, Li Q, Liu X, Ma X, Yong J, Gao S, Wu X, Wei Y, Wang X, Wang W, Li R, Yan J, Zhu X, Wen L, et al. Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution. Cell Research. PMID 32884136 DOI: 10.1038/s41422-020-00401-9  0.336
2020 Wang M, Wang D, Zhang K, Ngo V, Fan S, Wang W. Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. Genetics. PMID 32816922 DOI: 10.1534/Genetics.120.303597  0.361
2020 Parkinson J, Hard R, Ainsworth RI, Li N, Wang W. Engineering a Histone Reader Protein by Combining Directed Evolution, Sequencing, and Neural Network Based Ordinal Regression. Journal of Chemical Information and Modeling. PMID 32786513 DOI: 10.1021/Acs.Jcim.0C00441  0.318
2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Wang W, et al. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 583: 744-751. PMID 32728240 DOI: 10.1038/S41586-020-2093-3  0.556
2020 Roussarie JP, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt EF, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, et al. Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. Neuron. PMID 32603655 DOI: 10.1016/J.Neuron.2020.06.010  0.499
2020 Arvanitis M, Tampakakis E, Zhang Y, Wang W, Auton A, Dutta D, Glavaris S, Keramati A, Chatterjee N, Chi NC, Ren B, Post WS, Battle A. Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure. Nature Communications. 11: 1122. PMID 32111823 DOI: 10.1038/S41467-020-14843-7  0.453
2020 Ai R, Boyle D, Hammaker D, Deane K, Holers VM, Matti A, Robinson W, Buckner J, Rao N, Baribaud F, Johnsen A, Nagpal S, Wang W, Firestein G. Op0337 Differential Methylation Of Peripheral Blood Adaptive Immune Cells In Individuals At High Risk For Ra And With Early Ra Compared With Controls Identifies Pathways Important In Transition To Arthritis Annals of the Rheumatic Diseases. 79: 207-207. DOI: 10.1136/Annrheumdis-2020-Eular.2989  0.311
2019 Wang Z, Zhao Y, Phipps-Green A, Liu-Bryan R, Ceponis A, Boyle DL, Wang J, Merriman TR, Wang W, Terkeltaub R. Differential DNA methylation of networked signaling, transcriptional, innate and adaptive immunity, and osteoclastogenesis genes and pathways in gout. Arthritis & Rheumatology (Hoboken, N.J.). PMID 31738005 DOI: 10.1002/Art.41173  0.346
2019 Wang M, Zhang K, Ngo V, Liu C, Fan S, Whitaker JW, Chen Y, Ai R, Chen Z, Wang J, Zheng L, Wang W. Identification of DNA motifs that regulate DNA methylation. Nucleic Acids Research. 47: 6753-6768. PMID 31334813 DOI: 10.1093/Nar/Gkz483  0.48
2019 Zhang K, Wang M, Zhao Y, Wang W. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. Science Advances. 5: eaav3262. PMID 30944857 DOI: 10.1126/Sciadv.Aav3262  0.425
2019 Wang W, Xu J, Limbo O, Fei J, Kassavetis GA, Chong J, Kadonaga JT, Russell P, Li B, Wang D. Molecular basis of chromatin remodeling by Rhp26, a yeast CSB ortholog. Proceedings of the National Academy of Sciences of the United States of America. PMID 30867290 DOI: 10.1073/Pnas.1818163116  0.374
2019 Ngo V, Chen Z, Zhang K, Whitaker JW, Wang M, Wang W. Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse. Proceedings of the National Academy of Sciences of the United States of America. PMID 30755522 DOI: 10.1073/Pnas.1813565116  0.492
2019 Fan S, Tang J, Li N, Zhao Y, Ai R, Zhang K, Wang M, Du W, Wang W. Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers. Npj Genomic Medicine. 4: 2. PMID 30729033 DOI: 10.1038/S41525-019-0077-8  0.438
2019 Ngo V, Wang M, Wang W. Finding de novo methylated DNA motifs. Bioinformatics (Oxford, England). PMID 30726880 DOI: 10.1093/Bioinformatics/Btz079  0.377
2018 Hard R, Li N, He W, Ross B, Mo GCH, Peng Q, Stein RSL, Komives E, Wang Y, Zhang J, Wang W. Deciphering and engineering chromodomain-methyllysine peptide recognition. Science Advances. 4: eaau1447. PMID 30417094 DOI: 10.1126/Sciadv.Aau1447  0.353
2018 Ainsworth RI, Ai R, Ding B, Li N, Zhang K, Wang W. Bayesian Networks Predict Neuronal Transdifferentiation. G3 (Bethesda, Md.). PMID 29848620 DOI: 10.1534/G3.118.200401  0.375
2018 Ai R, Laragione T, Hammaker D, Boyle DL, Wildberg A, Maeshima K, Palescandolo E, Krishna V, Pocalyko D, Whitaker JW, Bai Y, Nagpal S, Bachman KE, Ainsworth RI, Wang M, ... ... Wang W, et al. Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nature Communications. 9: 1921. PMID 29765031 DOI: 10.1038/S41467-018-04310-9  0.36
2018 Treen N, Heist T, Wang W, Levine M. Depletion of Maternal Cyclin B3 Contributes to Zygotic Genome Activation in the Ciona Embryo. Current Biology : Cb. PMID 29576477 DOI: 10.1016/J.Cub.2018.02.046  0.397
2018 Milner JJ, Toma C, Yu B, Zhang K, Omilusik K, Phan AT, Wang D, Getzler AJ, Nguyen T, Crotty S, Wang W, Pipkin ME, Goldrath AW. Erratum: Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours. Nature. PMID 29320476 DOI: 10.1038/Nature25445  0.308
2017 Local A, Huang H, Albuquerque CP, Singh N, Lee AY, Wang W, Wang C, Hsia JE, Shiau AK, Ge K, Corbett KD, Wang D, Zhou H, Ren B. Identification of H3K4me1-associated proteins at mammalian enhancers. Nature Genetics. PMID 29255264 DOI: 10.1038/S41588-017-0015-6  0.599
2017 Milner JJ, Toma C, Yu B, Zhang K, Omilusik K, Phan AT, Wang D, Getzler AJ, Nguyen T, Crotty S, Wang W, Pipkin ME, Goldrath AW. Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours. Nature. 552: 253-257. PMID 29211713 DOI: 10.1038/Nature24993  0.39
2017 Matsuda S, Hammaker D, Topolewski K, Briegel KJ, Boyle DL, Dowdy S, Wang W, Firestein GS. Regulation of the Cell Cycle and Inflammatory Arthritis by the Transcription Cofactor LBH Gene. Journal of Immunology (Baltimore, Md. : 1950). PMID 28807995 DOI: 10.4049/Jimmunol.1700719  0.3
2017 Yu B, Zhang K, Milner JJ, Toma C, Chen R, Scott-Browne JP, Pereira RM, Crotty S, Chang JT, Pipkin ME, Wang W, Goldrath AW. Epigenetic landscapes reveal transcription factors that regulate CD8(+) T cell differentiation. Nature Immunology. PMID 28288100 DOI: 10.1038/Ni.3706  0.408
2016 Spreafico R, Rossetti M, Whitaker JW, Wang W, Lovell DJ, Albani S. Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways. Proceedings of the National Academy of Sciences of the United States of America. PMID 27849614 DOI: 10.1073/Pnas.1524056113  0.364
2016 Rhead B, Holingue C, Cole M, Shao X, Quach HL, Quach D, Shah K, Sinclair E, Graf J, Link T, Harrison R, Rahmani E, Halperin E, Wang W, Firestein GS, et al. Rheumatoid arthritis naïve T cells share hypermethylation sites with synoviocytes. Arthritis & Rheumatology (Hoboken, N.J.). PMID 27723282 DOI: 10.1002/Art.39952  0.305
2016 Zhang K, Li N, Ainsworth RI, Wang W. Systematic identification of protein combinations mediating chromatin looping. Nature Communications. 7: 12249. PMID 27461729 DOI: 10.1038/Ncomms12249  0.426
2016 Ai R, Hammaker D, Boyle DL, Morgan R, Walsh AM, Fan S, Firestein GS, Wang W. Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Nature Communications. 7: 11849. PMID 27282753 DOI: 10.1038/Ncomms11849  0.312
2016 Hammaker D, Whitaker JW, Maeshima K, Boyle DL, Ekwall AH, Wang W, Firestein GS. Limb Bud and Heart Development Gene Transcription is Regulated by the Interplay of an Enhancer Risk Allele and DNA Methylation in Rheumatoid Arthritis. Arthritis & Rheumatology (Hoboken, N.J.). PMID 27159840 DOI: 10.1002/Art.39746  0.338
2016 Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W. Constructing 3D interaction maps from 1D epigenomes. Nature Communications. 7: 10812. PMID 26960733 DOI: 10.1038/Ncomms10812  0.399
2016 Fan S, Huang K, Ai R, Wang M, Wang W. Predicting CpG methylation levels by integrating Infinium HumanMethylation450 BeadChip array data. Genomics. PMID 26921858 DOI: 10.1016/J.Ygeno.2016.02.005  0.372
2016 Fan S, Li C, Ai R, Firestein GS, Wang W. Computationally expanding Infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. Bioinformatics (Oxford, England). PMID 26883487 DOI: 10.1093/Bioinformatics/Btw089  0.326
2015 Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, ... ... Wang W, et al. Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. PMID 26605523 DOI: 10.1038/Nature16179  0.69
2015 Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, ... ... Wang W, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 523: 212-6. PMID 26030523 DOI: 10.1038/Nature14465  0.721
2015 Whitaker JW, Boyle DL, Bartok B, Ball ST, Gay S, Wang W, Firestein GS. Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets. Plos One. 10: e0124254. PMID 25901943 DOI: 10.1371/Journal.Pone.0124254  0.304
2015 Ekwall AK, Whitaker JW, Hammaker D, Bugbee WD, Wang W, Firestein GS. The Rheumatoid Arthritis Risk Gene LBH Regulates Growth in Fibroblast-like Synoviocytes. Arthritis & Rheumatology (Hoboken, N.J.). 67: 1193-202. PMID 25707478 DOI: 10.1002/Art.39060  0.314
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Wang W, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.723
2015 Whitaker JW, Nguyen TT, Zhu Y, Wildberg A, Wang W. Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods (San Diego, Calif.). 72: 86-94. PMID 25461775 DOI: 10.1016/J.Ymeth.2014.10.008  0.336
2015 Whitaker JW, Chen Z, Wang W. Predicting the human epigenome from DNA motifs. Nature Methods. 12: 265-72, 7 p followin. PMID 25240437 DOI: 10.1038/Nmeth.3065  0.378
2014 Greer EL, Beese-Sims SE, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizábal-Corrales D, Chen S, Badeaux AI, Jin Q, Wang W, Strahl BD, Colaiácovo MP, Shi Y. A histone methylation network regulates transgenerational epigenetic memory in C. elegans. Cell Reports. 7: 113-26. PMID 24685137 DOI: 10.1016/J.Celrep.2014.02.044  0.348
2013 Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (Oxford, England). 29: 3204-3210. PMID 24078702 DOI: 10.1093/Bioinformatics/Btt558  0.412
2013 Zhu Y, Sun L, Chen Z, Whitaker JW, Wang T, Wang W. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Research. 41: 10032-43. PMID 24038352 DOI: 10.1093/Nar/Gkt826  0.362
2013 Li N, Stein RS, He W, Komives E, Wang W. Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. Molecular & Cellular Proteomics : McP. 12: 2750-60. PMID 23842000 DOI: 10.1074/Mcp.O112.025015  0.373
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, ... ... Wang W, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022  0.729
2013 Whitaker JW, Shoemaker R, Boyle DL, Hillman J, Anderson D, Wang W, Firestein GS. An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype. Genome Medicine. 5: 40. PMID 23631487 DOI: 10.1186/Gm444  0.696
2013 Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. Plos Computational Biology. 9: e1002968. PMID 23526891 DOI: 10.1371/Journal.Pcbi.1002968  0.729
2013 Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, Ren B, Wang W. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Research. 41: 4423-32. PMID 23482391 DOI: 10.1093/Nar/Gkt143  0.554
2013 Stein RS, Li N, He W, Komives E, Wang W. Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. Journal of Proteome Research. 12: 1467-77. PMID 23320494 DOI: 10.1021/Pr3011205  0.324
2013 Nakano K, Whitaker JW, Boyle DL, Wang W, Firestein GS. DNA methylome signature in rheumatoid arthritis. Annals of the Rheumatic Diseases. 72: 110-7. PMID 22736089 DOI: 10.1136/Annrheumdis-2012-201526  0.354
2013 Whitaker JW, Chen Z, Wang W. Interplay between DNA sequence motifs and the human epigenome Embnet.Journal. 19: 32-33. DOI: 10.14806/Ej.19.A.615  0.4
2012 Won KJ, Xu Z, Zhang X, Whitaker JW, Shoemaker R, Ren B, Xu Y, Wang W. Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells Nucleic Acids Research. 40: 8199-8209. PMID 22730289 DOI: 10.1093/Nar/Gks584  0.762
2011 Chang R, Shoemaker R, Wang W. Systematic search for recipes to generate induced pluripotent stem cells Plos Computational Biology. 7. PMID 22215993 DOI: 10.1371/Journal.Pcbi.1002300  0.696
2011 Xu Z, Hou T, Li N, Xu Y, Wang W. Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray. Molecular & Cellular Proteomics : McP. 11: O111.010389. PMID 22023807 DOI: 10.1074/Mcp.O111.010389  0.307
2011 Ding S, Wang W. Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae Bmc Systems Biology. 5: 50-50. PMID 21486480 DOI: 10.1186/1752-0509-5-50  0.331
2011 Chang R, Shoemaker R, Wang W. A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention Ieee/Acm Transactions On Computational Biology and Bioinformatics. 8: 1170-1182. PMID 21282866 DOI: 10.1109/Tcbb.2011.18  0.695
2011 Stein RS, Wang W. The recognition specificity of the CHD1 chromodomain with modified histone H3 peptides. Journal of Molecular Biology. 406: 527-41. PMID 21195088 DOI: 10.1016/J.Jmb.2010.12.030  0.351
2011 Shoemaker R, Wang W, Zhang K. Mediators and dynamics of DNA methylation Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 3: 281-298. PMID 20878927 DOI: 10.1002/Wsbm.124  0.748
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, ... ... Wang W, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/J.Stem.2010.03.018  0.747
2010 Shoemaker R, Deng J, Wang W, Zhang K. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Research. 20: 883-9. PMID 20418490 DOI: 10.1101/Gr.104695.109  0.729
2009 Hon G, Wang W, Ren B. Discovery and annotation of functional chromatin signatures in the human genome. Plos Computational Biology. 5: e1000566. PMID 19918365 DOI: 10.1371/Journal.Pcbi.1000566  0.739
2009 Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology. 27: 353-60. PMID 19330000 DOI: 10.1038/Nbt.1530  0.731
2008 Won KJ, Chepelev I, Ren B, Wang W. Prediction of regulatory elements in mammalian genomes using chromatin signatures Bmc Bioinformatics. 9. PMID 19094206 DOI: 10.1186/1471-2105-9-547  0.54
2008 Hon G, Ren B, Wang W. ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome Plos Computational Biology. 4. PMID 18927605 DOI: 10.1371/Journal.Pcbi.1000201  0.731
2008 Shen L, Liu J, Wang W. GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach Bmc Bioinformatics. 9: 395-395. PMID 18811979 DOI: 10.1186/1471-2105-9-395  0.334
2008 Yu RX, Liu J, True N, Wang W. Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16. Plos One. 3. PMID 18350157 DOI: 10.1371/Journal.Pone.0001821  0.338
2007 Philibert P, Stoessel A, Wang W, Sibler AP, Bec N, Larroque C, Saven JG, Courtête J, Weiss E, Martineau P. A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm. Bmc Biotechnology. 7: 81. PMID 18034894 DOI: 10.1186/1472-6750-7-81  0.314
2007 Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics. 39: 311-318. PMID 17277777 DOI: 10.1038/Ng1966  0.737
2006 Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling. 25: 247-60. PMID 16458552 DOI: 10.1016/J.Jmgm.2005.12.005  0.444
2006 Chung JL, Wang W, Bourne PE. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins. 62: 630-40. PMID 16329107 DOI: 10.1002/Prot.20741  0.303
2005 Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H. Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proceedings of the National Academy of Sciences of the United States of America. 102: 1998-2003. PMID 15684073 DOI: 10.1073/Pnas.0405537102  0.468
2005 Park S, Kono H, Wang W, Boder ET, Saven JG. Progress in the development and application of computational methods for probabilistic protein design Computers and Chemical Engineering. 29: 407-421. DOI: 10.1016/J.Compchemeng.2004.07.037  0.311
2004 Cole AM, Wang W, Waring AJ, Lehrer RI. Retrocyclins: Using past as prologue Current Protein and Peptide Science. 5: 373-381. PMID 15544532 DOI: 10.2174/1389203043379657  0.303
2003 Li H, Wang W. Dissecting the transcription networks of a cell using computational genomics. Current Opinion in Genetics & Development. 13: 611-616. PMID 14638323 DOI: 10.1016/J.Gde.2003.10.012  0.351
2002 Wang W, Cherry JM, Botstein D, Li H. A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 99: 16893-8. PMID 12482955 DOI: 10.1073/Pnas.252638199  0.471
2002 Wang W, Saven JG. Designing gene libraries from protein profiles for combinatorial protein experiments. Nucleic Acids Research. 30: e120. PMID 12409479 DOI: 10.1093/Nar/Gnf119  0.303
2002 Wang J, Wang W, Huo S, Lee M, Kollman PA. Solvation model based on weighted solvent accessible surface area Journal of Physical Chemistry B. 105: 5055-5067. DOI: 10.1021/Jp0102318  0.445
2001 Wang W, Kollman PA. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proceedings of the National Academy of Sciences of the United States of America. 98: 14937-42. PMID 11752442 DOI: 10.1073/Pnas.251265598  0.439
2001 Wang J, Morin P, Wang W, Kollman PA. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. Journal of the American Chemical Society. 123: 5221-30. PMID 11457384 DOI: 10.1021/Ja003834Q  0.463
2001 Wang W, Lim WA, Jakalian A, Wang J, Wang J, Luo R, Bayly CI, Kollman PA. An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. Journal of the American Chemical Society. 123: 3986-94. PMID 11457149 DOI: 10.1021/Ja003164O  0.471
2001 Wang W, Donini O, Reyes CM, Kollman PA. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annual Review of Biophysics and Biomolecular Structure. 30: 211-43. PMID 11340059 DOI: 10.1146/Annurev.Biophys.30.1.211  0.609
2000 Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33: 889-97. PMID 11123888 DOI: 10.1021/Ar000033J  0.726
2000 Wang W, Kollman PA. Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. Journal of Molecular Biology. 303: 567-82. PMID 11054292 DOI: 10.1006/Jmbi.2000.4057  0.447
1999 Wang W, Wang J, Kollman PA. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins. 34: 395-402. PMID 10024025 DOI: 10.1002/(Sici)1097-0134(19990215)34:3<395::Aid-Prot11>3.0.Co;2-4  0.449
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