68. Anna-Karin H. Ekwall, John W. Whitaker, Deepa Hammaker, William Bugbee,
Wei Wang* and Gary S. Firestein*. The Rheumatoid Arthritis Risk Gene, LBH, Regulates Growth in Fibroblast-like Synoviocytes. Arthritis & Rheumatology. 2015, DOI 10.1002/art.39060 (* corresponding authors) [HTML][PDF]

67. Bo Ding#, Lina Zheng#, Yun Zhu, Nan Li, Haiyang Jia, Rizi Ai, Andre Wildberg, Wei Wang. Normalization and noise reduction for single cell RNA-seq experiments. Bioinformatics, 2015,Advance Access.(# equal contribution) [HTML][PDF]

66. John W. Whitaker, Tung T. Nguyen, Yun Zhu, Andre Wildberg, Wei Wang. Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods, 2015, 72, 86-94. [HTML][PDF]

65. John W. Whitaker, Zhao Chen, Wei Wang. Predicting the human epigenome using DNA motifs. Nature Methods, 2015, 12, 265-272. [HTML][PDF]

64. Eric L. Greer, Sara E. Beese-Sims, Emily Brookes, Ruggero Spadafora, Yun Zhu, Scott B. Rothbart, David Aristizábal-Corrales, Shuzhen Chen, Aimee I. Badeaux, Qiuye Jin, Wei Wang, Brian D. Strahl, Monica P. Colaiácovo, Yang Shi. A Histone Methylation Network Regulates Transgenerational Epigenetic Memory in C. elegans. Cell Reports, 2014, 7, 113-126 [HTML][PDF]

63. Tao Wang, Jie Liu, Li Shen, Julian Tonti-Filippini, Yun Zhu, Haiyang Jia, Ryan Lister, John W. Whitaker, Joseph R. Ecker, A. Harvey Millar, Bing Ren, Wei Wang. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics, 2013, 29, 3204-3210. [HTML][PDF][STAR Browser][STAR Download]

62. Nan Li#, Richard S.L. Stein#, Wei He#, Elizabeth Komives, Wei Wang. Identification of methyllysine peptides binding to CBX6 chromodomain in the human proteome. Molecular & Cellular Proteomics, 2013, 12, 2750-2760. [HTML][PDF]

61. Yun Zhu, Lin Sun#, Zhao Chen#, John W. Whitaker, Tao Wang, Wei Wang. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Research, 2013, 41, 10032-10043. (# equal contribution) [HTML] [PDF]

60. Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren. RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State. Plos Computational Biology, 2013,9,e1002968. [HTML][PDF]

59. Wei Xie, Matthew D. Schultz#, Ryan Lister#, Zhonggang Hou#, Nisha Rajagopal#, Pradipta Ray#, John W. Whitaker#, Shulan Tian#, R. David Hawkins#, Danny Leung#, Hongbo Yang, Tao Wang, Ah Young Lee, Scott A. Swanson, Jiuchun Zhang, Yun Zhu, Audrey Kim, Joseph R. Nery, Mark A. Urich, Samantha Kuan, Chia-an Yen, Sarit Klugman, Pengzhi Yu, Kran Suknuntha, Nicholas E. Propson, Huaming Chen, Lee E. Edsall, Ulrich Wagner, Yan Li, Zhen Ye, Ashwinikumar Kulkarni, Zhenyu Xuan, Wen-Yu Chung, Neil C. Chi, Jessica E. Antosiewicz-Bourget, Igor Slukvin, Ron Stewart, Michael Q. Zhang*, Wei Wang*, James A. Thomson*, Joseph R. Ecker*, Bing Ren*. Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 2013,153,1134-1148. (# equal contribution; * equal contribution) [HTML][PDF]

58. John W. Whitaker, Robert Shoemaker, David L. Boyle, Josh Hillman, David Anderson, Wei Wang*, Gary S. Firestein*. An Imprinted Rheumatiod Arthritis Methylome Signature Reflects Pathogenic Phenotype. Genome Medicine, 2013,5,40. (* corresponding authors) [HTML][PDF]

57. Bo Ding, Nan Li, Wei Wang. Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures. Journal of Chemical Information and Modeling, 2013, 53,1213-1222 [HTML][PDF]

56. Kyoung-Jae Won, Xian Zhang, Tao Wang, Bo Ding, Debasish Raha, Michael Snyder, Bing Ren, Wei Wang. Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Research, 2013,41,4423-4432. [HTML][PDF]

55. Wei Wang. Therapeutic Hints from Analyzing the Attractor Landscape of the p53 Regulatory Circuit. Science Signaling, 2013, 6, pe5 [HTML][PDF]

54. Richard S.L. Stein#, Nan Li#, Wei He#, Elizabeth Komives, Wei Wang. Recognition of Methylated Peptides by Drosophila melanogaster Polycomb Chromodomain. Journal of Proteome Research, 2013, 12, 1467-1477 (# equal contribution) [HTML][PDF]

53. Bo Ding, Jian Wang, Nan Li, Wei Wang. Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening. Journal of Chemical Information and Modeling, 2013, 53, 114-122. [HTML][PDF]

52. Kazuhisa Nakano, John W. Whitaker, David L Boyle, Wei Wang, Gary S Firestein. DNA methylome signature in rheumatoid arthritis. Annals of the Rheumatic Diseases, 2013, 72, 110-117. [HTML][PDF]

51. Tingjun Hou*, Nan Li, Youyong Li, Wei Wang*.Characterization of Domain-Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein-Protein Interaction Network in Yeast by Generic Structure-Based Models.Journal of Proteome Research, 2012, 11, 2982-2995. (* corresponding authors) [HTML] [PDF]

50. Kyoung-Jae Won#, Zheng Xu#, Xian Zhang#, John W. Whitaker, Robert Shoemaker, Bing Ren, Yang Xu, Wei Wang. Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells. Nucleic Acids Research, 2012, 49, 8199-8209 (# equal contribution) [HTML] [PDF]

49. Zheng Xu#, Tingjun Hou#, Nan Li#, Yang Xu, Wei Wang. Proteome-wide detection of Abl1 SH3 binding peptides by integrating computational prediction and peptide microarray. Molecular & Cellular Proteomics, 2012, 11:O111.010389. (# equal contribution) [HTML] [PDF]

48. Robert Shoemaker, Wei Wang, Kun Zhang. Mediators and dynamics of DNA methylation. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2011, 3, 281-298. [HTML] [PDF]

47. Rui Chang, Robert Shoemaker, Wei Wang. Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells.Plos Computational Biology, 2011, 7, 12, e1002300. [HTML] [PDF]

46. Nan Li, Tingjun Hou, Bo Ding, Wei Wang. Characterization of PDZ domain-peptide interaction interface based on energetic patterns. Proteins: Structure, Function, and Bioinformatics, 2011, 79, 3208-3220 [HTML] [PDF]

45. Rui Chang, Robert Shoemaker, Wei Wang. A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8, 1170-1182 [HTML] [PDF]

44. Tingjun Hou*, Youyong Li, Wei Wang*. Prediction of peptides binding to the PKA RII{alpha} subunit using a hierarchical strategy. Bioinformatics, 2011, 27, 1814-1821. (* corresponding authors) [HTML] [PDF]

43. Shengchao Ding, Wei Wang. Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. BMC System Biology, 2011, 5:50 [HTML] [PDF]

42. Richard S.L. Stein, Wei Wang. The recognition specificity of the CHD1 Chromodomain with modified histone H3 peptides. Journal of Molecular Biology, 2011, 406, 527-541. [HTML] [PDF]

41. William A. McLaughlin*, Tingjun Hou, Susan S. Taylor, Wei Wang. The identification of novel cyclic AMP-dependent protein kinase anchoring proteins using bioinformatic filters and peptide arrays. Protein engineering design & selection, 2011, 24, 333-339. (* corresponding authors) [HTML] [PDF]

40. Tingjun Hou*, Junmei Wang, Youyong Li, Wei Wang*. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry, 2011, 32, 866-877. (* corresponding authors) [HTML] [PDF]

39. Tingjun Hou*, Junmei Wang, Youyong Li, Wei Wang*. Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 2011, 51, 69-82. (* corresponding authors) [HTML] [PDF]

38. Li Shen, Iouri Chepelev, Jie Liu, Wei Wang. Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation. BMC System Biology, 2010, 4, 128. [HTML] [PDF]

37. R. David Hawkins, Gray C. Hon, Leonard K. Lee, QueMinh Ngo, Ryan Lister, Mattia Pelizzola, Lee E. Edsall, Samantha Kuan, Ying Luu, Sarit Klugman, Jessica Antosiewicz-Bourget, Zhen Ye, Celso Espinoza, Saurabh Agarwahl, Li Shen, Victor Ruotti, Wei Wang, Ron Stewart, James A. Thomson, Josephe R. Ecker and Bing Ren. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell, 2010, 6, 479-491. [HTML] [PDF]

36. Robert Shoemaker#, Jie Deng#, Wei Wang*, and Kun Zhang*. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Research, 2010, 20, 883-889.(# equal contribution; * corresponding authors) [HTML] [PDF]

35. Kyoung-Jae Won, Bing Ren, Wei Wang. Genome-wide prediciton of transcription factor binding sites using an intergrated model. Genome Biology, 2010, 11, R7. [HTML] [PDF] [Chromia Download]

34. Jiang Zhang#, Tingjun Hou#, Wei Wang*, Jun S. Liu*. Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. Proceeding of the National Academy of Sciences of the United States of America, 2010, 107, 1321-1326. (# equal contribution; * corresponding authors) [HTML] [PDF]
(This paper was reported by UCSD News Center: )

33. Gary Hon, Wei Wang*, Bing Ren*, Discovery and annotation of functional chromatin signatures in the human genome, Plos Computational Biology, 2009, 5, 11, e1000566. (* corresponding authors) [HTML] [PDF]

32. Kyoung-Jae Won, Saurabh Agarwal, Li Shen, Robert Shoemaker, Bing Ren*, Wei Wang*, An integrated approach to identifying cis-regulatory modules in the human genome, Plos One, 2009, 4, 5, e5501. (* corresponding authors) [HTML] [PDF]

31. Jie Deng, Robert Shoemaker, Bin Xie, Athurva Gore, Emily M LeProust, Jessica Antosiewicz-Bourget, Dieter Egli, Nimet Maherali, In-Hyun Park, Junying Yu, George Q Daley, Kevin Eggan, Konrad Hochedlinger, James Thomson, Wei Wang, Yuan Gao and Kun Zhang, Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming, Nature Biotechnology, 2009, 27, 353-360. [HTML] [PDF]

30. Tingjun Hou#, Zheng Xu#, Wei Zhang, William A. McLaughlin, David A. Case, Yang Xu and Wei Wang, Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains, Molecular & Cellular Proteomics, 2009, 8, 639-649. (# equal contribution) [HTML] [PDF]

29. Tingjun Hou, Wei Zhang, Jian Wang and Wei Wang, Predicting drug resistance of the HIV-1 protease using molecular interaction energy components, Proteins: Structure, Function, and Bioinformatics, 2009, 74, 837-846. [HTML] [PDF]

28. Kyoung-Jae Won, Iouri Chepelev, Bing Ren and Wei Wang, Prediction of Regulatory Elements in Mammalian Genomes Using Chromatin Signatures, BMC Bioinformatics, 2008, 9, 547. [HMTL] [PDF] [Chromia Download]

27. Li Shen, Jie Liu and Wei Wang, GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach, BMC Bioinformatics, 2008, 9, 395. [HTML] [PDF] [GBNet Download]

26. Gary Hon, Bing Ren* and Wei Wang*, ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome, PLoS Computational Biology, 2008, 4, 10, e1000201. (* corresponding authors) [HTML] [PDF] [ChromaSig Download]
(This paper was highlighted by Nature Reviews Genetics, 9, 895, 2008.)

25. Chia-en A. Chang#*, William A. McLaughlin#*, Riccardo Baron, Wei Wang And J. Andrew McCammon, Entropic contributions and the influcence of the hydrophobic environment in promiscuous protein-protein association, Proceeding of the National Academy of Sciences of the United States of America, 2008, 105, 21, 7456-7461. (# equal contribution. * corresponding authors) [HTML] [PDF]

24. Ron Yu, Jie Liu, Wei Wang, Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16, PLoS one, 2008, 3, e1821.[HTML] [PDF] [Transmodis Download]

23. Tingjun Hou, Wei Zhang, David Case, Wei Wang, Characterization of domain-peptide interaction interface: A case study on the amphiphysin-1 SH3 domain, Journal of Molecular Biology, 2008, 376, 1201-1214. [HTML] [PDF]

22. Tingjun Hou, William McLaughlin, Wei Wang, Evaluating the potency of HIV-1 protease drugs to combat resistance, Proteins: Structure, Function, and Bioinformatics, 2008, 71, 1163-1174. [HTML] [PDF]

21. Bin Fu and Wei Wang, Geometric Separators and their applications to protein folding in the HP-model, SIAM Journal on Computing, 2007, 37, 4, 1014-1029. [HTML] [PDF]

20. William McLaughlin, Ken Chen, Tingjun Hou, Wei Wang, On the detection of functionally coherent groups of protein domains with an extension to protein annotation, BMC Bioinformatics. 2007, 8, 390. [HTML] [PDF]

19. Chung JL, Wei Wang , Bourne PE. High-throughput identification of interacting protein-protein binding sites, BMC Bioinformatics, 2007, 8, 223. [HTML] [PDF]

18. Nathaniel D Heintzman, Rhona K Stuart, Gary Hon, Yutao Fu, Christina W Ching, R David Hawkins, Leah O Barrera, Sara Van Calcar, Chunxu Qu, Keith A Ching, Wei Wang, Zhiping Weng, Roland D Green, Gregory E Crawford and Bing Ren, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome, Nature Genetics, 2007, 39, 311-318. [HTML] [PDF]

17. Tingjun Hou, Junmei Wang, Wei Zhang, Wei Wang, Xiaojie Xu, Recent advances in computational prediction of drug absorption and permeability in drug discovery, Current Medicinal Chemistry, 2006, 13, 2653-2667.[HTML] [PDF]

16. Junmei Wang, Wei Wang, Peter A. Kollman and David A. Case, Automatic atom type and bond type perception in molecular mechanical calculations, Journal of Molecular Graphics and Modelling, 2006, 25, 247-260. [HTML] [PDF]

15. Chung JL, Wei Wang and Bourne PE. Exploiting sequence and structure homologs to identify protein-protein binding sites, Proteins: Structure, Function and Genetics, 2006, 62, 630-40. [HTML] [PDF]

14. William A. McLaughlin, Tingjun Hou , Wei Wang, Prediction of Binding Sites of Peptide Recognition Domains: An Application on Grb2 and SAP SH2 Domains. Journal of Molecular Biology, 2006, 357, 1322-1334.[HTML] [PDF]

13. Tingjun Hou, Ken Chen, William A. McLaughlin, Benzhuo Lu and Wei Wang, Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain, PLoS Computational Biology, 2006, 2, 0046-0055. [HTML] [PDF]
(This paper was recommendedy by Falculty 1000,

12. Tingjun Hou, William A. McLaughlin, Benzhuo Lu, Ken Chen and Wei Wang, Prediction of Binding Affinities between the Human Amphiphysin-1 SH3 Domain and Its Peptide Ligands Using Homology Modeling, Molecular Dynamics and Molecular Field Analysis, Journal of Proteome Research, 2006, 5, 32-43. [HTML] [PDF]

11. Wei Wang , J. Michael Cherry, Yigal Nochomovitz, Emmitt Jolly, David Botstein and Hao Li, Inference of combinatorial regulation in yeast transcirptional networks: A case study of sporulation, Proceeding of the National Academy of Sciences of the United States of America, 2005, 102, 6, 1998-2003. [HTML] [PDF]
(An article about this paper in Genomics & Proteomics Feb. 10, 2005: "Deciphering Regulatory Networks")

10. Hao Li and Wei Wang, Dissecting the transcription networks of a cell using computational genomics, Current Opinion in Genetics & Development, 2003, 13, 6, 611-616. [HTML] [PDF]

9. Wei Wang , J. Michael Cherry, David Botstein and Hao Li, A systematic approach to reconstructing transcirption networks in Saccharomyces cerevisiae, Proceeding of the National Academy of Sciences of the United States of America, 2002, 99, 26, 16893-16898. [HTML] [PDF]

8. Wei Wang and Peter A. Kollman, Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance, Proceeding of the National Academy of Sciences of the United States of America, 2001, 98, 26, 14937-14942. [HTML] [PDF]
(This paper was selected as a highlight by Nature Reviews Drug Discovery, "Hit where it hurts", Nature Reviews Drug Discovery 1, 2, 97, 2002.)

7. Wei Wang, Wendell A. Lim, Araz Jakalian, Jian Wang, Junmei Wang, Ray Luo Christopher Bayly and Peter A. Kollman, 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, 2001, 123, 17, 3986-3994. [HTML] [PDF]
(This paper was selected as a further reading paper in the highlight "Hit where it hurts", Nature Reviews Drug Discovery 1, 2, 97, 2002.)

6. Wei Wang, Oreola Donnii, Carolina M. Reyes and Peter A. Kollman, Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis and protein-ligand, protein-protein and protein-nucleic acid non-covalent interactions, Annual Review of Biophysics and Biomolecular Structure, 2001, 30, 211-243. [HTML] [PDF]

5. Junmei Wang, Paul Morin, Wei Wang and Peter A. Kollman, 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, 2001, 123, 22, 5221-5230. [HTML] [PDF]

4. Junmei Wang, Wei Wang, Shuanghong Huo, Matthew Lee and Peter A. Kollman, Solvation Model Based on Weighted Solvent Accessible Surface Area. The Journal of Physical Chemistry B, 2001, 105, 21, 5055-5067. [HTML] [PDF]

3. Wei Wang and Peter A. Kollman Free energy calculations on the HIV-1 protease dimmer stability using molecular dynamics and a continuum model. Journal of Molecular Biology, 2000, 303, 4, 567-582. [HTML] [PDF]

2. Peter A. Kollman, Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, Taisung Lee, Yong Duan, Wei Wang, Oreola Donini, Piotr Cieplak, Jaysharee Srinivasan, Dave Case and Thomas E. Cheatham, III Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research, 2000, 33, 12, 889-897. [HTML] [PDF]

1. Wei Wang, Jian Wang, and Peter A. Kollman, 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: Structure, Function and Genetics, 1999, 34, 3, 395-402. [HTML] [PDF]