2024
Young Su Ko, Jonathan Parkinson, Cong Liu, Wei Wang. TUnA: An uncertainty aware transformer model for sequence-based protein-protein interaction prediction, Briefings in Bioinformatics, 2024, in revision; bioRxiv, 2024, Feb. 21.
Jonathan Parkinson, Wei Wang. For antibody sequence generative modeling, mixture models may be all you need, Bioinformatics, 2024, 40, 5; bioRxiv, 2024, Jan. 30.
Eunice Choi, Camilla R L Machado, Takaichi Okano, David Boyle, Wei Wang#*, Gary S Firestein#*. Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity, 2024, JCI Insight, May 23; bioRxiv. 2024 Jan 23. (# equal contribution, * corresponding authors) (# equal contribution, * corresponding authors)
Benjamin Van Espen#, Edward B. Prideaux#, Andrew R. Wilson#, Grégory Seumois, Cristiano Sacchetti, Anna Belongia, Narayanan B. Perumal, Pandurangan Vijayanand, Robert J. Benschop, Wei Wang, Gary S. Firestein, Nunzio Bottini and Stephanie M. Stanford. Laser capture microscopy (LCM)-RNAseq for topological mapping of synovial pathology during rheumatoid arthritis, 2024, Arthritis & Rheumatology, Mar. 31. #equal contribution. (# equal contribution)
Hyeonjeong Lee, Camilla R L Machado, Deepa Hammaker, Eunice Choi, Edward B. Prideaux, Wei Wang, David L Boyle, Gary Firestein. Joint-Specific regulation of Homeobox D10 Expression in Rheumatoid Arthritis Fibroblast-Like Synoviocytes, PLoS One, 2024.
2023
Peiyao Wu, Mina Yao, Wei Wang. Distinct 3D contacts and phenotypic consequences of adjacent non-coding loci in the epigenetically quiescent regions, 2024, Nucleic Acids Research, accepted; bioRxiv, 2023, Sept. 23.
Jonathan Parkinson#, Ryan Hard#, Wei Wang. The RESP AI model accelerates the identification of tight-binding antibodies, 2023, Jan. 28, Nature Communications, 14, 454. #equal contribution. (# equal contribution)
Jonathan Parkinson, Wei Wang. Linear-scaling kernels for protein sequences and small molecules outperform deep learning while providing uncertainty quantitation and improved interpretability, 2023, Journal of Chemical Information and Modeling, 63, 15, 4589-4601.
Paul Hsu#, Eunice J. Choi#, William H. Wong, Yun Hsuan Lin, Sara A. Vandenburgh, Yi Chia Liu, Priscilla Yao, Cynthia S. Indralingam, Eugene W. Yeo, Elina I. Zuniga, Ananda W. Goldrath, Wei Wang, John T. Chang. [Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner], 2023, Science Immunology, in review, #equal contribution. (# equal contribution)
Sho Sendo, Camilla, Machado, David Boyle, Robert Benschop, Narayanan Perumal, Eunice Choi, Wei Wang, Gary Firestein. Dysregulated NUB1 and neddylation enhances rheumatoid arthritis fibroblast-like synoviocyte inflammatory responses, 2023, Arthritis & Rheumatology, Apr. 2.
H. Kay Chung#, Cong Liu#, Eduardo Casillas, Brent Chick, Bryan Mcdonald, Jun Wang, Peixiang He, Ming Sun, Shixin Ma, Qiyuan Yang, Dan Chen, Filipe Hoffmann, Siva Karthik Varanasi, Victoria Tripple, Yuqing Hang, Ukrae H. Cho, Josephine Ho, April Williams, Yingxiao Wang, Diana Hargreaves, Susan M. Kaech*, Wei Wang*. Multiomics atlas-assisted discovery of transcription factors enables specific cell state programming, 2023, Jan. 3, bioRxiv, #equal contribution. *corresponding authors. (# equal contribution, * corresponding authors)
Xiaoyu Yang#, Ian R. Jones#, Poshen B. Chen#, Han Yang#, Xingjie Ren#, Lina Zheng, Bin Li, Yang E. Li, Quan Sun, Jia Wen, Cooper Beaman, Xiekui Cui, Yun Li, Wei Wang, Ming Hu, Bing Ren*, Yin Shen*. Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons, 2023, in review. Aug. 30, bioRxiv, #equal contribution. * corresponding authors. (# equal contribution, * corresponding authors)
Cong Liu#, Zengmiao Wang#, Jun Wang#, Chengyu Liu, Mengchi Wang, Vu Ngo, Wei Wang. Predicting regional somatic mutation rates using DNA motifs, 2023, PLoS Computational Biology, 19, 10, e1011536. #equal contribution, BioRxiv. (# equal contribution)
Eddie A. James#, V. Michael Holers#, Radhika Iyer#, E. Barton Prideaux#, Navin L. Rao, Cliff Rims, Virginia S. Muir, Sylvia E. Posso, Michelle S. Bloom, Amin Zia, Serra E. Elliott, Julia Z. Adamska, Rizi Ai, R. Camille Brewer, Jennifer A. Seifert, LauraKay Moss, Saman Barzideh, M. Kristen Demoruelle, Christopher C. Striebich, Yuko Okamoto, Enkhtsogt Sainbayar, Alexandra A. Crook, Ryan A. Peterson, Lauren A. Vanderlinden, Wei Wang, David L. Boyle, William H. Robinson*, Jane H. Buckner*, Gary S. Firestein*, Kevin D. Deane*. Multifaceted Immune Dysregulation in Potentially Modifiable Pathways Characterizes Individuals At-Risk for Rheumatoid Arthritis, 2023, Nature Communications, 14, 7637. #equal contribution. * corresponding author. (# equal contribution, * corresponding authors)
Paul Hsu#, Eunice J. Choi#, Shefali A. Patel, William H. Wong, Jocelyn G. Olvera, Priscilla Yao,Yi Chia Liu, Matthew S. Tsai, Wei Wang, Brigid S. Boland, John T. Chang. Responsiveness to vedolizumab therapy in ulcerative colitis is associated with alterations in immune cell-cell communications, 2023, Inflammatory Bowel Diseases, May 26, izad084. #equal contribution. (# equal contribution)
David A. McBride, Matthew D. Kerr, Wade Johnson, Anders Nguyen, Martina Zoccheddu, Mina Yao, Edward B. Prideaux, Nicholas C. Dorn, Wei Wang, Mattias N.D. Svensson, Nunzio Bottini*, Nisarg J. Shah*. Immunomodulatory microparticles epigenetically modulate T cells and systemically ameliorate autoimmune arthritis, 2023, Advanced Science, 10, 11, 2202720. * corresponding author.
Wade T. Johnson, David McBride, Matthew Kerr, Anders Nguyen, Martina Zoccheddu, Miriam Bollmann, Xiaofu Wei, Ryan M. Jones, Wei Wang, Mattias N. D. Svensson, Nunzio Bottini*, and Nisarg J. Shah*. Immunomodulatory Nanoparticles for Modulating Arthritis Flares, Nov 28, 2023, ACS Nano, published online. (* corresponding authors)
Han G. Duong#, Eunice J. Choi#, Hsu, Paul#, Natalie R. Chiang, Shefali A. Patel, Jocelyn G. Olvera, Yi Chia Liu, Yun Hsuan Lin, Priscilla Yao, William H. Wong, Cynthia S. Indralingam, Matthew S. Tsai, Brigid S. Boland, Wei Wang, John T. Chang. Identification of CD8+ T cell - immune cell communications in ileal Crohn’s disease, 2023, Mar. 1, Clinical and Translational Gastroenterology. #equal contribution. (# equal contribution)
2022
Lina Zheng, Wei Wang*. Regulation associated modules reflect 3D genome modularity associated with chromatin activity. Nature Communications 13, 5281. 8 Sep 2022. (* corresponding authors)
Chengyu Liu, Sam Shen, Wei Wang*. Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression. bioRxiv. 2022. (* corresponding authors)
Song Wang, Wei Wang*. Interpretable Prediction of mRNA Abundance from Promoter Sequence using Contextual Regression Models. bioRxiv. 2022 (* corresponding authors)
Cong Liu#, Zengmiao Wang#, Jun Wang#, Chengyu Liu, Mengchi Wang, Vu Ngo, Wei Wang*. Predicting regional somatic mutation rates using DNA motifs. submitted, bioRxiv. 2022 (# equal contribution, * corresponding authors)
Cong Liu#, Kyla Omilusik#, Clara Toma, Nadia S. Kurd, John T. Chang, Ananda W. Goldrath*, Wei Wang*. Systems-level identification of key transcription factors in immune cell specification. PLoS Computational Biology, in press. 2022 (# equal contribution, * corresponding authors)
Jonathan Parkinson#, Ryan Hard#, Richard Ainsworth, Wei Wang*. Engineering Human JMJD2A Tudor Domains For An Improved Understanding of Histone Peptide Recognition. Proteins. 4 Aug 2022. (# equal contribution, * corresponding authors)
Richard I. Ainsworth, Deepa Hammaker, Gyrid Nygaard, Cecilia Ansalone, Kai Zhang, Lina Zheng, Andre Wildberg, Amanda Kuhs, Mattias N. D. Svensson, David L. Boyle, Gary S. Firestein*, and Wei Wang*. [Personalized systems-biology analysis of rheumatoid arthritis patients reveals key regulators and enables mechanism-based stratification]. Nature Communications, in revision. 2022. (* corresponding authors)
David L. Boyle, Edward B. Prideaux, Joshua Hillman, Wei Wang* and Gary S. Firestein*. Improving transcriptome fidelity following synovial tissue disaggregation. Frontiers in Medicine. 10 Aug 2022. (* corresponding authors)
Ying Liu#, Bo Ding#, Lina Zheng#, Ping Xu#, Zhiheng Liu, Zhao Chen, Peiyao Wu, Ying Zhao, Qian Pan, Yu Guo, Wei Wang*, Wensheng Wei*. Regulatory elements can be essential for maintaining broad chromatin organization and cell viability. Nucleic Acids Research. 7 Apr 2022. (# equal contribution, * corresponding authors)
Alyssa Torres#, Brian Pedersen#, Isidoro Cobo, Rizi Ai, Roxana Coras, Jessica Murillo-Saich, Gyrid Nygaard, Elsa Sanchez-Lopez, Anne Murphy, Wei Wang, Gary S Firestein and Monica Guma. Epigenetic Regulation of Metabolic Transporters in Rheumatoid Arthritis Fibroblast-Like Synoviocytes, Arthritis & Rheumatology, Feb. 6, 2022 doi: 10.1002/art.42077. PMID: 35128827. #equal contribution. (# equal contribution)
Cecilia Ansalone, Richard I. Ainsworth, Gyrid Nygaard, Rizi Ai, Edward B. Prideaux, Deepa Hammaker, Narayanan B. Perumal, Ken Weichert, Frances Tung, Lalitha Kodandapani, J. Michael Sauder, Elisabeth C. Mertsching, Robert J. Benschop, David L. Boyle, Wei Wang*, Gary S. Firestein*. Caspa se-8 Variant G Regulates Rheumatoid Arthritis Fibroblast-Like Synoviocyte Aggressive Behavior. ACR Open Rheumatology, Vol. 4, No. 4, April 2022. (* corresponding authors)
David A. McBride, Nicholas C. Dorn, Mina Yao, Wade T. Johnson, Wei Wang, Nunzio Bottini, Nisarg J. Shah. Short‑chain fatty acid‑mediated epigenetic modulation of inflammatory T cells in vitro, 2022, Drug Delivery and Translational Research, Dec. 24.
Poshen B. Chen, Patrick C. Fiaux, Bin Li, Kai Zhang, Naoki Kubo, Shan Jiang, Rong Hu, Sihan Wu, Mengchi Wang, Wei Wang, Graham McVicker, Paul S. Mischel, Bing Ren. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation, 2022, Cell Reports, 41, 6, 111630.
2021
Bohan Zhu#, Richard I. Ainsworth#, Zengmiao Wang, Salvador Sierra, Chengyu Deng, Luis F. Callado, J. Javier Meana, Wei Wang*, Chang Lu*, JavierGonzález-Maeso*. Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia. submitted; bioRxiv, 2021. (# equal contribution, * corresponding authors)
Bo Ding#, Ying Liu#, Zhiheng Liu#, Lina Zheng#, Ping Xu, Zhao Chen, Peiyao Wu, Ying Zhao, Qian Pan, Yu Guo, Wensheng Wei*, Wei Wang*. Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability. Science Advances. 3 Nov 2021: Vol. 7, no. 45, abi6020. (# equal contribution, * corresponding authors)
Jun Wang#, Cong Liu#, Yue Chen#, Wei Wang*. Taiji-reprogram: a framework to uncover cell-type specific regulators and predict cellular reprogra mming cocktails, NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab100. (# equal contribution, * corresponding authors)
Xingjie Ren, Mengchi Wang, Bingkun Li, Kirsty Jamieson, Lina Zheng, Ian R. Jones, Bin Li, Maya Asami Takagi, Jerry Lee, Lenka Maliskova, Tsz WaiTam, Miao Yu, Rong Hu, Lindsay Lee, Armen Abnousi, Gang Li, Yun Li, Ming Hu, Bing Ren, Wei Wang, Yin Shen*. Parallel characterization of cis-r egulatory elements for multiple genes using CRISPRpath. Science Advances. 15 Sep 2021: Vol. 7, no. 38, abi4360. (* corresponding authors)
Rizi Ai#, David L. Boyle#, Wei Wang*, Gary S. Firestein*. Distinct DNA Methylation Patterns of Rheumatoid Arthritis Peripheral Blood and Synov ial Tissue T Cells. ACR Open Rheumatology, Vol. 3, No. 3, March 2021. (# equal contribution, * corresponding authors)
Bohan Zhu#, Richard I. Ainsworth#, Zengmiao Wang, Salvador Sierra, Chengyu Deng, Luis F. Callado, J. Javier Meana, Wei Wang,Chang Lu, Javier González-Maeso*. Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia. bioRxiv. 14 July 2021. (# equal contribution, * corresponding authors)
Mengchi Wang, Vu Ngo and Wei Wang*. Deciphering the genetic code of DNA methylation . Briefings in Bioinformatics, Volume 22, Issue 5, September 2021, bbaa424. (* corresponding authors)
Denise Beckmann, Anja Römer-Hillmann, Annika Krause, Uwe Hansen, Corinna Wehmeyer, Johanna Intemann, David J.J. de Gorter, Berno Dankbar, Jan Hillen, Marianne Heitzmann, Isabell Begemann, Milos Galic, Toni Weinhage, Dirk Föll, Rizi Ai, Jochen Kremerskothen, Hans P. Kiener, Thomas Kamradt, Christopher Schröder, Elsa Leitão, Bernhard Horsthemke, Philip Rosenstiel, Karl Nordström, Nina Gasparoni, Jörn Walter, Na Li, Xinyi Yang, Ho-Ryun Chung, Hermann Pavenstädt, Nico Lindemann, Hans J. Schnittler, Wei Wang, Gary S. Firestein, Thomas Pap and Adelheid Korb-Pap*. Lasp1 regulates adherens junction dynamics and fibroblast transformation in destructive arthritis, Nature Communications, 2021, 12, 3624.
2020
Rizi Ai#, David L. Boyle#, Wei Wang*, Gary S. Firestein*. Distinct DNA Methylation Patterns of Rheumatoid Arthritis Peripheral Blood and Synov ial Tissue T Cells. ACR Open Rheumatology, Vol. 3, No. 3, March 2021. (# equal contribution, * corresponding authors)
Bohan Zhu#, Richard I. Ainsworth#, Zengmiao Wang, Salvador Sierra, Chengyu Deng, Luis F. Callado, J. Javier Meana, Wei Wang,Chang Lu, Javier González-Maeso*. Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia. bioRxiv. 14 July 2021. (# equal contribution, * corresponding authors)
Poshen B. Chen, Patrick C. Fiaux, Bin Li, Kai Zhang, Naoki Kubo, Shan Jiang, Rong Hu, Sihan Wu, Mengchi Wang, Wei Wang, Graham McVicker, Paul S.Mischel, Bing Ren*. Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells. bioRxiv, 04 Feb 2021. (* corresponding authors)
Anusorn Mudla, Yanfei Jiang, Kei-ichiro Arimoto, Bingxian Xu, Adarsh Rajesh, Andy P Ryan, Wei Wang, Matthew D Daugherty, Dong-Er Zhang, Nan Hao*. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. eLife 2020;9:e58825. (* corresponding authors)
Jonathan Parkinson, Ryan Hard, Richard Ainsworth, Wei Wang. Engineering a histone reader protein by combining directed evolution, sequencing and neural network based ordinal regression, Journal of Chemical Information and Modeling. 2020, Aug. 5.
Mengchi Wang, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, Wei Wang. Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. Genetics, 2020, Aug. 20.
Liangliang Wang#, Yan Gao#, Gao Zhang#, Dan Li#, Zhenda Wang, Jie Zhang, Leandro C. Hermida, Lei He, Zhisong Wang, Jingwen Si, Shuang Geng, Rizi Ai, Fei Ning, Chaoran Cheng, Haiteng Deng, Dimiter S. Dimitrov, Yan Sun, Yanyi Huang, Dong Wang, Xiaoyu Hu*, Zhi Wei*, Wei Wang*, Xuebin Liao*. Targeting KDM5A induction and TLR activation to improve response to immune checkpoint blockade. Science Translational Medicine, 2020, in press. (# equal contribution, * corresponding authors)
David Gorkin, Iros Barozzi, Yanxiao Zhang, Ah Young Lee, Bin Li, Yuan Zhao, Andre Wildberg, Bo Ding, Bo Zhang, Mengchi Wang, J. Strattan, Jean Da vidson, Yunjiang Qiu, Veena Afzal, Jennifer Akiyama, Ingrid Plajzer-Frick, Catherine Pickle, Momoe Kato, Tyler Garvin, Quan Pham, Anne Harrington, Brandon Mannion, Elizabeth Lee, Yoko Fukuda-Yuzawa, Yupeng He, Sebastian Preissl, Sora Chee, Brian Williams, Diane Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Yin Shen, Joseph Ecker, Wei Wang, Diane Dickel, Axel Visel, Len Pennacchio, Hui Huang, Jee Yun Han, Joshua Chiou, Kyle Gaulton, Bing Ren. An atlas of dynamic chromatin landscapes in the developing mouse fetus. Nature, 2020, Jul. 30.
The ENCODE Project Consortium#, Jill E. Moore*, Michael J. Purcaro*, Henry E. Pratt*, Charles B.Epstein*, Noam Shoresh*, Jessika Adrian*, Trupti Kawli*, Carrie A. Davis*, Alexander Dobin*,Rajinder Kaul*, Jessica Halow*, Eric L. Van Nostrand*, Peter Freese*, David U. Gorkin*, Yin Shen*, Yupeng He*, Mark Mackiewicz*, Florencia Pauli-Behn*,Brian A. Williams, Cheryl A.Keller, Xiao-Ou Zhang, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, XiaofengWang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lécuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigó, Peggy J.Farnham, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B.Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, Zhiping Weng. Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. Nature, 2020, Jul 30. (# equal contribution, * corresponding authors)
Mattias N.D. Svensson, Martina Zoccheddu, Shen Yang, Gyrid Nygaard, Christian Secchi, Karen M. Doody, Kamil Slowikowski, Fumitaka Mizoguchi, Frances Humby, Rebecca Hands, Eugenio Santelli, Cristiano Sacchetti, Kuninobu Wakabayashi, Dennis J. Wu, Christopher Barback, Rizi Ai, Wei Wang, Gary P. Sims, Piotr Mydel, Tsuyoshi Kasama, David L. Boyle, Francesco Galimi, David Vera, Michel L. Tremblay, Soumya Raychaudhuri, Michael B. Brenner, Gary S. Firestein, Costantino Pitzalis, Anna-Karin H. Ekwall, Stephanie M. Stanford, Nunzio Bottini. Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal. Science Advances, 6, 26, eeba4353, 2020.
2019
Mengchi Wang, Kai Zhang, Vu Ngo, Chengyu Liu, Shicai Fan, John W Whitaker, Yue Chen, Rizi Ai, Zhao Chen, Jun Wang, Lina Zheng, Wei Wang. Identification of DNA motifs that regulate DNA methylation. Nucleic Acids Research, 2019, gkz483.
Angel Bottini, Dennis J Wu, Rizi Ai, Michelle Le Roux, Beatrix Bartok, Michele Bombardieri, Karen M Doody, Vida Zhang, Cristiano Sacchetti, Martina Zoccheddu, Ana Lonic, Xiaochun Li, David L Boyle, Deepa Hammaker, Tzu-Ching Meng, Lin Liu, Maripat Corr, Stephanie M Stanford, Myles Lewis, Wei Wang, Gary S Firestein, Yeesim Khew-Goodall, Costantino Pitzalis, Nunzio Bottini. PTPN14 phosphatase and YAP promote TGFβ signalling in rheumatoid synoviocytes. Ann Rheum Dis. 2019 May;78(5):600-609.
Vu Ngo, Mengchi Wang, Wei Wang. Finding de novo methylated DNA motifs. Bioinformatics. 2019 Feb 6.
Kai Zhang, Mengchi Wang, Ying Zhao, Wei Wang. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. Science Advances. 27 Mar 2019: Vol. 5, no. 3, eaav3262
Vu Ngo#, Zhao Chen#, Kai Zhang, John W. Whitaker, Mengchi Wang, Wei Wang. Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse. PNAS, February 26, 2019 116 (9) 3668-3677; first published February 12, 2019 . (# equal contribution)
Shicai Fan, Jianxiong Tang, Nan Li, Ying Zhao, Rizi Ai, Kai Zhang, Mengchi Wang, Wei Du, Wei Wang. Integrative analysis of TCGA data with expanded DNA methylation data reveals common key regulators and pathways in cancers. Npj Genomic Medicine. 2019, 4, Article number: 2.
2018
Ryan Hard#, Nan Li#, Wei He#, Brian Ross, Gary C. H. Mo, Qin Peng, Richard S. L. Stein, Elizabeth Komives, Yingxiao Wang, Jin Zhang, Wei Wang. Deciphering and engineering chromodomain-methyllysine peptide recognition. Science Advances. 2018, 4, 11, eaau1447. (# equal contribution)
Rizi Ai, Teresina Laragione, Deepa Hammaker, David L. Boyle, Andre <U+200E>Wildberg, Keisuke Maeshima, Emanuele Palescandolo, Vinod Krishna, David Pocalyko, John W. Whitaker, Yuchen Bai, Sunil Nagpal, Kurtis E. Bachman, Richard I. Ainsworth, Mengchi Wang, Bo Ding, Percio S. Gulko*, Wei Wang*, Gary S. Firestein*. Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Reveals Pathogenic Pathways. Nature Communications. 2018, 9, 1, 1921. (* corresponding authors)
Richard I Ainsworth, Rizi Ai, Bo Ding, Nan Li, Kai Zhang, Wei Wang. Bayesian Networks Predict Neuronal Transdifferentiation. G3: Genes, Genomes,Genetics. 2018, g3. 200401.2018.
2017
Chengyu Liu, Wei Wang*. Contextual regression: an accurate and conveniently interpretable nonlinear model for mining discovery from scientific data. arXiv preprint arXiv:1710.10728, 2017 (* corresponding authors)
Shinji Matsuda, Deepa Hammaker, Katharyn Topolewski, Karoline J. Briegel, David L. Boyle, Steven Dowdy, Wei Wang, Gary S. Firestein. Regulation of the Cell Cycle and Inflammatory Arthritis by the Transcription Cofactor LBH Gene. Journal of Immunology. 2017, 199, 7, 2316-2322.k
J Justin Milner, Clara Toma, Bingfei Yu, Kai Zhang, Kyla Omilusik, Anthony T Phan, Dapeng Wang, Adam J Getzler, Toan Nguyen, Shane Crotty, Wei Wang, Matthew E Pipkin, Ananda W Goldrath. Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours. Nature. 2017/12.
Bo Ding#, Lina Zheng#, Wei Wang. Assessment of Single Cell RNA-Seq Normalization Methods. G3: GENES, GENOMES, GENETICS. July 1, 2017. (# equal contribution)
Bingfei Yu#, Kai Zhang#, J Justin Milner, Clara Toma, Runqiang Chen, James P Scott-Browne, Renata M Pereira, Shane Crotty, John T Chang, Matthew E Pipkin, Wei Wang* and Ananda W Goldrath*. Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation. Nature Immunology. March 13, 2017. (# equal contribution, * corresponding authors)
2016
Roberto Spreafico, Maura Rossetti, John W. Whitaker, Wei Wang, Daniel J. Lovell, and Salvatore Albani. Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways. PNAS. November 14, 2016.
Kai Zhang, Nan Li, Richard Ainsworth, Wei Wang. Systematic identification of protein combinations mediating chromatin looping. Nature Communications. 2016.
Blue B. Lake#, Rizi Ai#, Gwendolyn E. Kaeser#, Neeraj S. Salathia#, Yun C. Yung, Rui Liu, Andre Wildberg, Derek Gao, Ho-Lim Fung, Song Chen, Raakhee Vijayaraghavan, Julian Wong, Allison Chen, Xiaoyan Sheng, Fiona Kaper, Richard Shen, Mostafa Ronaghi, Jian-Bing Fan*, Wei Wang*, Jerold Chun*, Kun Zhang*. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 2016. (# equal contribution, * corresponding authors)
Rizi Ai, Deepa Hammaker, David L. Boyle, Rachel Morgan, Shicai Fan, Gary S. Firestein*, Wei Wang*. Joint-specific DNA methylation signature of rheumatoid arthritis identifies distinct pathogenic processes in different joints. Nature Communications. 2016. (* corresponding authors)
Deepa Hammaker, John W. Whitaker, Keisuke Maeshima, David L. Boyle, Anna-Karin H. Ekwall, Wei Wang, Gary S. Firestein. 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. 2016, May 9, Advance publication online.
Keisuke Maeshima, Stephanie M. Stanford, Deepa Hammaker, Cristiano Sacchetti, Li-fan Zeng, Rizi Ai, Vida Zhang, David L. Boyle, German R. Aleman Muench, Gen-Sheng Feng, John W. Whitaker, Zhong-Yin Zhang, Wei Wang, Nunzio Bottini, and Gary S. Firestein. Abnormal PTPN11 enhancer methylation promotes rheumatoid arthritis fibroblast-like synoviocyte aggressiveness and joint inflammation. JCI Insight. 2016, 7, e86580.
Yun Zhu#, Zhao Chen#, Kai Zhang, Mengchi Wang, David Medovoy, John W. Whitaker, Bo Ding, Nan Li, Lina Zheng, Wei Wang. Constructing 3D interaction maps from 1D epigenomes. Nature Communications. 2016. (# equal contribution)
Shicai Fan, Chengzhe Li, Rizi Ai, Mengchi Wang, Gary S. Firestein*, Wei Wang*. Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. Bioinformatics. 2016, Advance Access. (* corresponding authors)
Shicai Fan*, Kang Huang, Rizi Ai, Mengchi Wang, Wei Wang*. Predicting CpG methylation levels by integrating Infinium HumanMethylation450 BeadChip array data. Genomics. 2016, Available online. (* corresponding authors)
Nan Li, Richard Ainsworth, Meixin Wu, Bo Ding, Wei Wang. MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction. Bioinformatics. 2016, 32, 940-942.
2015
Bo Ding, Lina Zheng, David Medovoy, Wei Wang*. Targeted mutations on 3D hub loci alter spatial interaction environment. bioRxiv, 2015. (* corresponding authors)
Na Zou, Yun Zhu, Ji Zhu, Mustafa Baydogan, Wei Wang, Jing Li. A transfer learning approach for predictive modeling of degenerate biological systems. Technometrics. 2015, 57, 3, 362.373.
Nan Li#, Richard Ainsworth#, Bo Ding, Tingjun Hou*, Wei Wang*. Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease. Journal of Chemical Information and Modeling. 2015, 55,1400-1412. (# equal contribution, * corresponding authors)
John W. Whitaker, David L. Boyle, Beatrix Bartok, Scott T. Ball, Steffen Gay, Wei Wang*, Gary S. Firestein*. Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets. PLOS ONE. 2015, 10, 4, e0124254. (* corresponding authors)
Rizi Ai, John W. Whitaker, David L. Boyle, Paul Peter Tak, Danielle M. Gerlag, Wei Wang*, Gary S. Firestein*. DNA Methylome Signature in Early Rheumatoid Arthritis Synoviocytes Compared with Longstanding Rheumatoid Arthritis and Other Inflammatory. Arthritis & Rheumatology. 2015, 67, 1978-1980. (* corresponding authors)
Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker. Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation. Nature. 2015, 523, 212-216.
Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis. Integrative analysis of 111 reference human epigenomes. Nature. 2015, 518, 317–330 (John W. Whitaker: equal contributors of integrative analysis leads; Wei Wang: co-principal investigators)
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, 67, 1193-1202. (* corresponding authors)
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, 31, 2225-2227. (# equal contribution)
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.
John W. Whitaker, Zhao Chen, Wei Wang. Predicting the human epigenome using DNA motifs. Nature Methods. 2015, 12, 265-272.
2014
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.
2013
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.
Nan Li#, Richard S. 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. (# equal contribution)
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)
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.
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, * corresponding authors)
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)
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.
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.
Wei Wang. Therapeutic Hints from Analyzing the Attractor Landscape of the p53 Regulatory Circuit. Science Signaling. 2013, 6, pe5.
Richard S. 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)
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.
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.
2012
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)
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)
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)
2011
Robert Shoemaker, Wei Wang, Kun Zhang. Mediators and dynamics of DNA methylation. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2011, 3, 281-298.
Rui Chang, Robert Shoemaker, Wei Wang. Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells.Plos Computational Biology. 2011, 7, 12, e1002300.
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.
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.
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)
Shengchao Ding, Wei Wang. Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. BMC System Biology. 2011, 5:50.
Richard S. Stein, Wei Wang. The recognition specificity of the CHD1 Chromodomain with modified histone H3 peptides. Journal of Molecular Biology. 2011, 406, 527-541.
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)
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)
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)
2010
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.
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.
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)
Kyoung-Jae Won, Bing Ren, Wei Wang. Genome-wide prediciton of transcription factor binding sites using an intergrated model. Genome Biology. 2010, 11, R7.
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. UCSD News (# equal contribution, * corresponding authors)
2009
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)
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)
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.
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)
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.
2008
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.
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.
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. (This paper was highlighted by Nature Reviews Genetics, 9, 895, 2008.) (* corresponding authors)
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)
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.
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.
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.
2007
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.
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.
Chung JL, Wei Wang , Bourne PE. High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics. 2007, 8, 223.
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.
2006
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.
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.
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.
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.
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. Falculty 1000
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.
2005
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. (An article about this paper in Genomics & Proteomics Feb. 10, 2005: “Deciphering Regulatory Networks”) 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.
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.
2000
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.
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.
1999
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.