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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
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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, May, Available
online. (# equal contribution; * equal contribution)
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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, Apr,
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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, 10.1021/ci400011c. [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
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54. Richard S.L. Stein#,
Nan
Li#, Wei
He#, Elizabeth
Komives, Wei
Wang. Recognition of Methylated
Peptides by Drosophila
melanogaster Polycomb Chromodomain.
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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
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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
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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
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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]
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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,
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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:
http://ucsdnews.ucsd.edu/newsrel/science/01-10HIV.asp )
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,
http://www.f1000biology.com/article/id/1030930/evaluation)
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,
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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,
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