Publications

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
Hyunghoon Cho, Bonnie Berger and Jian Peng
Research in Computational Molecular Biology (RECOMB), 2015 (accepted)
Quality Score Compression Improves Genotyping Accuracy
Yun William Yu, Deniz Yorukoglu, Jian Peng and Bonnie Berger
Nature Biotechnology, 2015 (in press)
A community computational challenge to predict the activity of pairs of compounds
Mukesh Bansal et al.
Nature Biotechnology, 2014
HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes
Florencia Pereyra, David Heckerman, Jonathan Carlson, Carl Kadie, Damien Soghoian, Daniel Karel, Ariel Goldenthal, Oliver Davis, Charles DeZiel, Tien-Ho Lin, Jian Peng, Alicja Piechocka-Trocha, Mary Carrington, and Bruce Walker
Journal of Virology, 2014
Selection bias at the heterosexual HIV-1 transmission bottleneck
Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung'u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J.R. Goulder, Todd M. Allen, Susan Allen, Eric Hunter
Science, 2014
A Quantitative Chaperone Interaction Network Reveals the Architecture of Cellular Protein Homeostasis Pathways
Mikko Taipale, George Tucker*, Jian Peng*, Irina Krykbaeva, Zhen-Yuan Lin, Brett Larsen, Hyungwon Choi, Bonnie Berger, Anne-Claude Gingras, and Susan Lindquist. (*-equal contribution)
Cell, 2014
A community effort to assess and improve drug sensitivity prediction algorithms
James C. Costello et al.
Nature Biotechnology, 2014
HapTree: A novel Bayesian framework for single individual polyplotyping using NGS data
Emily Berger, Deniz Yorukoglu, Jian Peng and Bonnie Berger
Research in Computational Molecular Biology (RECOMB), 2014
PLoS Computational Biology, 2014
Crowdsourcing for structured labeling with applications to protein folding
Jian Peng, Qiang Liu, Alex Ihler and Bonnie Berger.
Machine Learning Meets Crowdsourcing Workshop, The 30th International Conference on Machine Learning (ICML), 2013 (accepted as an oral presentation)
Compressive genomics for protein databases
Noah Daniels, Andrew Gallant, Jian Peng, Lenore Cowen, Michael Baym and Bonnie Berger.
Intelligent Systems for Molecular Biology (ISMB), 2013
Bioinformatics, 2013
Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling.
Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu.
Artificial Intelligence and Statistics (AISTATS), 2013 (accepted as an oral presentation)
Computational solutions for 'omics data.
Bonnie Berger*, Jian Peng* and Mona Singh*. (*-equal contribution, alphabetically ordered)
Nature Review Genetics, 2013
Protein structure alignment beyond spatial proximity.
Sheng Wang, Jianzhu Ma, Jian Peng and Jinbo Xu.
Scientific Reports, 2013
(Warren DeLano Award for Structural Bioinformatics and Computational Biophysics in ISMB 3DSIG 2012)
Frequent and Variable Cytotoxic-T-Lymphocyte Escape-associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins
Christian Boutwell, Jonathan Carlson, Tien-Ho Lin, Aaron Seese, Karen Power, Jian Peng, Yanhua Tang, Zabrina Brumme, David Heckerman, Arne Schneidewind, and Todd Allen
Journal of Virology, 2013
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.
Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska and Bonnie Berger.
Genome Biology, 2012
Template-based protein structure modeling using the RaptorX web server.
Morten Kallberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu and Jinbo Xu.
Nature Protocols, 2012
Variational inference for crowdsourcing.
Qiang Liu, Jian Peng, Alex Ihler.
Neural Information and Processing Systems (NIPS), 2012
A Conditional Neural Fields model for protein threading.
Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu. (*-equal contribution)
Intelligent Systems for Molecular Biology (ISMB), 2012
Bioinformatics, 2012 [Web Server]
Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs.
Tamir Hazan, Jian Peng, Amnon Shashua.
Uncertainty in Artificial Intelligence (UAI), 2012
Approximate Inference by Intersecting Semidefinite Bound and Local Polytope.
Jian Peng, Tamir Hazan, Nathan Srebro and Jinbo Xu.
Artificial Intelligence and Statistics (AISTATS), 2012
Modeling large regions in proteins: Applications to loops, termini and folding.
Aashish N. Adhikari, Jian Peng, Michael Wilde, Jinbo Xu, Karl F. Freed and Tobin R. Sosnick.
Protein Science, 2012
Protein 8-class Secondary Structure Prediction Using Conditional Neural Fields.
Zhiyong Wang, Feng Zhao, Jian Peng and Jinbo Xu.
Proteomics, 2011 [Software Download]
RaptorX: exploiting structure information for protein alignment by statistical inference.
Jian Peng and Jinbo Xu.
Proteins: Structure, Function, and Bioinformatics, 2011 Invited paper to CASP9 special issue
Alignment of distantly-related protein structures: algorithm, bound and implications to homology modeling.
Sheng Wang, Jian Peng and Jinbo Xu.
Bioinformatics, 2011 [Download 3DCOMB]
A multiple-template approach to protein threading.
Jian Peng and Jinbo Xu.
Proteins: Structure, Function, and Bioinformatics, 2011 [Web Server]
Integrating expression profiles and drug similarities for prediction of drug response.
Raghavendra Hosur*, Jian Peng* and Bonnie Berger. (*-equal contribution)
Critical Assessment of Genome Interpretation 2011 (CAGI), 2011 Top performer on breast cancer cell line pharmacogenomics challenge
Convex Max-Product Algorithms for Continuous MRFs with Applications to Protein Folding.
Jian Peng, Tamir Hazan, David McAllester and Raquel Urtasun.
International Conference of Machine Learning (ICML), 2011
Structural Stability and Protein-Protein Binding Affinity Explains Fitness Effects of Common HLA Escape and Compensatory Mutations.
Jian Peng, Jonathan M. Carlson and David Heckerman.
The 18th Conference on Retroviruses and Opportunistic Infections (CROI), 2011 Young Investigator Award
A probabilistic and continuous model of protein conformational space for template-free modeling.
Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick and Jinbo Xu.
Journal of Computational Biology, 2010
Low-homology protein threading
Jian Peng and Jinbo Xu.
Intelligent Systems for Molecular Biology (ISMB), 2010
Bioinformatics, 2010 [Web Server]
Fragment-free Approach to Protein Folding Using Conditional Neural Fields
Feng Zhao, Jian Peng and Jinbo Xu.
Intelligent Systems for Molecular Biology (ISMB), 2010
Bioinformatics, 2010
[Software Download] [User Guide]
Protein 8-class Secondary Structure Prediction Using Conditional Neural Fields.
Zhiyong Wang, Feng Zhao, Jian Peng and Jinbo Xu.
IEEE International Conference on Bioinformatics & Biomedicine (BIBM), 2010
Conditional Neural Fields
Jian Peng, Liefeng Bo and Jinbo Xu.
Neural Information and Processing Systems (NIPS), 2009 [Software Download] [Another implementation by Kei Uchiumi on Google Code]
Feng Zhao*, Jian Peng*, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick and Jinbo Xu (*-equal contribution).
A Probabilistic Graphical Model for Ab Initio Folding
Research in Computational Molecular Biology (RECOMB), 2009
Boosting Protein Threading Accuracy
Jian Peng and Jinbo Xu.
Research in Computational Molecular Biology (RECOMB), 2009 A poster on this paper won Best Poster Award in RECOMB 2009
Template-based and free modeling by RAPTOR++ in CASP8
Jinbo Xu, Jian Peng and Feng Zhao.
Proteins: Structure, Function, and Bioinformatics, 2009 Invited paper to CASP8 special issue