Publications

(*-equal contribution, #-corresponding author/lead contact)

  • Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks
    Yang Liu*, Perry Palmedo*, Qing Ye, Bonnie Berger, Jian Peng#
    Cell Systems, (accepted)
     
  • Large-Scale Integration of Heterogeneous Pharmacogenomic Data for Identifying Drug Mechanism of Action
    Yunan Luo, Sheng Wang, Jinfeng Xiao and Jian Peng#
    PSB, (accepted), 2018
     
  • Annotating gene sets by mining large literature collections with protein networks
    Sheng Wang*, Jianzhu Ma*, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng#, Trey Ideker#
    PSB, (accepted), 2018
     
  • Genetic Policy Optimization
    Tanmay Gangwani, Jian Peng
    arXiv:1711.01012, 2017
     
  • Sample-efficient Policy Optimization with Stein Control Variate
    Hao Liu*, Yihao Feng*, Yi Mao, Dengyong Zhou, Jian Peng, Qiang Liu
    arXiv:1710.11198, 2017
     
  • Empower Sequence Labeling with Task-Aware Neural Language Model
    Liyuan Liu, Jingbo Shang, Frank Xu, Xiang Ren, Huan Gui, Jian Peng, Jiawei Han
    arXiv:1709.04109, 2017
     
  • Stochastic Variance Reduction for Policy Gradient Estimation
    Tianbing Xu, Qiang Liu, Jian Peng
    arXiv:1710.06034, 2017
     
  • Energy-efficient Amortized Inference with Cascaded Deep Classifiers
    Jiaqi Guan, Yang Liu, Qiang Liu, Jian Peng
    arXiv:1710.03368, 2017
     
  • Efficient Localized Inference for Large Graphical Models
    Jinglin Chen, Jian Peng, Qiang Liu
    arXiv:1710.10404, 2017
     
  • DPPred: An Effective Prediction Framework with Concise Discriminative Patterns
    Jingbo Shang, Meng Jiang, Wenzhu Tong, Jinfeng Xiao, Jian Peng, Jiawei Han
    TKDE, 2017
     
  • A Network Integration Approach for Drug-Target Interaction Prediction and Drug Repositioning
    Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng#, Ligong Chen# and Jianyang Zeng#
    Nature Communications, 2017
     
  • Identification of Pathways Associated with Chemosensitivity through Network Embedding
    Sheng Wang, Edward Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha
    bioRxiv:168450, 2017
     
  • GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes
    Guangxiang Zhu, Wenxuan Deng, Hailin Hu, Rui Ma, Sai Zhang, Jinglin Yang, Jian Peng, Tommy Kaplan, Jianyang Zeng
    bioRxiv:161208, 2017
     
  • Learning Structural Motif Representations For Efficient Protein Structure Search
    Yang Liu, Qing Ye, Liwei Wang, Jian Peng#
    bioRxiv:137828, 2017
     
  • Network-Assisted Target Identification for Haploinsufficiency and Homozygous Profiling Screens
    Sheng Wang and Jian Peng#
    PLOS Computational Biology, 2017
     
  • Metagenomic binning through low density hashing
    Yunan Luo, Y. William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng#
    bioRxiv:133116, 2017
     
  • Stein Variational Policy Gradient
    Yang Liu, Prajit Ramachandran, Qiang Liu, Jian Peng
    UAI, arXiv:1704.02399, 2017
     
  • On the Interpretability of Conditional Probability Estimates in the Agnostic Setting
    Yihan Gao, Aditya Parameswaran, Jian Peng
    AISTATS, 2017 (oral presentation)
     
  • Genome-scale molecular networks link diverse neurodegenerative disease genes and processes to alpha-synuclein
    Khurana V*, Peng J*, Chung CY*, Auluck PK, Tardiff DF, Fanning S, Bartels T, Koeva M, Benyamini H, Lou Y, Nutter-Upham A, Tuncbag N, Baru V, Freyzon Y, Costanzo M, San-Luis B, Schöndorf DC, Barrasa MI, Caraveo G, Ehsani S, Sanjana N, Zhong Q, Gasser T, Vidal M, Deleidi M, Boone C, Fraenkel E#, Berger B#, Lindquist S#.
    Cell Systems, (Cover Article), 2017
     
  • A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information
    Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng#, Ligong Chen# and Jianyang Zeng#
    RECOMB, 2017
     
  • Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening
    Frank S. He, Yang Liu, Alexander Schwing, Jian Peng
    ICLR, 2017, [openreview]
     
  • Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
    Justin Guinney et al
    Lancet Oncology, 2017
     
  • ProSNet: integrating homology with molecular networks for protein function prediction
    Sheng Wang, Meng Qu, Jian Peng#
    PSB, 2017
     
  • Scalable Visualization for High-dimensional Single-cell Data
    Juho Kim, Nate Russell, Jian Peng#
    PSB, 2017
     
  • Exploiting Temporal Divergence of Topic Distributions for Event Detection
    Rongda Zhu, Aston Zhang, Jian Peng, ChengXiang Zhai
    IEEE Bigdata, 2016
     
  • Meta-Path Guided Embedding for Similarity Search in Large-Scale Heterogeneous Information Networks
    Jingbo Shang, Meng Qu, Jialu Liu, Lance M. Kaplan, Jiawei Han, Jian Peng
    arXiv:1610.09769
     
  • DWCox: A Density-Weighted Cox Model for Robust Prediction of Prostate Cancer Survival
    Jinfeng Xiao, Sheng Wang, Jingbo Shang, Henry Lin, Doris Xin, Xiang Ren, Jiawei Han, and Jian Peng
    F1000Research, 2016
     
  • Compact Integration of Multi-Network Topology for Functional Analysis of Genes
    Hyunghoon Cho, Bonnie Berger#, Jian Peng#
    Cell Systems, [F1000Prime Recommendation], 2016
     
  • Reconstructing Causal Biological Networks through Active Learning
    Hyunghoon Cho, Bonnie Berger and Jian Peng#
    PLOS ONE, 2016
     
  • Compressive Mapping for Next-Generation Sequencing
    Deniz Yorukoglu, William Y Yu, Jian Peng and Bonnie Berger
    Nature Biotechnology, 2016
     
  • Low-density locality-sensitive hashing boosts metagenomic binning
    Yunan Luo, Jianyang Zeng, Bonnie Berger# and Jian Peng#
    RECOMB, 2016
     
  • Complexes detection in biological networks via diversified dense subgraph mining
    Xiuli Ma, Guangyu Zhou, Jingjing Wang, Jian Peng# and Jiawei Han#
    Journal of Computational Biology, 2017
    RECOMB, 2016
     
  • DPClass: An Effective but Concise Discriminative Patterns-Based Classification Framework
    Jingbo Shang, Wenzhu Tong, Jian Peng# and Jiawei Han#
    SDM, 2016
     
  • MACFP: Maximal Approximate Consecutive Frequent Pattern Mining under Edit Distance
    Jingbo Shang, Jian Peng# and Jiawei Han#
    SDM, 2016
     
  • Protein secondary structure prediction using deep convolutional neural fields
    Sheng Wang, Jian Peng, Jianzhu Ma and Jinbo Xu
    Scientific Reports, 2016
     
  • Bermuda: Bidirectional de novo assembly of transcripts with new insights for handling uneven coverage
    Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma and Jinbo Xu
    ACM-BCB, 2015
     
  • Discovering what dimensionality reducion really tells us about RNA-seq data
    Sean Simmons, Jian Peng, Jadwiga Bienkowska and Bonnie Berger
    Journal of Computational Biology, 2015
     
  • Estimating the Partition Function by Discrimnance Sampling
    Qiang Liu*, Jian Peng*, Alex Ihler and John Fisher
    UAI, 2015 (plenary presentation)
    also in ICML Deep Learning Workshop, 2015
     
  • Exploiting Ontology Graph for Predicting Sparsely Annotated Gene Function
    Sheng Wang*, Hyunghoon Cho*, ChengXiang Zhai, Bonnie Berger and Jian Peng#
    ISMB/ECCB, 2015
    Bioinformatics, 2015
     
  • Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
    Hyunghoon Cho, Bonnie Berger# and Jian Peng#
    RECOMB, 2015
     
  • iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition
    Jian Peng, Raghavendra Hosur, Bonnie Berger, Jinbo Xu
    arXiv:1504.05467
     
  • Exact Hybrid Covariance Thresholding for Joint Graphical Lasso
    Qingming Tang, Chao Yang, Jian Peng, Jinbo Xu
    ECML/PKDD, 2015
     
  • Widespread Specific Macromolecular Interaction Perturbations in Human Genetic Disorders
    Sahni, N.*, Yi S.*, Taipale M.*, Fuxman Bass JI*, Coulombe-Huntington J.*, Yang F., Peng J., Weile J., Karras GI, Wang Y., Kovács IA, Kamburov A., Krykbaeva I., Lam MH, Tucker G., Khurana V., Sharma A., Liu YY, Yachie N., Zhong Q., Shen Y., Palagi A., San-Miguel A., Fan C., Balcha D., Dricot A., Jordan DM, Walsh JM, Shah AA, Yang X., Stoyanova AK, Leighton A., Calderwood MA, Jacob Y., Cusick ME, Salehi-Ashtiani K., Whitesell LJ, Sunyaev S., Berger B., Barabási AL, Charloteaux B., Hill DE, Hao T., Roth FP, Xia Y., Walhout AJ, Lindquist S.#, and Vidal M.#
    Cell, 2015
     
  • Quality Score Compression Improves Genotyping Accuracy
    Yun William Yu, Deniz Yorukoglu, Jian Peng and Bonnie Berger
    Nature Biotechnology, 2015
     

  • Before 2015

     
  • 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
    Cell, 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
     
  • 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
     
  • A community effort to assess and improve drug sensitivity prediction algorithms
    James C. Costello et al
    Nature Biotechnology, 2014
     
  • A community computational challenge to predict the activity of pairs of compounds
    Mukesh Bansal 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
    RECOMB, 2014
    PLOS Computational Biology, 2014
     
  • Computational solutions for 'omics data
    Bonnie Berger*, Jian Peng* and Mona Singh*. (alphabetically ordered)
    Nature Review Genetics, 2013
     
  • Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling.
    Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu
    AISTATS, 2013 (oral presentation)
     
  • Compressive genomics for protein databases
    Noah Daniels, Andrew Gallant, Jian Peng, Lenore Cowen, Michael Baym and Bonnie Berger
    ISMB/ECCB, 2013
    Bioinformatics, 2013
     
  • 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
     
  • Protein structure alignment beyond spatial proximity
    Sheng Wang, Jianzhu Ma, Jian Peng and Jinbo Xu
    Scientific Reports, 2013
    (Warren DeLano Award in ISMB 3DSIG 2012)
     
  • Crowdsourcing for structured labeling with applications to protein folding
    Jian Peng, Qiang Liu, Alex Ihler and Bonnie Berger
    Machine Learning Meets Crowdsourcing Workshop, ICML, 2013 (oral presentation)
     
  • 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
     
  • Approximate Inference by Intersecting Semidefinite Bound and Local Polytope
    Jian Peng, Tamir Hazan, Nathan Srebro and Jinbo Xu
    AISTATS, 2012
     
  • A Conditional Neural Fields model for protein threading
    Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu
    ISMB, 2012
    Bioinformatics, 2012 [Web Server]
     
  • Variational inference for crowdsourcing
    Qiang Liu, Jian Peng, Alex Ihler
    NIPS, 2012
     
  • Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs
    Tamir Hazan, Jian Peng, Amnon Shashua
    UAI, 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
     
  • 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
     
  • Convex Max-Product Algorithms for Continuous MRFs with Applications to Protein Folding
    Jian Peng, Tamir Hazan, David McAllester and Raquel Urtasun
    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 multiple-template approach to protein threading
    Jian Peng and Jinbo Xu
    Proteins: Structure, Function, and Bioinformatics, 2011 [Web Server]
     
  • Alignment of distantly-related protein structures: algorithm, bound and implications to homology modeling
    Sheng Wang, Jian Peng and Jinbo Xu
    Bioinformatics, 2011 [Download 3DCOMB]
     
  • Protein 8-class Secondary Structure Prediction Using Conditional Neural Fields
    Zhiyong Wang, Feng Zhao, Jian Peng and Jinbo Xu
    Proteomics, 2011 [Software Download]
     
  • Integrating expression profiles and drug similarities for prediction of drug response
    Raghavendra Hosur*, Jian Peng* and Bonnie Berger
    Critical Assessment of Genome Interpretation 2011
    (CAGI), 2011
    Top performer on breast cancer cell line pharmacogenomics challenge
     
  • Low-homology protein threading
    Jian Peng and Jinbo Xu
    ISMB, 2010
    Bioinformatics, 2010 [Web Server]
     
  • Fragment-free Approach to Protein Folding Using Conditional Neural Fields
    Feng Zhao, Jian Peng and Jinbo Xu
    ISMB, 2010
    Bioinformatics, 2010
    [Software Download] [User Guide]
     
  • 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
     
  • Protein 8-class Secondary Structure Prediction Using Conditional Neural Fields
    Zhiyong Wang, Feng Zhao, Jian Peng and Jinbo Xu
    BIBM, 2010
     
  • Conditional Neural Fields
    Jian Peng, Liefeng Bo and Jinbo Xu
    NIPS, 2009 [Software Download] [Another implementation by Kei Uchiumi on Google Code]
     
  • Boosting Protein Threading Accuracy
    Jian Peng and Jinbo Xu
    RECOMB, 2009
    A poster on this paper won Best Poster Award in RECOMB 2009
     
  • A Probabilistic Graphical Model for Ab Initio Folding
    Feng Zhao*, Jian Peng*, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick and Jinbo Xu
    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