Selected Papers:

(*-equal contribution, #-corresponding author/lead contact)
(for collaborative papers, authors from my group are underlined.)
 
  • Integrating Deep Neural Networks and Symbolic Inference for Organic Reactivity Prediction
    Wesley Wei Qian*, Nathan T. Russell*, Claire L. W. Simons, Yunan Luo, Martin D. Burke, Jian Peng#
    ChemRxiv, 2020
     
  • Evolutionary context-integrated deep sequence modeling for protein engineering
    Yunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu, Wesley Wei Qian, Huimin Zhao and Jian Peng#
    RECOMB, 2020
     
  • Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning
    Yunan Luo*, Jianzhu Ma*, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker and Jian Peng#
    RECOMB, 2019
     
  • Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction
    Yufeng Su, Yunan Luo, Xiaoming Zhao, Yang Liu, Jian Peng#
    PLOS Computational Biology, 2019
     
  • Robust Single-Cell Hi-C Clustering by Convolution and Random Walk based Imputation
    Jingtian Zhou*, Jianzhu Ma*, Yusi Chen, Chuankai Cheng, Bokan Bao, Jian Peng, Terrence J. Sejnowski, Jesse R. Dixon, Joseph R Ecker
    PNAS, 2019
     
  • Identification of Pathways Associated with Chemosensitivity through Network Embedding
    Sheng Wang, Edward Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha
    PLOS Computational Biology, 2019
     
  • Typing tumors using pathways selected by somatic evolution
    Sheng Wang*, Jianzhu Ma*, Wei Zhang, John Paul Shen, Justin Huang, Jian Peng#, Trey Ideker#
    Nature Communications, 2018
     
  • Learning Structural Motif Representations For Efficient Protein Structure Search
    Yang Liu, Qing Ye, Liwei Wang, Jian Peng#
    ECCB, 2018
    Bioinformatics, 2018
     
  • Generalizable and Scalable Visualization of Single Cell Data Using Neural Networks
    Hyunghoon Cho, Bonnie Berger#, Jian Peng#
    RECOMB, 2018
    Cell Systems, 2018
     
  • Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach
    Robert Kueffner*, Neta Zach*, Maya Bronfeld, Raquel Norel, Nazem Atassi, Venkat Balagurusamy, Barbara di Camillo, Adriano Chio, Merit Cudkowicz, Donna Dillenberger, Javier Garcia-Garcia, Orla Hardiman, Bruce Hoff, Joshua Knight, Melanie L Leitner, Guang Li, Lara Mangravite, Thea Norman, Liuxia Wang, The ALS Stratification Consortium, Jinfeng Xiao, Wen-Chieh Fang, Jian Peng, Gustavo Stolovitzky
    Scientific Reports, (co-winner of the ALS DREAM challenge), 2018
     
  • Deciphering signaling specificity with interpretable deep neural networks
    Yunan Luo*, Jianzhu Ma*, Yang Liu, Qing Ye, Trey Ideker, Jian Peng#
    RECOMB, 2018
     
  • Metagenomic binning through low density hashing
    Yunan Luo, Y. William Yu, Jianyang Zeng, Bonnie Berger#, Jian Peng#
    Bioinformatics, 2018
     
  • Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks
    Yang Liu*, Perry Palmedo*, Qing Ye, Bonnie Berger#, Jian Peng#
    Cell Systems, 2018
     
  • 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
     
  • Network-Assisted Target Identification for Haploinsufficiency and Homozygous Profiling Screens
    Sheng Wang and Jian Peng#
    PLOS Computational Biology, 2017
     
  • 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
     
  • Compact Integration of Multi-Network Topology for Functional Analysis of Genes
    Hyunghoon Cho, Bonnie Berger#, Jian Peng#
    Cell Systems, [F1000Prime Recommendation], 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
     
  • 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
     
  • 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
     
  • 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
     
  • Computational solutions for 'omics data
    Bonnie Berger*, Jian Peng* and Mona Singh*. (alphabetically ordered)
    Nature Review Genetics, 2013
     
  • Compressive genomics for protein databases
    Noah Daniels, Andrew Gallant, Jian Peng, Lenore Cowen, Michael Baym and Bonnie Berger
    ISMB/ECCB, 2013
    Bioinformatics, 2013
  • 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
     
  • A Conditional Neural Fields model for protein threading
    Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu
    ISMB, 2012
    Bioinformatics, 2012 [Web Server]
     
  • 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
     
  • A multiple-template approach to protein threading
    Jian Peng and Jinbo Xu
    Proteins: Structure, Function, and Bioinformatics, 2011 [Web Server]
     
  • Low-homology protein threading
    Jian Peng and Jinbo Xu
    ISMB, 2010
    Bioinformatics, 2010 [Web Server]
     
  • 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