Jian Peng

Machine Learning and other CS Papers

(papers in major machine learning or CS related conferences)

A 3D Generative Model for Structure-Based Drug Design
Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng
NeurIPS, 2021
PALM: Probabilistic Area Loss Minimization for Protein Sequence Alignment
Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue
UAI, 2021
Learning Neural Generative Dynamics for Molecular Conformation Generation
Minkai Xu, Shitong Luo, Yoshua Bengio, Jian Peng, Jian Tang
ICLR, 2021
DAP: Detection-Aware Pre-Training With Weak Supervision
Yuanyi Zhong, Jianfeng Wang, Lijuan Wang, Jian Peng, Yu-Xiong Wang, Lei Zhang
CVPR, 2021
Pixel Contrastive-Consistent Semi-Supervised Semantic Segmentation
Yuanyi Zhong, Bodi Yuan, Hong Wu, Zhiqiang Yuan, Jian Peng, Yu-Xiong Wang
ICCV, 2021
Learning Guidance Rewards with Trajectory-space Smoothing
Tanmay Gangwani, Yuan Zhou, Jian Peng
NeurIPS, 2020
Harnessing Distribution Ratio Estimators for Learning Agents with Quality and Diversity
Tanmay Gangwani, Jian Peng, Yuan Zhou
CoRL, 2020
Off-Policy Interval Estimation with Lipschitz Value Iteration
Ziyang Tang, Yihao Feng, Na Zhang, Jian Peng, Qiang Liu
NeurIPS, 2020
Causality in machine learning: When causal inference meets deep neural networks
Yunan Luo, Jian Peng and Jianzhu Ma
Nature Machine Intelligence, 2020
A Chance-Constrained Generative Framework for Sequence Optimization
Xianggen Liu, Sen Song, Qiang Liu, Jian Peng
ICML, 2020
Mutual Information Based Knowledge Transfer Under State-Action Dimension Mismatch
Michael Wan, Tanmay Gangwani, Jian Peng
UAI, 2020
Boosting Weakly Supervised Object Detection with Progressive Knowledge Transfer
Yuanyi Zhong, Jianfeng Wang, Jian Peng, Lei Zhang
ECCV, 2020
HAL: Computer System for Scalable Deep Learning
Volodymyr Kindratenko, Dawei Mu, Yan Zhan, John Maloney, Sayed Hadi Hashemi, Ben Rabe, Ke Xu, Roy Campbell, Jian Peng and William Gropp
PEARC, 2020
Stein Variational Inference for Discrete Distributions
Jun Han, Fan Ding, Xianglong Liu, Lorenzo Torresani, Jian Peng, Qiang Liu
AISTATS, 2020
A PTAS for the Bayesian Thresholding Bandit Problem
Yue Qin, Jian Peng, Yuan Zhou
AISTATS, 2020
State-only Imitation with Transition Dynamics Mismatch
Tanmay Gangwani, Jian Peng
ICLR, 2020
√n-Regret for Learning in Markov Decision Processes with Function Approximation and Low Bellman Rank
Kefan Dong, Jian Peng, Yining Wang, Yuan Zhou
COLT, 2020
Exploration via Hindsight Goal Generation
Zhizhou Ren, Kefan Dong, Yuan Zhou, Qiang Liu, Jian Peng
NeurIPS, 2019
Thresholding Bandit with Optimal Aggregate Regret
Chao Tao, Saúl Blanco, Jian Peng, Yuan Zhou
NeurIPS, 2019
HeteSpaceyWalk: A Heterogeneous Spacey Random Walk for Heterogeneous Information Network Embedding
Yu He, Yangqiu Song, Jianxin Li, Cheng Ji, Jian Peng and Hao Peng
CIKM, (long paper), 2019
Sequence Modeling of Temporal Credit Assignment for Episodic Reinforcement Learning
Yang Liu, Yunan Luo, Yuanyi Zhong, Xi Chen, Qiang Liu, Jian Peng
arXiv:1905.13420, 2019
Stochastic Variance Reduction for Deep Q-learning
Wei-Ye Zhao, Xi-Ya Guan, Yang Liu, Xiaoming Zhao, Jian Peng
AAMAS, 2019
Learning Belief Representations for Imitation Learning in POMDPs
Tanmay Gangwani, Joel Lehman, Qiang Liu, Jian Peng
UAI, 2019
REINAM: Reinforcement Learning for Input-Grammar Inference
Zhengkai Wu, Evan N. Johnson, Wei Yang, Osbert Bastani, Dawn Song, Jian Peng, Tao Xie
ESEC/FSE, 2019
Quantile Stein Bayesian Optimization
Chengyue Gong, Jian Peng, Qiang Liu
ICML, 2019
A gradual, semi-discrete approach to generative network training via explicit Wasserstein minimization
Yucheng Chen, Matus Telgarsky, Chao Zhang, Bolton Bailey, Daniel Hsu, Jian Peng
ICML, 2019
Large-Margin Classification in Hyperbolic Space
Hyunghoon Cho, Benjamin DeMeo, Jian Peng, Bonnie Berger
AISTATS, 2019
Off-Policy Evaluation and Learning from Logged Bandit Feedback: Error Reduction via Surrogate Policy
Yuan Xie, Boyi Liu, Qiang Liu, Zhaoran Wang, Yuan Zhou, Jian Peng
ICLR, 2019
Learning Self-Imitating Diverse Policies
Tanmay Gangwani, Qiang Liu, Jian Peng
ICLR, 2019
Accelerating Nonconvex Learning via Replica Exchange Langevin Diffusion
Yi Chen, Jinglin Chen, Jing Dong, Jian Peng, Zhaoran Wang
ICLR, 2019
Knowledge Flow: Improve Upon Your Teachers
Iou-Jen Liu, Jian Peng, Alexander Schwing
ICLR, 2019
emrQA: A Large Corpus for Question Answering on Electronic Medical Records
Anusri Pampari, Preethi Raghavan, Jennifer Liang and Jian Peng
EMNLP (oral presentation), 2018
Efficient Contextualized Representation: Language Model Pruning for Sequence Labeling
Liyuan Liu, Xiang Ren, Jingbo Shang, Jian Peng, Jiawei Han
EMNLP (oral presentation), 2018
SemRegex: A Semantics-Based Approach for Generating Regular Expressions from Natural Language Specifications
Zexuan Zhong, Jiaqi Guo, Wei Yang, Jian Peng, Tao Xie, Jian-Guang Lou, Ting Liu and Dongmei Zhang
EMNLP, 2018
Learning to Explore via Meta Policy Gradient
Tianbing Xu, Qiang Liu, Liang Zhao, Jian Peng
ICML, 2018
Policy Optimization by Genetic Distillation
Tanmay Gangwani, Jian Peng
ICLR, 2018
Action-dependent Control Variates for Policy Optimization via Stein Identity
Hao Liu*, Yihao Feng*, Yi Mao, Dengyong Zhou, Jian Peng, Qiang Liu
ICLR, 2018
Fast and Accurate Text Classification: Skimming, Rereading and Early Stopping
Keyi Yu, Yang Liu, Alexander G Schwing, Jian Peng
ICLR Workshop, 2018
Energy-efficient Amortized Inference with Cascaded Deep Classifiers
Jiaqi Guan, Yang Liu, Qiang Liu, Jian Peng
IJCAI, 2018
Efficient Localized Inference for Large Graphical Models
Jinglin Chen, Jian Peng, Qiang Liu
IJCAI, 2018
Empower Sequence Labeling with Task-Aware Neural Language Model
Liyuan Liu, Jingbo Shang, Frank Xu, Xiang Ren, Huan Gui, Jian Peng, Jiawei Han
AAAI, 2018
Similarity Modeling on Heterogeneous Networks via Automatic Path Discovery
Carl Yang, Mengxiong Liu, Frank He, Xikun Zhang, Jian Peng, and Jiawei Han
ECML-PKDD, 2018
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]
On the interpretability of conditional probability estimates in the agnostic setting
Yihan Gao, Aditya Parameswaran, Jian Peng
Electronic Journal of Statistics, 2017
AISTATS, 2017 (oral presentation)
Stochastic Variance Reduction for Policy Gradient Estimation
Tianbing Xu, Qiang Liu, Jian Peng
arXiv:1710.06034, 2017
DPPred: An Effective Prediction Framework with Concise Discriminative Patterns
Jingbo Shang, Meng Jiang, Wenzhu Tong, Jinfeng Xiao, Jian Peng, Jiawei Han
TKDE, 2017
Stein Variational Policy Gradient
Yang Liu, Prajit Ramachandran, Qiang Liu, Jian Peng
UAI, 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
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
Estimating the Partition Function by Discriminance Sampling
Qiang Liu*, Jian Peng*, Alex Ihler and John Fisher
UAI, 2015 (plenary presentation)
also in ICML Deep Learning Workshop, 2015
Exact Hybrid Covariance Thresholding for Joint Graphical Lasso
Qingming Tang, Chao Yang, Jian Peng, Jinbo Xu
ECML/PKDD, 2015
Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling.
Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu
AISTATS, 2013 (oral presentation)
Approximate Inference by Intersecting Semidefinite Bound and Local Polytope
Jian Peng, Tamir Hazan, Nathan Srebro and Jinbo Xu
AISTATS, 2012
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
Convex Max-Product Algorithms for Continuous MRFs with Applications to Protein Folding
Jian Peng, Tamir Hazan, David McAllester and Raquel Urtasun
ICML, 2011
Conditional Neural Fields
Jian Peng, Liefeng Bo and Jinbo Xu
NIPS, 2009

Bioinformatics and other Scientific Papers

(*-equal contribution, #-corresponding author/lead contact)
(for collaborative papers, authors from my group are underlined.)

JUMPER Enables Discontinuous Transcript Assembly in Coronaviruses
Palash Sashittal, Chuanyi Zhang, Jian Peng, Mohammed El-Kebir
Nature Communications, (accepted), 2021
Protein engineering using an evolutionary context-integrated deep learning framework
Yunan Luo*, Guangde Jiang*, Tianhao Yu, Yang Liu, Lam Vo, Hantian Ding, Yufeng Su, Wesley Wei Qian, Huimin Zhao#, Jian Peng#
Nature Communications, 2021
Deep geometric representations for modeling effects of mutations on protein-protein binding affinity
Xianggen Liu, Yunan Luo, Pengyong Li, Sen Song, Jian Peng#
PLOS Computational Biology, 2021
Bayesian Information Sharing Enhances Detection of Regulatory Associations in Rare Cell Types
Alexander P. Wu, Jian Peng, Bonnie Berger and Hyunghoon Cho
ISMB/ECCB, 2021
Bioinformatics, 2021
Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains
Benjamin L. Piette, Nader Alerasool, Zhen-Yuan Lin, Jessica Lacoste, Mandy Hiu Yi Lam, Wesley Wei Qian, Stephanie Tran,Brett Larsen, Eric Campos, Jian Peng, Anne-Claude Gingras, Mikko Taipale
Molecular Cell, 2021
Crowdsourced mapping of unexplored target space of kinase inhibitors
Anna Cichonska, et al
Nature Communications, 2021
Learning predictive models of drug response that translate across biological contexts
Jianzhu Ma, Samson Fong, Yunan Luo, Christopher Bakkenist, John-Paul Shen, Soufiane Mourragui, Lodewyk Wessels, Marc Hafner, Roded Sharan, Jian Peng, Trey Ideker#
Nature Cancer, 2021
A marine microbiome antifungal targets urgent-threat drug-resistant fungi
Fan Zhang, Miao Zhao, Doug R. Braun, Spencer S. Ericksen, Jeff S. Piotrowski, Justin Nelson, Jian Peng, Gene E. Ananiev, Shaurya Chanana, Kenneth Barns, Jen Fossen, Hiram Sanchez, Marc G. Chevrette, Ilia A. Guzei, Changgui Zhao, Le Guo, Weiping Tang, Cameron R. Currie, Scott R. Rajski, Anjon Audhya, David R. Andes#, and Tim S. Bugni#
Science, 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
Batch Equalization with a Generative Adversarial Network
Wesley Wei Qian, Cassandra Xia, Subhashini Venugopalan, Arunachalam Narayanaswamy, Michelle Dimon, George Ashdown, Jake Baum, Jian Peng, D. Michael Ando
ECCB, 2020
Bioinformatics, 2020
Characterization of SARS-CoV-2 viral diversity within and across hosts
Palash Sashittal*, Yunan Luo*, Jian Peng#, Mohammed El-Kebir#
BioRxiv, 2020
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
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
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
Integrating satellite and climate data to predict wheat yield in Australia using machine learning approaches
Yaping Cai, Kaiyu Guan, David Lobell, Andries B Potgieter, Shaowen Wang, Jian Peng, Tianfang Xu, Senthold Asseng, Yongguang Zhang, Liangzhi You, Bin Peng
Agricultural and Forest Meteorology, 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
A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction
Michael Menden et al
Nature Communications, 2019
Toward building a transparent statistical model for improving crop yield prediction: Modeling rainfed corn in the US
Yan Li, Kaiyu Guan, Albert Yu, Bin Peng, Lei Zhao, Bo Li, Jian Peng
Field Crops Research, 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
STAIR: A generic and fully-automated method to fuse multiple sources of optical satellite data to generate a high-resolution, daily and cloud-/gap-free surface reflectance product
Yunan Luo, Kaiyu Guan#, Jian Peng#
Remote Sensing of Environment, 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
Large-Scale Integration of Heterogeneous Pharmacogenomic Data for Identifying Drug Mechanism of Action
Yunan Luo, Sheng Wang, Jinfeng Xiao and Jian Peng#
PSB, 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, 2018
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
Nucleic Acids Research, bioRxiv:161208, 2018
A high-performance and in-season classification system of field-level crop types using time-series Landsat data and a machine learning approach
Yaping Cai, Kaiyu Guan#, Jian Peng#, Shaowen Wang, Christopher Seifert, Brian Wardlow, Zhan Li
Remote Sensing of Environment, 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
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
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
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
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 reduction really tells us about RNA-seq data
Sean Simmons, Jian Peng, Jadwiga Bienkowska and Bonnie Berger
Journal of Computational Biology, 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
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
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
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)
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)
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
A Conditional Neural Fields model for protein threading
Jianzhu Ma*, Jian Peng*, Sheng Wang and Jinbo Xu
ISMB, 2012
Bioinformatics, 2012 [Web Server]
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
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 the 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
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