Publication

Senior author paper

  • NEW! Modeling Gene Regulatory Networks Using Neural Network Architectures
    Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma
    Nature Computational Science 2021

  • NEW! Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns
    Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li and Jianzhu Ma
    KDD 2021

  • NEW! Predicting MHC-peptide binding affinity by differential boundary tree
    Peiyuan Feng, Jianyang Zeng and Jianzhu Ma
    ISMB 2021

  • NEW! Disease Gene Prediction with Privileged Information and Heteroscedastic Dropout
    Juan Shu, Yu Li, Sheng Wang, Bowei Xi and Jianzhu Ma
    ISMB 2021

  • NEW! AirSign: Smartphone Authentication by Signing in the Air
    Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma
    Sensor 2021

  • NEW! Towards the prediction of higher-order genetic interactions
    Ruochi Zhang, Jianzhu Ma, Jian Ma
    RECOMB 2021

  • Predicting drug response and synergy using a deep learning model of a cancer cell
    Brent Kuenzi, Jisoo Park, Samson H. Fong, Kyle Salinas Sanchez, Jason F. Kreisberg, Jianzhu Ma, Trey Ideker
    Cancer Cell in press 2020

  • Causality in machine learning: When causal inference meets deep neural networks
    Yunan Luo, Jian Peng, Jianzhu Ma
    Nature Machine intelligence 2020

First or co-first author paper

  • 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 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

  • DDOT: A Swiss-Army Knife for Investigating Data-Driven Biological Ontologies
    Michael Ku Yu, Jianzhu Ma, Keiichiro Ono, Fan Zheng, Samson H. Fong, Aaron Gary, Jing Chen, Barry Demchak, Dexter Pratt, Trey Ideker
    Cell Systems 2019

  • Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning
    Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng
    RECOMB 2019

  • Visible Machine Learning for Biomedicine
    Michael Ku Yu, Jianzhu Ma, Jasmin Fisher, Jason F. Kreisberg, Benjamin J. Raphael, Trey Ideker
    Cell 2018

  • Typing tumors using pathways selected by somatic evolution
    Sheng Wang, Jianzhu Ma, Wei Zhang, John Shen, Justin Huang, Jian Peng, Trey Ideker
    Nature Communications 2018

  • Classifying tumors by supervised network propagation
    Wei Zhang, Jianzhu Ma, Trey Ideker
    ISMB 2018 and bioinformatics

  • Using deep learning to model the hierarchical structure and function of a cell
    Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak, Roded Sharan, Trey Ideker
    Nature Methods 2018

  • Deciphering signaling specificity with deep neural networks
    Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng
    RECOMB 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
    Pacific Symposium on Biocomputing, 2018

  • DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields
    Mingfu Shao, Jianzhu Ma, Sheng Wang
    ISMB 2017 and Bioinformatics

  • AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multi-Task Learning Framework under the Conditional Random Fields Model
    Jianzhu Ma and Sheng Wang
    BioMed Research International 2015

  • Structure Learning Constrained by Node-Specific Degree Distribution
    Jianzhu Ma, Sheng Wang and Jinbo Xu
    UAI 2015

  • Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning
    Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu
    RECOMB and PLOS Computational Biology 2015

  • MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
    Jianzhu Ma, Sheng Wang, Jinbo Xu
    RECOMB and PLOS Computational Biology 2014
    This work also won the following awards:

    • Best Paper Award of RECOMB 2014

    • Best Poster Award of 2nd Zing Conference on Protein and RNA Structure Prediction

    • Warren DeLano Award of 3DSIG 2014

  • Algorithms, Applications and Challenges of Protein Structure Alignment
    Jianzhu Ma and Sheng Wang
    Journal of Advances in Protein Chemistry and Structural Biology 2014

  • Protein Threading Using Context-Specific Alignment Potential
    Jianzhu Ma, Sheng Wang and Jinbo Xu
    ISMB and Bioinformatics 2013

  • Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling
    Jianzhu Ma, Jian Peng, Sheng Wang and Jinbo Xu
    AI & Statistics 2013

  • A Conditional Neural Fields Model for Protein Threading
    Jianzhu Ma, Jian Peng, Sheng Wang and Jinbo Xu
    ISMB and Bioinformatics 2012

  • Design and Implementation of a Cooperate Framework for Autonomous Component based on Rule Injection
    Jianzhu Ma, Jiyu Huang and Wenpin Jiao
    NASAC 2009

Co-author paper

  • NEW! PALM: Probabilistic Area Loss Minimization for Protein Sequence Alignment
    Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue
    UAI 2021

  • NEW! XOR-CD: Linearly Convergent Constrained Structure Generation
    Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue
    ICML 2021 oral presentation

  • NEW! SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through ACE2-independent interactions via C-type lectin receptors and TTYH2
    Qiao Lu, Jia Liu, Shuai Zhao, Maria Florencia Gomez Castro, Maudry Laurent-Rolle, Jianbo Dong, Xiaojuan Ran, Payal Damani-Yokota, Hongzheng Tang, Triantafyllia Karakousi, Juhee Son, Maria E. Kaczmarek, Ze Zhang, Stephen T. Yeung, Broc T. McCune, Rita E. Chen, Fei Tang, Xianwen Ren, Xufeng Chen, Jack C.C. Hsu, Marianna Teplova, Betty Huang, Haijing Deng, Zhilin Long, Tenny Mudianto, Shumin Jin, Peng Lin, Jasper Du, Ruochen Zang, Tina Tianjiao Su, Alberto Herrera, Ming Zhou, Renhong Yan, Jia Cui, James Zhu, Qiang Zhou, Tao Wang, Jianzhu Ma, Sergei B. Koralov, Zemin Zhang, Iannis Aifantis, Leopoldo N. Segal, Michael S. Diamond, Kamal M. Khanna, Kenneth A. Stapleford, Peter Cresswel, Yue Liu, Siyuan Ding, Qi Xie, Jun Wang
    Immunity 2021 (Impact Factor=22)

  • A conserved epigenetic progression aligns dog and human age
    Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander and Trey Ideker
    Cell Systems 2020

  • Artificial-Cell-Type Aware Cell Type Classification in CITE-seq
    Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu and Kong Chen
    ISMB 2020 and Bioinformatics

  • AUCpreD: proteome-level protein disorder prediction by AUC-maximized Deep Convolutional Neural Fields
    Sheng Wang, Jianzhu Ma, Jinbo Xu
    ECCB 2016 and Bioinformatics

  • ModuleAlign: Module-based global alignment of protein-protein interaction networks
    Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu
    ECCB 2016 and Bioinformatics

  • Protein secondary structure prediction using deep convolutional neural fields
    Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
    Scientific Reports 2016

  • Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage
    Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
    ACM BCB 2016

  • Predicting diverse M-best protein contact maps
    Siqi Sun,Jianzhu Ma, Jinbo Xu
    BIBM 2015

  • DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields
    Sheng Wang, Jianzhu Ma, Jinbo Xu
    International Journal of Molecular Sciences 2015

  • An Integrative Computational Approach for Prioritization of Genomic Variants
    Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Börnigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex R Paciorkowski, Ghayda M Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al-Gazali, Christopher E Mason, M Elizabeth Ross, Natalia Maltsev and T Conrad Gilliam
    PLOS ONE 2015

  • Fast and Automatic Pairwise Structure Alignment Algorithm close to Manually-Curated Precision
    Scientific Reports and 3DSIG 2012. Warren DeLano Award

  • A Self-Adaptive Mechanism for Software Configuration Based on Case-based Reasoning and Policy
    Maoguang Wang, Hong Mei, Wenpin Jiao, Junjing Jie and Jianzhu Ma
    AICI 2010

  • An Empirical Study on the Impacts of Autonomy of Components on Qualities of Software Systems
    Shiting Xun, Jianzhu Ma, Wenpin Jiao and Fanjing Meng
    EASe 2011

  • A Two-way Selections based Approach to Automated Integration of Multi-Agent Systems
    Xi Fang, Jianzhu Ma, Maoguang Wang and Wenpin Jiao
    3rd National Conference on Agent Theory and Application 2010

  • A Browser-based Framework for Data Cache in Web-Delivered Service Composition
    Jiyu Huang, Xuanzhe Liu, Qi Zhao, Jianzhu Ma and Gang Huang
    SOCA 2010 (Best paper running up)

Book Chapter

  • Protein Homology Detection Through Alignment of Markov Random Fields: Using MRFalign
    Jinbo Xu, Sheng Wang and Jianzhu Ma
    Springer Book 2015

  • RaptorX Server: A Resource for Template-based Protein Structure Modeling
    Morten Källberg, Gohar Margaryan, Sheng Wang, Jianzhu Ma and Jinbo Xu
    Methods in Molecular Biology 2013

  • Protein Structure Prediction by Protein Alignments
    Jianzhu Ma
    Dissertation 2015