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
  

• • ScienceDaily: DrugCell: New experimental AI platform matches tumor to best drug combo
    

  • Health IT Analytics: Deep Learning Model Could Enhance Cancer Precision Medicine
    

  • Med India: New AI Platform Matches Tumor to Right Drug Combination

  • AZO Life Sciences: Experimental AI platform predicts best approach to cancer treatment

  • UC San Diego Health Newsroom: DrugCell: New Experimental AI Platform Matches Tumor to Best Drug Combo

• 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
  

  • SALK NEWS: NEW COMPUTATIONAL TOOL LETS RESEARCHERS IDENTIFY CELLS BASED ON THEIR CHROMOSOME SHAPE
    

  • GenomeWeb: PNAS Studies Look at Lung Cancer LncRNA, Hi-C Clustering, and More

• 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
  

  • Cover Art: Nature Methods About the Cover: April 2018 Vol 15 No 4
    

  • IEEE SPECTRUM: Cracking Open the Black Box of AI with Cell Biology
    

  • UCSD Health: How a Yeast Cell Helps Crack Open the “Black Box” Behind Artificial Intelligence
    

  • GenomeWeb: Deep Learning-Based Cell Model May Predict Patient Tumor Cell Growth Someday
    

  • Nature: Deep learning takes on tumours
    

• 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