Biology Papers

• NEW! Group retrosynthetic planning as neurosymbolic programming
  Xuefeng Zhang, Haowei Lin, Muhan Zhang, Yuan Zhou, and Jianzhu Ma
  Nature Communications 2024 corresponding author
  

   

• NEW! Large Scale Foundation Model on Single-cell Transcriptomics
  Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Le Song, Xuegong Zhang
  Nature Methods 2024 corresponding author
  

   

• Single-cell transcriptomics reveals the heterogeneity of the immune landscape of IDH-wildtype high-grade gliomas
  Xiaojuan Ran, Jian Zheng, Linchao Chen, Zhen Xia, Yin Wang, Chengfang Sun, Chen Guo, Peng Lin, Fuyi Liu, Chun Wang, Jianguo Zhou, Chongyuan Sun, Qichang Liu, Jianzhu Ma , Zhiyong Qin, Xiangdong Zhu, Qi Xie
  Cancer Immunology Research 2023
  

   

• Extrapolating Heterogeneous Time-Series Gene Expression Data using Sagittarius
  Addie Woicik, Mingxin Zhang, Janelle Chan, Jianzhu Ma, Sheng Wang
  Nature Machine Intelligence 2023
  

   

• Con-AAE: Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration
  Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma and Yu Li
  Bioinformatics 2023
  

   

• Characterizing the interaction conformation between T cell receptors and epitopes with deep learning
  Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma , Dan Zhao and Jianyang Zeng
  Nature Machine Intelligence 2023
  

   

• Pisces: A combo-wise contrastive learning approach to synergistic drug combination prediction
  Jiacheng Lin, Hanwen Xu, Addie Woicik, Jianzhu Ma and Sheng Wang
  RECOMB 2023
  

   

• Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data
  Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng and Jianzhu Ma
  Briefings in Bioinformatics 2022
  

   

• Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma
  Qi Xie, Zhilin Long, Chengfang Sun, Min Tang, Yin Wang, Jiayan Ma, Jichuan Yu, Jingchao Wei, Jianzhu Ma , Bohan Wang, and Jiaming Wen
  Cell Discovery 2022
  

   

• Deep learning guided optimization of human antibody against SARS-Cov-2 variants with broad neutralization
  Sisi Shan, Shitong Luo, Ziqing Yang, Junxian Hong, Yufeng Su, Fan Ding, Chengyu Li, Peng Chen, Jianzhu Ma, Xuanling Shi, Qi Zhang, Bonnie Berger, Linqi Zhang, Jian Peng
  PNAS 2022
  

   

• scPretrain: Multi-task self-supervised learning for cell type classification
  Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang
  Bioinformatics 2022
  

   

• Next decade’s AI-based drug development features the tight integration of data and computation
  Yunan Luo, Jian Peng, Jianzhu Ma
  Health Data Science 2021
  

   

• A multi-scale map of cell structure fusing protein images and interactions
  Yue Qin, Edward L. Huttlin, Casper F. Winsnes, Maya L. Gosztyla, Ludivine Wacheul, Marcus R. Kelly, Steven M. Blue, Fan Zheng, Michael Chen, Leah V. Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J. Lee, Wei Ouyang, Sophie N. Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F. Kreisberg, Steven P. Gygi, Jianzhu Ma, J. Wade Harper, Gene W. Yeo, Denis L. J. Lafontaine, Emma Lundberg，Trey Ideker
  Nature 2021
  

   

• 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)
  

   

• 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
  

   

• ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways
  Xiaoqing Huang, Kun Huang, Travis Johnson, Milan Radovich, Jie Zhang, Jianzhu Ma, Yijie Wang
  NAR genomics and bioinformatics 2021 corresponding author
  

   

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

   

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

   

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

   

• 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 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

• 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
  

   

• Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients
  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 co-first author
  

  • 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 co-first author
  

   

• 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 co-first author
  

   

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

   

• 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 co-first author
  

   

• Classifying tumors by supervised network propagation
  Wei Zhang, Jianzhu Ma, Trey Ideker
  ISMB 2018 co-first author
  

   

• 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 co-first author
  

   

• 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 co-first author
  

   

• DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields
  Mingfu Shao, Jianzhu Ma, Sheng Wang
  ISMB 2017 co-first author
  

   

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

   

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

   

• 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
  

   

• 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
  

   

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

• 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
  

   

• 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 2013
  

   

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

   

• 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)

   

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