Senior author paper
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
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
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
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
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