Jian Ma

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 39

Top Topics

Interactive Visualization

Convex Optimization

Gene Expression

Top Venues

Publications

Muyu Yang, Jian Ma
UNADON: transformer-based model to predict genome-wide chromosome spatial position. Bioinform. 39 (Supplement-1) (2023)
Muyu Yang, Jian Ma
UNADON: Transformer-based model to predict genome-wide chromosome spatial position. CoRR (2023)
Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma
Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing. RECOMB (2022)
Jian Ma
Guest Editorial for Selected Papers From ACM-BCB 2019. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Ruochi Zhang, Tianming Zhou, Jian Ma
Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi. RECOMB (2022)
Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
Assessing the contribution of tumor mutational phenotypes to cancer progression risk. PLoS Comput. Biol. 17 (3) (2021)
Ruochi Zhang, Yuesong Zou, Jian Ma
Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. ICLR (2020)
Yang Zhang, Yunxuan Xiao, Muyu Yang, Jian Ma
Cancer mutational signatures representation by large-scale context embedding. Bioinform. 36 (Supplement-1) (2020)
Neeraj Kumar, Ruchika Verma, Deepak Anand, Yanning Zhou, Omer Fahri Onder, Efstratios Tsougenis, Hao Chen, Pheng-Ann Heng, Jiahui Li, Zhiqiang Hu, Yunzhi Wang, Navid Alemi Koohbanani, Mostafa Jahanifar, Neda Zamani Tajeddin, Ali Gooya, Nasir M. Rajpoot, Xuhua Ren, Sihang Zhou, Qian Wang, Dinggang Shen, Cheng-Kun Yang, Chi-Hung Weng, Wei-Hsiang Yu, Chao-Yuan Yeh, Shuang Yang, Shuoyu Xu, Pak-Hei Yeung, Peng Sun, Amirreza Mahbod, Gerald Schaefer, Isabella Ellinger, Rupert Ecker, Örjan Smedby, Chunliang Wang, Benjamin Chidester, That-Vinh Ton, Minh-Triet Tran, Jian Ma, Minh N. Do, Simon Graham, Quoc Dang Vu, Jin Tae Kwak, Akshaykumar Gunda, Raviteja Chunduri, Corey Hu, Xiaoyang Zhou, Dariush Lotfi, Reza Safdari, Antanas Kascenas, Alison O'Neil, Dennis Eschweiler, Johannes Stegmaier, Yanping Cui, Baocai Yin, Kailin Chen, Xinmei Tian, Philipp Grüning, Erhardt Barth, Elad Arbel, Itay Remer, Amir Ben-Dor, Ekaterina Sirazitdinova, Matthias Kohl, Stefan Braunewell, Yuexiang Li, Xinpeng Xie, Linlin Shen, Jun Ma, Krishanu Das Baksi, Mohammad Azam Khan, Jaegul Choo, Adrián Colomer, Valery Naranjo, Linmin Pei, Khan M. Iftekharuddin, Kaushiki Roy, Debotosh Bhattacharjee, Aníbal Pedraza, Maria Gloria Bueno, Sabarinathan Devanathan, Saravanan Radhakrishnan, Praveen Koduganty, Zihan Wu, Guanyu Cai, Xiaojie Liu, Yuqin Wang, Amit Sethi
A Multi-Organ Nucleus Segmentation Challenge. IEEE Trans. Medical Imaging 39 (5) (2020)
Ruochi Zhang, Jian Ma
Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. RECOMB (2020)
Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. Bioinform. 36 (Supplement-1) (2020)
Benjamin Chidester, Tianming Zhou, Minh N. Do, Jian Ma
Rotation equivariant and invariant neural networks for microscopy image analysis. Bioinform. 35 (14) (2019)
Benjamin Chidester, That-Vinh Ton, Minh-Triet Tran, Jian Ma, Minh N. Do
Enhanced Rotation-Equivariant U-Net for Nuclear Segmentation. CVPR Workshops (2019)
Ruochi Zhang, Yuesong Zou, Jian Ma
Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. CoRR (2019)
Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz
Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases. ISMCO (2019)
Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark deCaestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma A. Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574 (7777) (2019)
Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. Quant. Biol. 7 (2) (2019)
Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. RECOMB (2019)
Jinghui Chen, Pan Xu, Lingxiao Wang, Jian Ma, Quanquan Gu
Covariate Adjusted Precision Matrix Estimation via Nonconvex Optimization. ICML (2018)
Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma
Predicting CTCF-mediated chromatin loops using CTCF-MP. Bioinform. 34 (13) (2018)
Shashank Singh, Barnabás Póczos, Jian Ma
Minimax Reconstruction Risk of Convolutional Sparse Dictionary Learning. AISTATS (2018)
Benjamin Chidester, Minh N. Do, Jian Ma
Discriminative bag-of-cells for imaging-genomics. PSB (2018)
Ashok Rajaraman, Jian Ma
Toward Recovering Allele-specific Cancer Genome Graphs. J. Comput. Biol. 25 (7) (2018)
Vaishnavi Subramanian, Benjamin Chidester, Jian Ma, Minh N. Do
Correlating cellular features with gene expression using CCA. ISBI (2018)
Yang Yang, Quanquan Gu, Takayo Sasaki, Julianna Crivello, Rachel O'Neill, David M. Gilbert, Jian Ma
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. RECOMB (2018)
Vaishnavi Subramanian, Weizhao Tang, Benjamin Chidester, Jian Ma, Minh N. Do
Integration of Spatial Distribution in Imaging-Genetics. MICCAI (2) (2018)
Benjamin Chidester, Minh N. Do, Jian Ma
Rotation Equivariance and Invariance in Convolutional Neural Networks. CoRR (2018)
Ashok Rajaraman, Jian Ma
Towards Recovering Allele-Specific Cancer Genome Graphs. RECOMB (2017)
Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma
Exploiting sequence-based features for predicting enhancer-promoter interactions. Bioinform. 33 (14) (2017)
Pan Xu, Jian Ma, Quanquan Gu
Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimization. NIPS (2017)
Chris Bryan, Gregory Guterman, Kwan-Liu Ma, Harris A. Lewin, Denis M. Larkin, Jaebum Kim, Jian Ma, Marta Farre
Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution. IEEE Trans. Vis. Comput. Graph. 23 (1) (2017)
Shashank Singh, Barnabás Póczos, Jian Ma
On the Reconstruction Risk of Convolutional Sparse Dictionary Learning. CoRR (2017)
Pan Xu, Jian Ma, Quanquan Gu
Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimizations. CoRR (2017)
Feifei He, Yang Li, Yu-Hang Tang, Jian Ma, Huaiqiu Zhu
Identifying micro-inversions using high-throughput sequencing reads. BMC Genom. 17 (S-1) (2016)
Ashok Rajaraman, Jian Ma
Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. BMC Bioinform. 17 (S-14) (2016)
Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic
A new correlation clustering method for cancer mutation analysis. CoRR (2016)
Yun Heo, Anand Ramachandran, Wen-mei W. Hwu, Jian Ma, Deming Chen
BLESS 2: accurate, memory-efficient and fast error correction method. Bioinform. 32 (15) (2016)
Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic
A new correlation clustering method for cancer mutation analysis. Bioinform. 32 (24) (2016)
Yang Li, Shiguo Zhou, David C. Schwartz, Jian Ma
Allele-Specific Quantification of Structural Variations in Cancer Genomes. RECOMB (2016)
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic
DNA-Based Storage: Trends and Methods. CoRR (2015)
Anand Ramachandran, Yun Heo, Wen-mei W. Hwu, Jian Ma, Deming Chen
FPGA accelerated DNA error correction. DATE (2015)
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic
DNA-Based Storage: Trends and Methods. IEEE Trans. Mol. Biol. Multi Scale Commun. 1 (3) (2015)
S. M. Hossein Tabatabaei Yazdi, Yongbo Yuan, Jian Ma, Huimin Zhao, Olgica Milenkovic
A Rewritable, Random-Access DNA-Based Storage System. CoRR (2015)
Yiyi Liu, Quanquan Gu, Jack P. Hou, Jiawei Han, Jian Ma
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. BMC Bioinform. 15 (2014)
Yun Heo, Xiaolong Wu, Deming Chen, Jian Ma, Wen-mei W. Hwu
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads. Bioinform. 30 (10) (2014)
Jaebum Kim, Jian Ma
PSAR-Align: improving multiple sequence alignment using probabilistic sampling. Bioinform. 30 (7) (2014)
Ken Daigoro Yokoyama, Yang Zhang, Jian Ma
Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework. PLoS Comput. Biol. 10 (8) (2014)
Jaebum Kim, Denis M. Larkin, Qingle Cai, Asan, Yongfen Zhang, Ri-Li Ge, Loretta Auvil, Boris Capitanu, Guojie Zhang, Harris A. Lewin, Jian Ma
Reference-assisted chromosome assembly. Proc. Natl. Acad. Sci. USA 110 (5) (2013)
Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma
TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq. RECOMB (2012)
Xiaolong Wu, Yun Heo, Izzat El Hajj, Wen-mei W. Hwu, Deming Chen, Jian Ma
TIGER: tiled iterative genome assembler. BMC Bioinform. 13 (S-19) (2012)
Jaebum Kim, Jian Ma
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract). RECOMB (2011)
Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler
Cactus Graphs for Genome Comparisons. J. Comput. Biol. 18 (3) (2011)
Yang Li, Jeremy Chien, David I. Smith, Jian Ma
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinform. 27 (12) (2011)
Jian Ma
Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges. J. Comput. Biol. 18 (7) (2011)
Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler
Cactus Graphs for Genome Comparisons. RECOMB (2010)
Jian Ma
A probabilistic framework for inferring ancestral genomic orders. BIBM (2010)
Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. J. Comput. Biol. 15 (8) (2008)
Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler
The infinite sites model of genome evolution. Proc. Natl. Acad. Sci. USA 105 (38) (2008)
Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. RECOMB-CG (2007)
Guoliang Li, Jian Ma, Louxin Zhang
Selecting Genomes for Reconstruction of Ancestral Genomes. RECOMB-CG (2007)