Jian Ma

According to our database, Jian Ma authored at least 55 papers between 2007 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

UNADON: transformer-based model to predict genome-wide chromosome spatial position.

Muyu Yang, Jian Ma

Bioinform., 2023

2022

Guest Editorial for Selected Papers From ACM-BCB 2019.

Jian Ma

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi.

Ruochi Zhang, Tianming Zhou, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2022

Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing.

Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2022

2021

Assessing the contribution of tumor mutational phenotypes to cancer progression risk.

Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz

PLoS Comput. Biol., 2021

2020

A Multi-Organ Nucleus Segmentation Challenge.

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

IEEE Trans. Medical Imaging, 2020

Cancer mutational signatures representation by large-scale context embedding.

Yang Zhang, Yunxuan Xiao, Muyu Yang, Jian Ma

Bioinform., 2020

Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.

Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz

Bioinform., 2020

Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning.

Ruochi Zhang, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2020

Hyper-SAGNN: a self-attention based graph neural network for hypergraphs.

Ruochi Zhang, Yuesong Zou, Jian Ma

Proceedings of the 8th International Conference on Learning Representations, 2020

2019

Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.

Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma

Quant. Biol., 2019

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

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 P. de Caestecker, 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 Anand 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

Nat., 2019

Rotation equivariant and invariant neural networks for microscopy image analysis.

Benjamin Chidester, Tianming Zhou, Minh N. Do, Jian Ma

Bioinform., 2019

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.

Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2019

Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases.

Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz

Proceedings of the Mathematical and Computational Oncology - First International Symposium, 2019

Enhanced Rotation-Equivariant U-Net for Nuclear Segmentation.

Benjamin Chidester, That-Vinh Ton, Minh-Triet Tran, Jian Ma, Minh N. Do

Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition Workshops, 2019

2018

Toward Recovering Allele-specific Cancer Genome Graphs.

Ashok Rajaraman, Jian Ma

J. Comput. Biol., 2018

Rotation Equivariance and Invariance in Convolutional Neural Networks.

Benjamin Chidester, Minh N. Do, Jian Ma

CoRR, 2018

Predicting CTCF-mediated chromatin loops using CTCF-MP.

Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma

Bioinform., 2018

Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.

Yang Yang, Quanquan Gu, Takayo Sasaki, Julianna Crivello, Rachel O'Neill, David M. Gilbert, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2018

Discriminative bag-of-cells for imaging-genomics.

Benjamin Chidester, Minh N. Do, Jian Ma

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Integration of Spatial Distribution in Imaging-Genetics.

Vaishnavi Subramanian, Weizhao Tang, Benjamin Chidester, Jian Ma, Minh N. Do

Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2018, 2018

Correlating cellular features with gene expression using CCA.

Vaishnavi Subramanian, Benjamin Chidester, Jian Ma, Minh N. Do

Proceedings of the 15th IEEE International Symposium on Biomedical Imaging, 2018

Covariate Adjusted Precision Matrix Estimation via Nonconvex Optimization.

Jinghui Chen, Pan Xu, Lingxiao Wang, Jian Ma, Quanquan Gu

Proceedings of the 35th International Conference on Machine Learning, 2018

Minimax Reconstruction Risk of Convolutional Sparse Dictionary Learning.

Shashank Singh, Barnabás Póczos, Jian Ma

Proceedings of the International Conference on Artificial Intelligence and Statistics, 2018

2017

Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution.

Chris Bryan, Gregory Guterman, Kwan-Liu Ma, Harris A. Lewin, Denis M. Larkin, Jaebum Kim, Jian Ma, Marta Farre

IEEE Trans. Vis. Comput. Graph., 2017

On the Reconstruction Risk of Convolutional Sparse Dictionary Learning.

Shashank Singh, Barnabás Póczos, Jian Ma

CoRR, 2017

Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimizations.

Pan Xu, Jian Ma, Quanquan Gu

CoRR, 2017

Exploiting sequence-based features for predicting enhancer-promoter interactions.

Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma

Bioinform., 2017

Towards Recovering Allele-Specific Cancer Genome Graphs.

Ashok Rajaraman, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2017

Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimization.

Pan Xu, Jian Ma, Quanquan Gu

Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017

2016

Identifying micro-inversions using high-throughput sequencing reads.

Feifei He, Yang Li, Yu-Hang Tang, Jian Ma, Huaiqiu Zhu

BMC Genom., 2016

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.

Ashok Rajaraman, Jian Ma

BMC Bioinform., 2016

A new correlation clustering method for cancer mutation analysis.

Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic

Bioinform., 2016

BLESS 2: accurate, memory-efficient and fast error correction method.

Yun Heo, Anand Ramachandran, Wen-mei W. Hwu, Jian Ma, Deming Chen

Bioinform., 2016

Allele-Specific Quantification of Structural Variations in Cancer Genomes.

Yang Li, Shiguo Zhou, David C. Schwartz, Jian Ma

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

DNA-Based Storage: Trends and Methods.

S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic

IEEE Trans. Mol. Biol. Multi Scale Commun., 2015

A Rewritable, Random-Access DNA-Based Storage System.

S. M. Hossein Tabatabaei Yazdi, Yongbo Yuan, Jian Ma, Huimin Zhao, Olgica Milenkovic

CoRR, 2015

FPGA accelerated DNA error correction.

Anand Ramachandran, Yun Heo, Wen-mei W. Hwu, Jian Ma, Deming Chen

Proceedings of the 2015 Design, Automation & Test in Europe Conference & Exhibition, 2015

2014

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework.

Ken Daigoro Yokoyama, Yang Zhang, Jian Ma

PLoS Comput. Biol., 2014

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.

Yiyi Liu, Quanquan Gu, Jack P. Hou, Jiawei Han, Jian Ma

BMC Bioinform., 2014

PSAR-Align: improving multiple sequence alignment using probabilistic sampling.

Jaebum Kim, Jian Ma

Bioinform., 2014

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads.

Yun Heo, Xiaolong Wu, Deming Chen, Jian Ma, Wen-mei W. Hwu

Bioinform., 2014

2013

Reference-assisted chromosome assembly.

Jaebum Kim, Denis M. Larkin, Qingle Cai, Asan, Yongfen Zhang, Ri-Li Ge, Loretta Auvil, Boris Capitanu, Guojie Zhang, Harris A. Lewin, Jian Ma

Proc. Natl. Acad. Sci. USA, 2013

2012

TIGER: tiled iterative genome assembler.

Xiaolong Wu, Yun Heo, Izzat El Hajj, Wen-mei W. Hwu, Deming Chen, Jian Ma

BMC Bioinform., 2012

TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq.

Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2012

2011

Cactus Graphs for Genome Comparisons.

Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler

J. Comput. Biol., 2011

Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges.

Jian Ma

J. Comput. Biol., 2011

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.

Yang Li, Jeremy Chien, David I. Smith, Jian Ma

Bioinform., 2011

PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract).

Jaebum Kim, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2011

2010

A probabilistic framework for inferring ancestral genomic orders.

Jian Ma

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2008

The infinite sites model of genome evolution.

Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler

Proc. Natl. Acad. Sci. USA, 2008

DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications.

Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler

J. Comput. Biol., 2008

2007

A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications.

Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler

Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007

Selecting Genomes for Reconstruction of Ancestral Genomes.

Guoliang Li, Jian Ma, Louxin Zhang

Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007