Jian Ma

66 papers A* 2A 2B 13Misc 1Journal 39Unranked 8
YearRankTypeTitle / Venue / Authors
2025 B conf
Steamboat: Attention-Based Multiscale Delineation of Cellular Interactions in Tissues.
RECOMB
Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma
2025 B conf
Unified Integration of Spatial Transcriptomics Across Platforms.
RECOMB
Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger
2024 J jnl
Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning.
Trans. Mach. Learn. Res.
Yihe Deng, Ruochi Zhang, Pan Xu, Jian Ma, Quanquan Gu
2024 J jnl
RECOMB 2024 Special Issue.
J. Comput. Biol.
Jian Ma, Mona Singh
2024 B ed.
Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings
RECOMB
Jian Ma
2023 J jnl
UNADON: Transformer-based model to predict genome-wide chromosome spatial position.
CoRR
Muyu Yang, Jian Ma
2023 J jnl
UNADON: transformer-based model to predict genome-wide chromosome spatial position.
Bioinform.
Muyu Yang, Jian Ma
2022 B conf
Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing.
RECOMB
Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma
2022 J jnl
Guest Editorial for Selected Papers From ACM-BCB 2019.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jian Ma
2022 B conf
Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi.
RECOMB
Ruochi Zhang, Tianming Zhou, Jian Ma
2021 J jnl
Assessing the contribution of tumor mutational phenotypes to cancer progression risk.
PLoS Comput. Biol.
Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
2020 J jnl
A Multi-Organ Nucleus Segmentation Challenge.
IEEE Trans. Medical Imaging
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
2020 J jnl
Cancer mutational signatures representation by large-scale context embedding.
Bioinform.
Yang Zhang, Yunxuan Xiao, Muyu Yang, Jian Ma
2020 A* conf
Hyper-SAGNN: a self-attention based graph neural network for hypergraphs.
ICLR
Ruochi Zhang, Yuesong Zou, Jian Ma
2020 B conf
Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning.
RECOMB
Ruochi Zhang, Jian Ma
2020 J jnl
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.
Bioinform.
Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz
2019 B conf
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
RECOMB
Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma
2019 — conf
Enhanced Rotation-Equivariant U-Net for Nuclear Segmentation.
CVPR Workshops
Benjamin Chidester, That-Vinh Ton, Minh-Triet Tran, Jian Ma, Minh N. Do
2019 J jnl
Hyper-SAGNN: a self-attention based graph neural network for hypergraphs.
CoRR
Ruochi Zhang, Yuesong Zou, Jian Ma
2019 — conf
Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases.
ISMCO
Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz
2019 J jnl
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.
Quant. Biol.
Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma
2019 — ed.
Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2019, Niagara Falls, NY, USA, September 7-10, 2019.
BCB
Xinghua Mindy Shi, Michael Buck, Jian Ma, Pierangelo Veltri
2019 J jnl
Rotation equivariant and invariant neural networks for microscopy image analysis.
Bioinform.
Benjamin Chidester, Tianming Zhou, Minh N. Do, Jian Ma
2019 J jnl
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
Nat.
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
2018 B conf
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.
RECOMB
Yang Yang, Quanquan Gu, Takayo Sasaki, Julianna Crivello, Rachel O'Neill, David M. Gilbert, Jian Ma
2018 — conf
Correlating cellular features with gene expression using CCA.
ISBI
Vaishnavi Subramanian, Benjamin Chidester, Jian Ma, Minh N. Do
2018 A* conf
Covariate Adjusted Precision Matrix Estimation via Nonconvex Optimization.
ICML
Jinghui Chen, Pan Xu, Lingxiao Wang, Jian Ma, Quanquan Gu
2018 Misc conf
Discriminative bag-of-cells for imaging-genomics.
PSB
Benjamin Chidester, Minh N. Do, Jian Ma
2018 — conf
Integration of Spatial Distribution in Imaging-Genetics.
MICCAI (2)
Vaishnavi Subramanian, Weizhao Tang, Benjamin Chidester, Jian Ma, Minh N. Do
2018 A conf
Minimax Reconstruction Risk of Convolutional Sparse Dictionary Learning.
AISTATS
Shashank Singh, Barnabás Póczos, Jian Ma
2018 J jnl
Predicting CTCF-mediated chromatin loops using CTCF-MP.
Bioinform.
Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma
2018 J jnl
Rotation Equivariance and Invariance in Convolutional Neural Networks.
CoRR
Benjamin Chidester, Minh N. Do, Jian Ma
2018 J jnl
Toward Recovering Allele-specific Cancer Genome Graphs.
J. Comput. Biol.
Ashok Rajaraman, Jian Ma
2017 J jnl
Exploiting sequence-based features for predicting enhancer-promoter interactions.
Bioinform.
Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma
2017 J jnl
On the Reconstruction Risk of Convolutional Sparse Dictionary Learning.
CoRR
Shashank Singh, Barnabás Póczos, Jian Ma
2017 — conf
Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimization.
NIPS
Pan Xu, Jian Ma, Quanquan Gu
2017 J jnl
Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimizations.
CoRR
Pan Xu, Jian Ma, Quanquan Gu
2017 J jnl
Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution.
IEEE Trans. Vis. Comput. Graph.
Chris Bryan, Gregory Guterman, Kwan-Liu Ma, Harris A. Lewin, Denis M. Larkin, Jaebum Kim, Jian Ma, Marta Farre
2017 B conf
Towards Recovering Allele-Specific Cancer Genome Graphs.
RECOMB
Ashok Rajaraman, Jian Ma
2016 J jnl
A new correlation clustering method for cancer mutation analysis.
Bioinform.
Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic
2016 J jnl
A new correlation clustering method for cancer mutation analysis.
CoRR
Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic
2016 B conf
Allele-Specific Quantification of Structural Variations in Cancer Genomes.
RECOMB
Yang Li, Shiguo Zhou, David C. Schwartz, Jian Ma
2016 J jnl
BLESS 2: accurate, memory-efficient and fast error correction method.
Bioinform.
Yun Heo, Anand Ramachandran, Wen-mei W. Hwu, Jian Ma, Deming Chen
2016 J jnl
Identifying micro-inversions using high-throughput sequencing reads.
BMC Genom.
Feifei He, Yang Li, Yu-Hang Tang, Jian Ma, Huaiqiu Zhu
2016 J jnl
Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.
BMC Bioinform.
Ashok Rajaraman, Jian Ma
2015 J jnl
A Rewritable, Random-Access DNA-Based Storage System.
CoRR
S. M. Hossein Tabatabaei Yazdi, Yongbo Yuan, Jian Ma, Huimin Zhao, Olgica Milenkovic
2015 J jnl
DNA-Based Storage: Trends and Methods.
CoRR
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic
2015 J jnl
DNA-Based Storage: Trends and Methods.
IEEE Trans. Mol. Biol. Multi Scale Commun.
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic
2015 A conf
FPGA accelerated DNA error correction.
DATE
Anand Ramachandran, Yun Heo, Wen-mei W. Hwu, Jian Ma, Deming Chen
2014 J jnl
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.
BMC Bioinform.
Yiyi Liu, Quanquan Gu, Jack P. Hou, Jiawei Han, Jian Ma
2014 J jnl
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads.
Bioinform.
Yun Heo, Xiaolong Wu, Deming Chen, Jian Ma, Wen-mei W. Hwu
2014 J jnl
PSAR-Align: improving multiple sequence alignment using probabilistic sampling.
Bioinform.
Jaebum Kim, Jian Ma
2014 J jnl
Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework.
PLoS Comput. Biol.
Ken Daigoro Yokoyama, Yang Zhang, Jian Ma
2013 J jnl
Reference-assisted chromosome assembly.
Proc. Natl. Acad. Sci. USA
Jaebum Kim, Denis M. Larkin, Qingle Cai, Asan, Yongfen Zhang, Ri-Li Ge, Loretta Auvil, Boris Capitanu, Guojie Zhang, Harris A. Lewin, Jian Ma
2012 J jnl
TIGER: tiled iterative genome assembler.
BMC Bioinform.
Xiaolong Wu, Yun Heo, Izzat El Hajj, Wen-mei W. Hwu, Deming Chen, Jian Ma
2012 B conf
TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq.
RECOMB
Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma
2011 J jnl
Cactus Graphs for Genome Comparisons.
J. Comput. Biol.
Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler
2011 J jnl
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
Bioinform.
Yang Li, Jeremy Chien, David I. Smith, Jian Ma
2011 B conf
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract).
RECOMB
Jaebum Kim, Jian Ma
2011 J jnl
Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges.
J. Comput. Biol.
Jian Ma
2010 — conf
A probabilistic framework for inferring ancestral genomic orders.
BIBM
Jian Ma
2010 B conf
Cactus Graphs for Genome Comparisons.
RECOMB
Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler
2008 J jnl
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications.
J. Comput. Biol.
Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler
2008 J jnl
The infinite sites model of genome evolution.
Proc. Natl. Acad. Sci. USA
Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler
2007 — conf
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications.
RECOMB-CG
Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler
2007 — conf
Selecting Genomes for Reconstruction of Ancestral Genomes.
RECOMB-CG
Guoliang Li, Jian Ma, Louxin Zhang