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ORCIDJian Ma 0004
Person information
- affiliation: Carnegie Mellon University, Computational Biology Department, Pittsburgh, PA, USA
- affiliation (2009 - 2015): University of Illinois at Urbana-Champaign, IL, USA
- affiliation (2007 - 2009): University of California at Santa Cruz, CA, USA
- affiliation (PhD 2006): Pennsylvania State University, PA, USA
Other persons with the same name
- Jian Ma — disambiguation page
- Jian Ma 0001 — Wuxi Sensingnet Industralization Research Institute, China (and 3 more)
- Jian Ma 0002 — University of Electronic Science and Technology of China, School of Microelectronics and Solid-State Electronics, Chengdu, China
- Jian Ma 0003
![[0000-0002-9091-2040]](https://dblp.org/img/orcid-mark.12x12.png "0000-0002-9091-2040")
— Shanghai Ocean University, College of Marine Sciences, China - Jian Ma 0005 — Shanghai University, Shanghai Institute for Advanced Communication and Data Science, China
- Jian Ma 0006 — Beihang University, School of Reliability and Systems Engineering, Beijing, China
- Jian Ma 0007 — Suzhou University of Science and Technology, School of Civil Engineering, China (and 1 more)
- Jian Ma 0008 — City University of Hong Kong, Department of Information Systems, Hong Kong (and 2 more)
- Jian Ma 0009 — Southwest Jiaotong University, School of Transportation and Logistics, Chengdu, China (and 1 more)
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2020 – today
- 2023
[j29]Muyu Yang, Jian Ma:
UNADON: transformer-based model to predict genome-wide chromosome spatial position. Bioinform. 39(Supplement-1): 553-562 (2023)- [i8]Muyu Yang, Jian Ma:
UNADON: Transformer-based model to predict genome-wide chromosome spatial position. CoRR abs/2304.13230 (2023) - 2022
- [j28]Jian Ma:
Guest Editorial for Selected Papers From ACM-BCB 2019. IEEE ACM Trans. Comput. Biol. Bioinform. 19(4): 1919 (2022) - [c23]Ruochi Zhang, Tianming Zhou, Jian Ma:
Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi. RECOMB 2022: 300-301 - [c22]Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma:
Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing. RECOMB 2022: 358-359 - 2021
- [j27]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) - 2020
- [j26]Yang Zhang, Yunxuan Xiao, Muyu Yang, Jian Ma:
Cancer mutational signatures representation by large-scale context embedding. Bioinform. 36(Supplement-1): i309-i316 (2020) - [j25]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): i407-i416 (2020) - [j24]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): 1380-1391 (2020) - [c21]Ruochi Zhang, Yuesong Zou, Jian Ma:
Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. ICLR 2020 - [c20]Ruochi Zhang, Jian Ma:
Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. RECOMB 2020: 276-277
2010 – 2019
- 2019
- [j23]Benjamin Chidester, Tianming Zhou, Minh N. Do, Jian Ma:
Rotation equivariant and invariant neural networks for microscopy image analysis. Bioinform. 35(14): i530-i537 (2019) - [j22]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:
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574(7777): 187-192 (2019) - [j21]Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma:
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. Quant. Biol. 7(2): 122-137 (2019) - [c19]Benjamin Chidester, That-Vinh Ton, Minh-Triet Tran, Jian Ma, Minh N. Do:
Enhanced Rotation-Equivariant U-Net for Nuclear Segmentation. CVPR Workshops 2019: 1097-1104 - [c18]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: 3-28 - [c17]Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma:
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. RECOMB 2019: 326-327 - [e1]Xinghua Mindy Shi, Michael Buck, Jian Ma, Pierangelo Veltri:
Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2019, Niagara Falls, NY, USA, September 7-10, 2019. ACM 2019, ISBN 978-1-4503-6666-3 [contents] - [i7]Ruochi Zhang, Yuesong Zou, Jian Ma:
Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. CoRR abs/1911.02613 (2019) - 2018
- [j20]Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma:
Predicting CTCF-mediated chromatin loops using CTCF-MP. Bioinform. 34(13): i133-i141 (2018) - [j19]Ashok Rajaraman, Jian Ma:
Toward Recovering Allele-specific Cancer Genome Graphs. J. Comput. Biol. 25(7): 624-636 (2018) - [c16]Shashank Singh, Barnabás Póczos, Jian Ma:
Minimax Reconstruction Risk of Convolutional Sparse Dictionary Learning. AISTATS 2018: 1327-1336 - [c15]Jinghui Chen, Pan Xu, Lingxiao Wang, Jian Ma, Quanquan Gu:
Covariate Adjusted Precision Matrix Estimation via Nonconvex Optimization. ICML 2018: 921-930 - [c14]Vaishnavi Subramanian, Benjamin Chidester, Jian Ma, Minh N. Do:
Correlating cellular features with gene expression using CCA. ISBI 2018: 805-808 - [c13]Vaishnavi Subramanian, Weizhao Tang, Benjamin Chidester, Jian Ma, Minh N. Do:
Integration of Spatial Distribution in Imaging-Genetics. MICCAI (2) 2018: 245-253 - [c12]Benjamin Chidester, Minh N. Do, Jian Ma:
Discriminative bag-of-cells for imaging-genomics. PSB 2018: 319-330 - [c11]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: 293-294 - [i6]Benjamin Chidester, Minh N. Do, Jian Ma:
Rotation Equivariance and Invariance in Convolutional Neural Networks. CoRR abs/1805.12301 (2018) - 2017
- [j18]Yang Yang, Ruochi Zhang, Shashank Singh, Jian Ma:
Exploiting sequence-based features for predicting enhancer-promoter interactions. Bioinform. 33(14): i252-i260 (2017) - [j17]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): 711-720 (2017) - [c10]Pan Xu, Jian Ma, Quanquan Gu:
Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimization. NIPS 2017: 1933-1944 - [c9]Ashok Rajaraman, Jian Ma:
Towards Recovering Allele-Specific Cancer Genome Graphs. RECOMB 2017: 224-240 - [i5]Pan Xu, Jian Ma, Quanquan Gu:
Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimizations. CoRR abs/1702.08651 (2017) - [i4]Shashank Singh, Barnabás Póczos, Jian Ma:
On the Reconstruction Risk of Convolutional Sparse Dictionary Learning. CoRR abs/1708.08587 (2017) - 2016
- [j16]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): 2369-2371 (2016) - [j15]Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic:
A new correlation clustering method for cancer mutation analysis. Bioinform. 32(24): 3717-3728 (2016) - [j14]Ashok Rajaraman, Jian Ma:
Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. BMC Bioinform. 17(S-14): 201-212 (2016) - [j13]Feifei He, Yang Li, Yu-Hang Tang, Jian Ma, Huaiqiu Zhu:
Identifying micro-inversions using high-throughput sequencing reads. BMC Genom. 17(S-1): 4 (2016) - [c8]Yang Li, Shiguo Zhou, David C. Schwartz, Jian Ma:
Allele-Specific Quantification of Structural Variations in Cancer Genomes. RECOMB 2016: 264 - [i3]Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic:
A new correlation clustering method for cancer mutation analysis. CoRR abs/1601.06476 (2016) - 2015
- [j12]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): 230-248 (2015) - [c7]Anand Ramachandran, Yun Heo, Wen-mei W. Hwu, Jian Ma, Deming Chen:
FPGA accelerated DNA error correction. DATE 2015: 1371-1376 - [i2]S. M. Hossein Tabatabaei Yazdi, Yongbo Yuan, Jian Ma, Huimin Zhao, Olgica Milenkovic:
A Rewritable, Random-Access DNA-Based Storage System. CoRR abs/1505.02199 (2015) - [i1]S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic:
DNA-Based Storage: Trends and Methods. CoRR abs/1507.01611 (2015) - 2014
- [j11]Jaebum Kim, Jian Ma:
PSAR-Align: improving multiple sequence alignment using probabilistic sampling. Bioinform. 30(7): 1010-1012 (2014) - [j10]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): 1354-1362 (2014) - [j9]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: 37 (2014) - [j8]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) - 2013
- [j7]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): 1785-1790 (2013) - 2012
- [j6]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): S18 (2012) - [c6]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: 163-164 - 2011
- [j5]Yang Li, Jeremy Chien, David I. Smith, Jian Ma:
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinform. 27(12): 1708-1710 (2011) - [j4]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): 469-481 (2011) - [j3]Jian Ma:
Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges. J. Comput. Biol. 18(7): 879-893 (2011) - [c5]Jaebum Kim, Jian Ma:
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract). RECOMB 2011: 134-135 - 2010
- [c4]Jian Ma:
A probabilistic framework for inferring ancestral genomic orders. BIBM 2010: 179-184 - [c3]Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler:
Cactus Graphs for Genome Comparisons. RECOMB 2010: 410-425
2000 – 2009
- 2008
- [j2]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): 1007-1027 (2008) - [j1]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): 14254-14261 (2008) - 2007
- [c2]Guoliang Li, Jian Ma, Louxin Zhang:
Selecting Genomes for Reconstruction of Ancestral Genomes. RECOMB-CG 2007: 110-121 - [c1]Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler:
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. RECOMB-CG 2007: 122-135
Coauthor Index
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