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Jian 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
— Shanghai Ocean University, College of Marine Sciences, China
- Jian Ma 0005
- Jian Ma 0006
- Jian Ma 0007
- Jian Ma 0008
- Jian Ma 0009
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2020 – today
- 2024
- [e2]Jian Ma
Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings. Lecture Notes in Computer Science 14758, Springer 2024, ISBN 978-1-0716-3988-7 [contents] - 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
Assessing the contribution of tumor mutational phenotypes to cancer progression risk. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j26]Yang Zhang
Cancer mutational signatures representation by large-scale context embedding. Bioinform. 36(Supplement-1): i309-i316 (2020) - [j25]Yifeng Tao
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. Bioinform. 36(Supplement-1): i407-i416 (2020) - [j24]Neeraj Kumar
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
Rotation equivariant and invariant neural networks for microscopy image analysis. Bioinform. 35(14): i530-i537 (2019) - [j22]Michael P. Snyder
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
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
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
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
Covariate Adjusted Precision Matrix Estimation via Nonconvex Optimization. ICML 2018: 921-930 - [c14]Vaishnavi Subramanian
Correlating cellular features with gene expression using CCA. ISBI 2018: 805-808 - [c13]Vaishnavi Subramanian
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
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
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
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
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
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
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
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
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinform. 27(12): 1708-1710 (2011) - [j4]Benedict Paten, Mark Diekhans
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
Cactus Graphs for Genome Comparisons. RECOMB 2010: 410-425
2000 – 2009
- 2008
- [j2]Jian Ma
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. J. Comput. Biol. 15(8): 1007-1027 (2008) - [j1]Jian Ma
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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last updated on 2024-11-13 23:49 CET by the dblp team
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