Selecting Genomes for Reconstruction of Ancestral Genomes. - Guoliang Li 002; Jian Ma 004; Louxin Zhang (RECOMB-CG, 2007)

A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. - Jian Ma 004; Aakrosh Ratan; Louxin Zhang; Webb Miller; David Haussler (RECOMB-CG, 2007)

DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. - Jian Ma 004; Aakrosh Ratan; Brian J. Raney; Bernard B. Suh; Louxin Zhang; Webb Miller; David Haussler (J. Comput. Biol., 2008)

The infinite sites model of genome evolution. - Jian Ma 004; Aakrosh Ratan; Brian J. Raney; Bernard B. Suh; Webb Miller; David Haussler (Proc. Natl. Acad. Sci. USA, 2008)

A probabilistic framework for inferring ancestral genomic orders. - Jian Ma 004 (BIBM, 2010)

PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling - (Extended Abstract). - Jaebum Kim; Jian Ma 004 (RECOMB, 2011)

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. - Yang Li; Jeremy Chien; David I. Smith; Jian Ma 004 (Bioinform., 2011)

Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges. - Jian Ma 004 (J. Comput. Biol., 2011)

Cactus Graphs for Genome Comparisons. - Benedict Paten; Mark Diekhans; Dent Earl; John St. John; Jian Ma 004; Bernard B. Suh; David Haussler (J. Comput. Biol., 2011)

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 004 (RECOMB, 2012)

TIGER: tiled iterative genome assembler. - Xiaolong Wu; Yun Heo; Izzat El Hajj; Wen-mei W. Hwu; Deming Chen; Jian Ma 004 (BMC Bioinform., 2012)

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 004 (Proc. Natl. Acad. Sci. USA, 2013)

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads. - Yun Heo; Xiaolong Wu; Deming Chen; Jian Ma 004; Wen-mei W. Hwu (Bioinform., 2014)

PSAR-Align: improving multiple sequence alignment using probabilistic sampling. - Jaebum Kim; Jian Ma 004 (Bioinform., 2014)

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. - Yiyi Liu; Quanquan Gu; Jack P. Hou; Jiawei Han 001; Jian Ma 004 (BMC Bioinform., 2014)

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework. - Ken Daigoro Yokoyama; Yang Zhang 042; Jian Ma 004 (PLoS Comput. Biol., 2014)

FPGA accelerated DNA error correction. - Anand Ramachandran 001; Yun Heo; Wen-mei W. Hwu; Jian Ma 004; Deming Chen (DATE, 2015)

A Rewritable, Random-Access DNA-Based Storage System. - S. M. Hossein Tabatabaei Yazdi; Yongbo Yuan; Jian Ma 004; Huimin Zhao; Olgica Milenkovic (CoRR, 2015)

DNA-Based Storage: Trends and Methods. - S. M. Hossein Tabatabaei Yazdi; Han Mao Kiah; Eva Ruiz Garcia; Jian Ma 004; Huimin Zhao; Olgica Milenkovic (IEEE Trans. Mol. Biol. Multi Scale Commun., 2015)

Allele-Specific Quantification of Structural Variations in Cancer Genomes. - Yang Li; Shiguo Zhou; David C. Schwartz; Jian Ma 004 (RECOMB, 2016)

BLESS 2: accurate, memory-efficient and fast error correction method. - Yun Heo; Anand Ramachandran 001; Wen-mei W. Hwu; Jian Ma 004; Deming Chen (Bioinform., 2016)

A new correlation clustering method for cancer mutation analysis. - Jack P. Hou; Amin Emad; Gregory J. Puleo; Jian Ma 004; Olgica Milenkovic (Bioinform., 2016)

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. - Ashok Rajaraman; Jian Ma 004 (BMC Bioinform., 2016)

Identifying micro-inversions using high-throughput sequencing reads. - Feifei He; Yang Li; Yu-Hang Tang; Jian Ma 004; Huaiqiu Zhu (BMC Genom., 2016)

Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimization. - Pan Xu 002; Jian Ma 004; Quanquan Gu (NIPS, 2017)

Towards Recovering Allele-Specific Cancer Genome Graphs. - Ashok Rajaraman; Jian Ma 004 (RECOMB, 2017)

Exploiting sequence-based features for predicting enhancer-promoter interactions. - Yang Yang 094; Ruochi Zhang; Shashank Singh 005; Jian Ma 004 (Bioinform., 2017)

Speeding Up Latent Variable Gaussian Graphical Model Estimation via Nonconvex Optimizations. - Pan Xu 002; Jian Ma 004; Quanquan Gu (CoRR, 2017)

On the Reconstruction Risk of Convolutional Sparse Dictionary Learning. - Shashank Singh 005; Barnabás Póczos; Jian Ma 004 (CoRR, 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 004; Marta Farre (IEEE Trans. Vis. Comput. Graph., 2017)

Minimax Reconstruction Risk of Convolutional Sparse Dictionary Learning. - Shashank Singh 005; Barnabás Póczos; Jian Ma 004 (AISTATS, 2018)

Covariate Adjusted Precision Matrix Estimation via Nonconvex Optimization. - Jinghui Chen; Pan Xu 002; Lingxiao Wang 001; Jian Ma 004; Quanquan Gu (ICML, 2018)

Correlating cellular features with gene expression using CCA. - Vaishnavi Subramanian; Benjamin Chidester; Jian Ma 004; Minh N. Do (ISBI, 2018)

Integration of Spatial Distribution in Imaging-Genetics. - Vaishnavi Subramanian; Weizhao Tang; Benjamin Chidester; Jian Ma 004; Minh N. Do (MICCAI (2), 2018)

Discriminative bag-of-cells for imaging-genomics. - Benjamin Chidester; Minh N. Do; Jian Ma 004 (PSB, 2018)

Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. - Yang Yang 094; Quanquan Gu; Takayo Sasaki; Julianna Crivello; Rachel O'Neill; David M. Gilbert; Jian Ma 004 (RECOMB, 2018)

Predicting CTCF-mediated chromatin loops using CTCF-MP. - Ruochi Zhang; Yuchuan Wang; Yang Yang 094; Yang Zhang 042; Jian Ma 004 (Bioinform., 2018)

Rotation Equivariance and Invariance in Convolutional Neural Networks. - Benjamin Chidester; Minh N. Do; Jian Ma 004 (CoRR, 2018)

Toward Recovering Allele-specific Cancer Genome Graphs. - Ashok Rajaraman; Jian Ma 004 (J. Comput. Biol., 2018)

Enhanced Rotation-Equivariant U-Net for Nuclear Segmentation. - Benjamin Chidester; That-Vinh Ton; Minh-Triet Tran; Jian Ma 004; Minh N. Do (CVPR Workshops, 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 004; Russell Schwartz (ISMCO, 2019)

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. - Yang Yang 094; Yang Zhang 042; Bing Ren; Jesse R. Dixon; Jian Ma 004 (RECOMB, 2019)

Rotation equivariant and invariant neural networks for microscopy image analysis. - Benjamin Chidester; Tianming Zhou; Minh N. Do; Jian Ma 004 (Bioinform., 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; et al. (Nat., 2019)

Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. - Shashank Singh 005; Yang Yang 094; Barnabás Póczos; Jian Ma 004 (Quant. Biol., 2019)

Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. - Ruochi Zhang; Yuesong Zou; Jian Ma 004 (ICLR, 2020)

Probing Multi-way Chromatin Interaction with Hypergraph Representation Learning. - Ruochi Zhang; Jian Ma 004 (RECOMB, 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 004; Russell Schwartz (Bioinform., 2020)

Cancer mutational signatures representation by large-scale context embedding. - Yang Zhang 042; Yunxuan Xiao; Muyu Yang; Jian Ma 004 (Bioinform., 2020)

A Multi-Organ Nucleus Segmentation Challenge. - Neeraj Kumar 002; Ruchika Verma; Deepak Anand; Yanning Zhou 001; Omer Fahri Onder; Efstratios Tsougenis; Hao Chen 011; Pheng-Ann Heng; Jiahui Li 005; Zhiqiang Hu; Yunzhi Wang; Navid Alemi Koohbanani; et al. (IEEE Trans. Medical Imaging, 2020)

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 003; Jian Ma 004; Russell Schwartz (PLoS Comput. Biol., 2021)

Concert: Genome-Wide Prediction of Sequence Elements That Modulate DNA Replication Timing. - Yang Yang 094; Yuchuan Wang; Yang Zhang 042; Jian Ma 004 (RECOMB, 2022)

Ultrafast and Interpretable Single-Cell 3D Genome Analysis with Fast-Higashi. - Ruochi Zhang; Tianming Zhou; Jian Ma 004 (RECOMB, 2022)

Guest Editorial for Selected Papers From ACM-BCB 2019. - Jian Ma 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

UNADON: transformer-based model to predict genome-wide chromosome spatial position. - Muyu Yang; Jian Ma 004 (Bioinform., 2023)