HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. - Zhaohui S. Qin; Jianjun Yu; Jincheng Shen; Christopher A. Maher; Ming Hu 001; Shanker Kalyana-Sundaram; Jindan Yu; Arul M. Chinnaiyan (BMC Bioinform., 2010)

HiCNorm: removing biases in Hi-C data via Poisson regression. - Ming Hu 001; Ke Deng; Siddarth Selvaraj; Zhaohui S. Qin; Bing Ren; Jun S. Liu (Bioinform., 2012)

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. - Ming Hu 001; Yu Zhu; Jeremy M. G. Taylor; Jun S. Liu; Zhaohui S. Qin (Bioinform., 2012)

Bayesian Inference of Spatial Organizations of Chromosomes. - Ming Hu 001; Ke Deng; Zhaohui S. Qin; Jesse R. Dixon; Siddarth Selvaraj; Jennifer Fang; Bing Ren; Jun S. Liu (PLoS Comput. Biol., 2013)

Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. - Ming Hu 001; Ke Deng; Zhaohui S. Qin; Jun S. Liu (Quant. Biol., 2013)

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. - Zheng Xu 010; Guosheng Zhang; Fulai Jin; Mengjie Chen; Terrence S. Furey; Patrick F. Sullivan; Zhaohui S. Qin; Ming Hu 001; Yun Li (Bioinform., 2016)

FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. - Zheng Xu 010; Guosheng Zhang; Cong Wu; Yun Li; Ming Hu 001 (Bioinform., 2016)

HUGIn: Hi-C Unifying Genomic Interrogator. - Joshua S. Martin; Zheng Xu 010; Alex P. Reiner; Karen L. Mohlke; Patrick F. Sullivan; Bing Ren; Ming Hu 001; Yun Li (Bioinform., 2017)

DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. - Zhe Sun; Ting Wang 003; Ke Deng; Xiao-Feng Wang; Robert Lafyatis; Ying Ding 003; Ming Hu 001; Wei Chen 074 (Bioinform., 2018)

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. - Ivan Juric; Miao Yu; Armen Abnousi; Ramya Raviram; Rongxin Fang; Yuan Zhao; Yan-Xiao Zhang; Yunjiang Qiu; Yuchen Yang; Yun Li; Bing Ren; Ming Hu 001 (PLoS Comput. Biol., 2019)

Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model. - Rongrong Zhang; Ming Hu 001; Yu Zhu; Zhaohui S. Qin; Ke Deng; Jun S. Liu (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. - Le Huang; Yuchen Yang; Gang Li 034; Minzhi Jiang; Jia Wen; Armen Abnousi; Jonathan D. Rosen; Ming Hu 001; Yun Li (Briefings Bioinform., 2022)

SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data. - Lindsay Lee; Miao Yu; Xiaoqi Li 018; Chenxu Zhu; Yanxiao Zhang; Hongyu Yu; Ziyin Chen; Shreya Mishra; Bing Ren; Yun Li; Ming Hu 001 (Briefings Bioinform., 2023)

SnapHiC-G: identifying long-range enhancer-promoter interactions from single-cell Hi-C data via a global background model. - Weifang Liu; Wujuan Zhong; Paola Giusti-Rodríguez; Zhiyun Jiang; Geoffery W. Wang; Huaigu Sun; Ming Hu 001; Yun Li (Briefings Bioinform., 2024)