Michael Q. Zhang

70 papers A* 1B 2Journal 62Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells.
Genom. Proteom. Bioinform.
Zhenyi Wang, Yuxin Miao, Hongjun Li, Wenyan Cheng, Minglei Shi, Gang Lv, Yating Zhu, Junyi Zhang, Tingting Tan, Jin Gu, Michael Q. Zhang, Jianfeng Li, Hai Fang, Zhu Chen, Saijuan Chen
2024 J jnl
Exact Power Spectrum in a Minimal Hybrid Model of Stochastic Gene Expression Oscillations.
SIAM J. Appl. Math.
Chen Jia, Hong Qian, Michael Q. Zhang
2023 J jnl
Dialog between artificial intelligence & natural intelligence.
Quant. Biol.
Michael Q. Zhang
2023 J jnl
Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection.
Comput. Biol. Medicine
Xiangting Guo, Yichu Guo, Hu Chen, Xiaoqing Liu, Ping-an He, Wenshu Li, Michael Q. Zhang, Qi Dai
2022 J jnl
HPVMD-C: a disease-based mutation database of human papillomavirus in China.
Database J. Biol. Databases Curation
Zhenyu Yang, Wenjing Yi, Jin Tao, Xiaoqing Liu, Michael Q. Zhang, Guiqian Chen, Qi Dai
2021 J jnl
A personal journey on cracking the genomic codes.
Quant. Biol.
Michael Q. Zhang
2021 J jnl
Deciphering hierarchical organization of topologically associated domains through change-point testing.
BMC Bioinform.
Haipeng Xing, Yingru Wu, Michael Q. Zhang, Yong Chen
2020 J jnl
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.
BMC Bioinform.
Rui Kong, Xinnan Xu, Xiaoqing Liu, Pingan He, Michael Q. Zhang, Qi Dai
2019 J jnl
Regulation by competition: a hidden layer of gene regulatory network.
Quant. Biol.
Lei Wei, Ye Yuan, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q. Zhang, Xiaowo Wang
2018 J jnl
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.
Bioinform.
Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q. Zhang, Xiangfeng Wang, Zhongfu Ni
2018 B conf
DE MERVLs are Enriched Around Two-Cell-Specific Genes During Zygotic Genome Activation in Mouse.
SMC
Yisi Li, Michael Q. Zhang, Wei Xie, Juntao Gao
2018 J jnl
MTGIpick allows robust identification of genomic islands from a single genome.
Briefings Bioinform.
Qi Dai, Chaohui Bao, Yabing Hai Hai, Sheng Ma, Tao Zhou, Cong Wang, Yunfei Wang, Wenwen Huo, Xiaoqing Liu, Yuhua Yao, Zhenyu Xuan, Min Chen, Michael Q. Zhang
2018 J jnl
NONCODEV5: a comprehensive annotation database for long non-coding RNAs.
Nucleic Acids Res.
Shuangsang Fang, LiLi Zhang, Jincheng Guo, Yiwei Niu, Yang Wu, Hui Li, Lianhe Zhao, Xiyuan Li, XueYi Teng, Xianhui Sun, Liang Sun, Michael Q. Zhang, Runsheng Chen, Yi Zhao
2017 J jnl
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes.
Bioinform.
Milos Pavlovic, Pradipta Ray, Kristina Pavlovic, Aaron Kotamarti, Min Chen, Michael Q. Zhang
2017 J jnl
HiC-3DViewer: a new tool to visualize Hi-C data in 3D space.
Quant. Biol.
Mohamed Nadhir Djekidel, Mengjie Wang, Michael Q. Zhang, Juntao Gao
2017 J jnl
Web3DMol: interactive protein structure visualization based on WebGL.
Nucleic Acids Res.
Maoxiang Shi, Juntao Gao, Michael Q. Zhang
2016 J jnl
Advances in computational ChIA-PET data analysis.
Quant. Biol.
Chao He, Guipeng Li, Mohamed Nadhir Djekidel, Yang Chen, Xiaowo Wang, Michael Q. Zhang
2016 J jnl
Developing bioimaging and quantitative methods to study 3D genome.
Quant. Biol.
Juntao Gao, Xusan Yang, Mohamed Nadhir Djekidel, Yang Wang, Peng Xi, Michael Q. Zhang
2016 J jnl
NONCODE 2016: an informative and valuable data source of long non-coding RNAs.
Nucleic Acids Res.
Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen
2015 J jnl
A novel method to identify topological domains using Hi-C data.
Quant. Biol.
Yang Wang, Yanjian Li, Juntao Gao, Michael Q. Zhang
2015 J jnl
ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.
Nucleic Acids Res.
Panwen Wang, Jing Qin, Yiming Qin, Yun Zhu, Lily Yan Wang, Mulin Jun Li, Michael Q. Zhang, Junwen Wang
2015 J jnl
Integrative analysis of 111 reference human epigenomes Open.
Nat.
Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis
2015 J jnl
MICC: an R package for identifying chromatin interactions from ChIA-PET data.
Bioinform.
Chao He, Michael Q. Zhang, Xiaowo Wang
2013 J jnl
Computational Identification of Active Enhancers in Model Organisms.
Genom. Proteom. Bioinform.
Chengqi Wang, Michael Q. Zhang, Zhihua Zhang
2013 J jnl
Population dynamics of cancer cells with cell state conversions.
Quant. Biol.
Da Zhou, Dingming Wu, Zhe Li, Minping Qian, Michael Q. Zhang
2013 J jnl
QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life.
Quant. Biol.
Michael Q. Zhang, Chao Tang
2012 — conf
Computational Modeling of Mammalian Promoters - (Invited Keynote Talk).
ISBRA
Michael Q. Zhang
2012 J jnl
Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data.
PLoS Comput. Biol.
Haipeng Xing, Yifan Mo, Will Liao, Michael Q. Zhang
2012 J jnl
Prioritizing Disease Genes and Understanding Disease Pathways.
Int. J. Knowl. Discov. Bioinform.
Xiaoyue Zhao, Lilia M. Iakoucheva, Michael Q. Zhang
2011 — conf
A method for finding novel associations between genome-wide copy number and dna methylation patterns.
GENSiPS
Man-Hung Eric Tang, Vinay Varadan, Sid Kamalakaran, Michael Q. Zhang, Nevenka Dimitrova, James Hicks
2011 J jnl
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.
Nucleic Acids Res.
Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, Junwen Wang
2011 — ch.
Computational Promoter Prediction in a Vertebrate Genome.
Handbook of Statistical Bioinformatics
Michael Q. Zhang
2011 J jnl
Correlated evolution of transcription factors and their binding sites.
Bioinform.
Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang, Junwen Wang
2011 J jnl
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.
BMC Bioinform.
Zhihua Zhang, Michael Q. Zhang
2011 J jnl
Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming.
BMC Syst. Biol.
Zhirui Hu, Minping Qian, Michael Q. Zhang
2011 J jnl
SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
Bioinform.
Jie Wu, Martin Akerman, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang
2010 J jnl
SFSSClass: an integrated approach for miRNA based tumor classification.
BMC Bioinform.
Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q. Zhang
2009 J jnl
Challenges in Understanding Genome-Wide DNA Methylation.
J. Comput. Sci. Technol.
Michael Q. Zhang, Andrew D. Smith
2009 J jnl
Gene set-based module discovery in the breast cancer transcriptome.
BMC Bioinform.
Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
2009 J jnl
The Seventh Asia Pacific Bioinformatics Conference (APBC2009).
BMC Bioinform.
Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang
2009 J jnl
Updates to the RMAP short-read mapping software.
Bioinform.
Andrew D. Smith, Wen-Yu Chung, Emily Hodges, Jude Kendall, Gregory J. Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang
2008 J jnl
Identification of Synaptic Targets of
PLoS Comput. Biol.
Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau
2008 J jnl
Identification of phylogenetically conserved microRNA
Bioinform.
Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li
2008 J jnl
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
BMC Bioinform.
Atsushi Niida, Andrew D. Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
2008 B conf
Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure.
IEEE Congress on Evolutionary Computation
Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Michael Q. Zhang, Xuegong Zhang
2008 J jnl
Using quality scores and longer reads improves accuracy of Solexa read mapping.
BMC Bioinform.
Andrew D. Smith, Zhenyu Xuan, Michael Q. Zhang
2008 J jnl
ZOOM! Zillions of oligos mapped.
Bioinform.
Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li
2007 J jnl
Computational analyses of eukaryotic promoters.
BMC Bioinform.
Michael Q. Zhang
2007 J jnl
Computational prediction of novel components of lung transcriptional networks.
Bioinform.
M. Juanita Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod
2007 J jnl
Computing exact
Bioinform.
Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang
2007 J jnl
Neighbor number, valley seeking and clustering.
Pattern Recognit. Lett.
Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li
2007 J jnl
OSCAR: One-class SVM for accurate recognition of
Bioinform.
Bo Jiang, Michael Q. Zhang, Xuegong Zhang
2007 J jnl
Statistical significance of cis-regulatory modules.
BMC Bioinform.
Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang
2007 J jnl
TRED: a transcriptional regulatory element database, new entries and other development.
Nucleic Acids Res.
C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang
2006 A* conf
Analysis and visualization of DNA spectrograms: open possibilities for the genome research.
ACM Multimedia
Nevenka Dimitrova, Yee Him Cheung, Michael Q. Zhang
2006 J jnl
Predicting methylation status of CpG islands in the human brain.
Bioinform.
Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang
2006 J jnl
Profiling alternatively spliced mRNA isoforms for prostate cancer classification.
BMC Bioinform.
Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu, Michael Q. Zhang
2005 — conf
Computational Molecular Biology of Genome Expression and Regulation.
PReMI
Michael Q. Zhang
2005 J jnl
DWE: Discriminating Word Enumerator.
Bioinform.
Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang
2005 — conf
Mining ChIP-chip data for transcription factor and cofactor binding sites.
ISMB (Supplement of Bioinformatics)
Andrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang
2005 J jnl
Similarity of position frequency matrices for transcription factor binding sites.
Bioinform.
Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang
2005 J jnl
TRED: a Transcriptional Regulatory Element Database and a platform for
Nucleic Acids Res.
Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang
2004 J jnl
Genome-wide prediction and analysis of function-specific transcription factor binding sites.
Silico Biol.
Fan Long, Hong Liu, Chang S. Hahn, Pavel Sumazin, Michael Q. Zhang, Asher Zilberstein
2003 J jnl
ESEfinder: a web resource to identify exonic splicing enhancers.
Nucleic Acids Res.
Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, Adrian R. Krainer
2001 J jnl
Identifying the 3'-terminal exon in human DNA.
Bioinform.
Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang
2001 J jnl
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes.
Bioinform.
Theresa Zhang, Michael Q. Zhang
2000 J jnl
Discriminant Analysis and Its Application in DNA Sequence Motif Recognition.
Briefings Bioinform.
Michael Q. Zhang
1999 J jnl
Promoter Analysis of Co-regulated Genes in the Yeast Genome.
Comput. Chem.
Michael Q. Zhang
1999 J jnl
SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
Bioinform.
Jian Zhu, Michael Q. Zhang
1993 J jnl
A weight array method for splicing signal analysis.
Comput. Appl. Biosci.
Michael Q. Zhang, T. G. Marr