Michael Q. Zhang

According to our database, Michael Q. Zhang authored at least 68 papers between 1993 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Dialog between artificial intelligence & natural intelligence.

Michael Q. Zhang

Quant. Biol., December, 2023

Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection.

Xiangting Guo, Yichu Guo, Hu Chen, Xiaoqing Liu, Ping-An He, Wenshu Li, Michael Q. Zhang, Qi Dai

Comput. Biol. Medicine, November, 2023

2022

HPVMD-C: a disease-based mutation database of human papillomavirus in China.

Zhenyu Yang, Wenjing Yi, Jin Tao, Xiaoqing Liu, Michael Q. Zhang, Guiqian Chen, Qi Dai

Database J. Biol. Databases Curation, 2022

2021

A personal journey on cracking the genomic codes.

Michael Q. Zhang

Quant. Biol., 2021

Deciphering hierarchical organization of topologically associated domains through change-point testing.

Haipeng Xing, Yingru Wu, Michael Q. Zhang, Yong Chen

BMC Bioinform., 2021

2020

2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.

Rui Kong, Xinnan Xu, Xiaoqing Liu, Pingan He, Michael Q. Zhang, Qi Dai

BMC Bioinform., 2020

2019

Regulation by competition: a hidden layer of gene regulatory network.

Lei Wei, Ye Yuan, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q. Zhang, Xiaowo Wang

Quant. Biol., 2019

2018

NONCODEV5: a comprehensive annotation database for long non-coding RNAs.

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

Nucleic Acids Res., 2018

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q. Zhang, Xiangfeng Wang, Zhongfu Ni

Bioinform., 2018

MTGIpick allows robust identification of genomic islands from a single genome.

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

Briefings Bioinform., 2018

DE MERVLs are Enriched Around Two-Cell-Specific Genes During Zygotic Genome Activation in Mouse.

Yisi Li, Michael Q. Zhang, Wei Xie, Juntao Gao

Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, 2018

2017

HiC-3DViewer: a new tool to visualize Hi-C data in 3D space.

Mohamed Nadhir Djekidel, Mengjie Wang, Michael Q. Zhang, Juntao Gao

Quant. Biol., 2017

Web3DMol: interactive protein structure visualization based on WebGL.

Maoxiang Shi, Juntao Gao, Michael Q. Zhang

Nucleic Acids Res., 2017

DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes.

Milos Pavlovic, Pradipta Ray, Kristina Pavlovic, Aaron Kotamarti, Min Chen, Michael Q. Zhang

Bioinform., 2017

2016

Advances in computational ChIA-PET data analysis.

Chao He, Guipeng Li, Mohamed Nadhir Djekidel, Yang Chen, Xiaowo Wang, Michael Q. Zhang

Quant. Biol., 2016

Developing bioimaging and quantitative methods to study 3D genome.

Juntao Gao, Xusan Yang, Mohamed Nadhir Djekidel, Yang Wang, Peng Xi, Michael Q. Zhang

Quant. Biol., 2016

NONCODE 2016: an informative and valuable data source of long non-coding RNAs.

Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen

Nucleic Acids Res., 2016

2015

A novel method to identify topological domains using Hi-C data.

Yang Wang, Yanjian Li, Juntao Gao, Michael Q. Zhang

Quant. Biol., 2015

Integrative analysis of 111 reference human epigenomes Open.

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

Nat., 2015

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.

Panwen Wang, Jing Qin, Yiming Qin, Yun Zhu, Lily Yan Wang, Mulin Jun Li, Michael Q. Zhang, Junwen Wang

Nucleic Acids Res., 2015

MICC: an R package for identifying chromatin interactions from ChIA-PET data.

Chao He, Michael Q. Zhang, Xiaowo Wang

Bioinform., 2015

2013

Population dynamics of cancer cells with cell state conversions.

Da Zhou, Dingming Wu, Zhe Li, Minping Qian, Michael Q. Zhang

Quant. Biol., 2013

QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life.

Michael Q. Zhang, Chao Tang

Quant. Biol., 2013

Computational Identification of Active Enhancers in Model Organisms.

Chengqi Wang, Michael Q. Zhang, Zhihua Zhang

Genom. Proteom. Bioinform., 2013

2012

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data.

Haipeng Xing, Yifan Mo, Will Liao, Michael Q. Zhang

PLoS Comput. Biol., 2012

Prioritizing Disease Genes and Understanding Disease Pathways.

Xiaoyue Zhao, Lilia M. Iakoucheva, Michael Q. Zhang

Int. J. Knowl. Discov. Bioinform., 2012

Computational Modeling of Mammalian Promoters - (Invited Keynote Talk).

Michael Q. Zhang

Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

2011

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.

Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, Junwen Wang

Nucleic Acids Res., 2011

Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming.

Zhirui Hu, Minping Qian, Michael Q. Zhang

BMC Syst. Biol., 2011

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.

Zhihua Zhang, Michael Q. Zhang

BMC Bioinform., 2011

Correlated evolution of transcription factors and their binding sites.

Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang, Junwen Wang

Bioinform., 2011

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Jie Wu, Martin Akerman, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang

Bioinform., 2011

A method for finding novel associations between genome-wide copy number and dna methylation patterns.

Man-Hung Eric Tang, Vinay Varadan, Sid Kamalakaran, Michael Q. Zhang, Nevenka Dimitrova, James Hicks

Proceedings of the 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, 2011

Computational Promoter Prediction in a Vertebrate Genome.

Michael Q. Zhang

Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010

SFSSClass: an integrated approach for miRNA based tumor classification.

Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q. Zhang

BMC Bioinform., 2010

2009

Challenges in Understanding Genome-Wide DNA Methylation.

Michael Q. Zhang, Andrew D. Smith

J. Comput. Sci. Technol., 2009

The Seventh Asia Pacific Bioinformatics Conference (APBC2009).

Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang

BMC Bioinform., 2009

Gene set-based module discovery in the breast cancer transcriptome.

Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama

BMC Bioinform., 2009

Updates to the RMAP short-read mapping software.

Andrew D. Smith, Wen-Yu Chung, Emily Hodges, Jude Kendall, Gregory J. Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang

Bioinform., 2009

2008

Identification of Synaptic Targets of <i>Drosophila</i> Pumilio.

Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau

PLoS Comput. Biol., 2008

Using quality scores and longer reads improves accuracy of Solexa read mapping.

Andrew D. Smith, Zhenyu Xuan, Michael Q. Zhang

BMC Bioinform., 2008

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.

Atsushi Niida, Andrew D. Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama

BMC Bioinform., 2008

Identification of phylogenetically conserved microRNA <i>cis</i>-regulatory elements across 12 <i>Drosophila</i> species.

Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li

Bioinform., 2008

ZOOM! Zillions of oligos mapped.

Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li

Bioinform., 2008

Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure.

Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Michael Q. Zhang, Xuegong Zhang

Proceedings of the IEEE Congress on Evolutionary Computation, 2008

2007

Neighbor number, valley seeking and clustering.

Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li

Pattern Recognit. Lett., 2007

TRED: a transcriptional regulatory element database, new entries and other development.

C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang

Nucleic Acids Res., 2007

Computational analyses of eukaryotic promoters.

Michael Q. Zhang

BMC Bioinform., 2007

Statistical significance of cis-regulatory modules.

Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang

BMC Bioinform., 2007

Computing exact <i>P</i>-values for DNA motifs.

Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang

Bioinform., 2007

Computational prediction of novel components of lung transcriptional networks.

M. Juanita Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod

Bioinform., 2007

OSCAR: One-class SVM for accurate recognition of <i>cis</i>-elements.

Bo Jiang, Michael Q. Zhang, Xuegong Zhang

Bioinform., 2007

2006

Profiling alternatively spliced mRNA isoforms for prostate cancer classification.

Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu, Michael Q. Zhang

BMC Bioinform., 2006

Predicting methylation status of CpG islands in the human brain.

Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang

Bioinform., 2006

Analysis and visualization of DNA spectrograms: open possibilities for the genome research.

Nevenka Dimitrova, Yee Him Cheung, Michael Q. Zhang

Proceedings of the 14th ACM International Conference on Multimedia, 2006

2005

TRED: a Transcriptional Regulatory Element Database and a platform for <i>in silico</i> gene regulation studies.

Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang

Nucleic Acids Res., 2005

DWE: Discriminating Word Enumerator.

Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang

Bioinform., 2005

Similarity of position frequency matrices for transcription factor binding sites.

Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang

Bioinform., 2005

Computational Molecular Biology of Genome Expression and Regulation.

Michael Q. Zhang

Proceedings of the Pattern Recognition and Machine Intelligence, 2005

Mining ChIP-chip data for transcription factor and cofactor binding sites.

Andrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004

Genome-wide prediction and analysis of function-specific transcription factor binding sites.

Fan Long, Hong Liu, Chang S. Hahn, Pavel Sumazin, Michael Q. Zhang, Asher Zilberstein

Silico Biol., 2004

2003

ESEfinder: a web resource to identify exonic splicing enhancers.

Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, Adrian R. Krainer

Nucleic Acids Res., 2003

2001

Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes.

Theresa Zhang, Michael Q. Zhang

Bioinform., 2001

Identifying the 3'-terminal exon in human DNA.

Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang

Bioinform., 2001

2000

Discriminant Analysis and Its Application in DNA Sequence Motif Recognition.

Michael Q. Zhang

Briefings Bioinform., 2000

1999

Promoter Analysis of Co-regulated Genes in the Yeast Genome.

Michael Q. Zhang

Comput. Chem., 1999

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

Jian Zhu, Michael Q. Zhang

Bioinform., 1999

1993

A weight array method for splicing signal analysis.

Michael Q. Zhang, T. G. Marr

Comput. Appl. Biosci., 1993