Michael Q. Zhang

Publication Activity (10 Years)

Years Active: 1993-2024
Publications (10 Years): 18

Top Topics

Gene Regulatory Networks

Gene Expression

Natural Intelligence

Top Venues

Nucleic Acids Res.

Publications

Chen Jia, Hong Qian, Michael Q. Zhang
Exact Power Spectrum in a Minimal Hybrid Model of Stochastic Gene Expression Oscillations. SIAM J. Appl. Math. 84 (3) (2024)
Michael Q. Zhang
Dialog between artificial intelligence & natural intelligence. Quant. Biol. 11 (4) (2023)
Xiangting Guo, Yichu Guo, Hu Chen, Xiaoqing Liu, Ping-An He, Wenshu Li, Michael Q. Zhang, Qi Dai
Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection. Comput. Biol. Medicine 166 (2023)
Zhenyu Yang, Wenjing Yi, Jin Tao, Xiaoqing Liu, Michael Q. Zhang, Guiqian Chen, Qi Dai
HPVMD-C: a disease-based mutation database of human papillomavirus in China. Database J. Biol. Databases Curation 2022 (2022) (2022)
Haipeng Xing, Yingru Wu, Michael Q. Zhang, Yong Chen
Deciphering hierarchical organization of topologically associated domains through change-point testing. BMC Bioinform. 22 (1) (2021)
Michael Q. Zhang
A personal journey on cracking the genomic codes. Quant. Biol. 9 (1) (2021)
Rui Kong, Xinnan Xu, Xiaoqing Liu, Pingan He, Michael Q. Zhang, Qi Dai
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. BMC Bioinform. 21 (1) (2020)
Lei Wei, Ye Yuan, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q. Zhang, Xiaowo Wang
Regulation by competition: a hidden layer of gene regulatory network. Quant. Biol. 7 (2) (2019)
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
NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res. 46 (Database-Issue) (2018)
Yisi Li, Michael Q. Zhang, Wei Xie, Juntao Gao
DE MERVLs are Enriched Around Two-Cell-Specific Genes During Zygotic Genome Activation in Mouse. SMC (2018)
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
MTGIpick allows robust identification of genomic islands from a single genome. Briefings Bioinform. 19 (3) (2018)
Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q. Zhang, Xiangfeng Wang, Zhongfu Ni
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinform. 34 (3) (2018)
Milos Pavlovic, Pradipta Ray, Kristina Pavlovic, Aaron Kotamarti, Min Chen, Michael Q. Zhang
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. Bioinform. 33 (19) (2017)
Mohamed Nadhir Djekidel, Mengjie Wang, Michael Q. Zhang, Juntao Gao
HiC-3DViewer: a new tool to visualize Hi-C data in 3D space. Quant. Biol. 5 (2) (2017)
Maoxiang Shi, Juntao Gao, Michael Q. Zhang
Web3DMol: interactive protein structure visualization based on WebGL. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen
NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res. 44 (Database-Issue) (2016)
Juntao Gao, Xusan Yang, Mohamed Nadhir Djekidel, Yang Wang, Peng Xi, Michael Q. Zhang
Developing bioimaging and quantitative methods to study 3D genome. Quant. Biol. 4 (2) (2016)
Chao He, Guipeng Li, Mohamed Nadhir Djekidel, Yang Chen, Xiaowo Wang, Michael Q. Zhang
Advances in computational ChIA-PET data analysis. Quant. Biol. 4 (3) (2016)
Chao He, Michael Q. Zhang, Xiaowo Wang
MICC: an R package for identifying chromatin interactions from ChIA-PET data. Bioinform. 31 (23) (2015)
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
Integrative analysis of 111 reference human epigenomes Open. Nat. 518 (7539) (2015)
Yang Wang, Yanjian Li, Juntao Gao, Michael Q. Zhang
A novel method to identify topological domains using Hi-C data. Quant. Biol. 3 (2) (2015)
Panwen Wang, Jing Qin, Yiming Qin, Yun Zhu, Lily Yan Wang, Mulin Jun Li, Michael Q. Zhang, Junwen Wang
ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Michael Q. Zhang, Chao Tang
QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life. Quant. Biol. 1 (1) (2013)
Da Zhou, Dingming Wu, Zhe Li, Minping Qian, Michael Q. Zhang
Population dynamics of cancer cells with cell state conversions. Quant. Biol. 1 (3) (2013)
Chengqi Wang, Michael Q. Zhang, Zhihua Zhang
Computational Identification of Active Enhancers in Model Organisms. Genom. Proteom. Bioinform. 11 (3) (2013)
Michael Q. Zhang
Computational Modeling of Mammalian Promoters - (Invited Keynote Talk). ISBRA (2012)
Xiaoyue Zhao, Lilia M. Iakoucheva, Michael Q. Zhang
Prioritizing Disease Genes and Understanding Disease Pathways. Int. J. Knowl. Discov. Bioinform. 3 (4) (2012)
Haipeng Xing, Yifan Mo, Will Liao, Michael Q. Zhang
Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data. PLoS Comput. Biol. 8 (7) (2012)
Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, Junwen Wang
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. 39 (Web-Server-Issue) (2011)
Jie Wu, Martin Akerman, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang
SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinform. 27 (21) (2011)
Man-Hung Eric Tang, Vinay Varadan, Sid Kamalakaran, Michael Q. Zhang, Nevenka Dimitrova, James Hicks
A method for finding novel associations between genome-wide copy number and dna methylation patterns. GENSiPS (2011)
Zhirui Hu, Minping Qian, Michael Q. Zhang
Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. BMC Syst. Biol. 5 (S-2) (2011)
Shu Yang, Hari Krishna Yalamanchili, Xinran Li, Kwok-Ming Yao, Pak Chung Sham, Michael Q. Zhang, Junwen Wang
Correlated evolution of transcription factors and their binding sites. Bioinform. 27 (21) (2011)
Zhihua Zhang, Michael Q. Zhang
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinform. 12 (2011)
Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q. Zhang
SFSSClass: an integrated approach for miRNA based tumor classification. BMC Bioinform. 11 (S-1) (2010)
Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
Gene set-based module discovery in the breast cancer transcriptome. BMC Bioinform. 10 (2009)
Andrew D. Smith, Wen-Yu Chung, Emily Hodges, Jude Kendall, Gregory J. Hannon, James Hicks, Zhenyu Xuan, Michael Q. Zhang
Updates to the RMAP short-read mapping software. Bioinform. 25 (21) (2009)
Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang
The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinform. 10 (S-1) (2009)
Michael Q. Zhang, Andrew D. Smith
Challenges in Understanding Genome-Wide DNA Methylation. J. Comput. Sci. Technol. 25 (1) (2009)
Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li
species. Bioinform. 24 (2) (2008)
Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li
ZOOM! Zillions of oligos mapped. Bioinform. 24 (21) (2008)
Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau
Pumilio. PLoS Comput. Biol. 4 (2) (2008)
Andrew D. Smith, Zhenyu Xuan, Michael Q. Zhang
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinform. 9 (2008)
Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Michael Q. Zhang, Xuegong Zhang
Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure. IEEE Congress on Evolutionary Computation (2008)
Atsushi Niida, Andrew D. Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinform. 9 (2008)
Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li
Neighbor number, valley seeking and clustering. Pattern Recognit. Lett. 28 (2) (2007)
Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang
Statistical significance of cis-regulatory modules. BMC Bioinform. 8 (2007)
Michael Q. Zhang
Computational analyses of eukaryotic promoters. BMC Bioinform. 8 (S-6) (2007)
C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang
TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 35 (Database-Issue) (2007)
Bo Jiang, Michael Q. Zhang, Xuegong Zhang
-elements. Bioinform. 23 (21) (2007)
Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang
-values for DNA motifs. Bioinform. 23 (5) (2007)
M. Juanita Martinez, Andrew D. Smith, Bilan Li, Michael Q. Zhang, Kevin S. Harrod
Computational prediction of novel components of lung transcriptional networks. Bioinform. 23 (1) (2007)
Nevenka Dimitrova, Yee Him Cheung, Michael Q. Zhang
Analysis and visualization of DNA spectrograms: open possibilities for the genome research. ACM Multimedia (2006)
Chaolin Zhang, Hai-Ri Li, Jian-Bing Fan, Jessica Wang-Rodriguez, Tracy Downs, Xiang-Dong Fu, Michael Q. Zhang
Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinform. 7 (2006)
Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang
Predicting methylation status of CpG islands in the human brain. Bioinform. 22 (18) (2006)
Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang
Similarity of position frequency matrices for transcription factor binding sites. Bioinform. 21 (3) (2005)
Andrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang
Mining ChIP-chip data for transcription factor and cofactor binding sites. ISMB (Supplement of Bioinformatics) (2005)
Michael Q. Zhang
Computational Molecular Biology of Genome Expression and Regulation. PReMI (2005)
Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang
DWE: Discriminating Word Enumerator. Bioinform. 21 (1) (2005)
Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang
gene regulation studies. Nucleic Acids Res. 33 (Database-Issue) (2005)
Fan Long, Hong Liu, Chang S. Hahn, Pavel Sumazin, Michael Q. Zhang, Asher Zilberstein
Genome-wide prediction and analysis of function-specific transcription factor binding sites. Silico Biol. 4 (4) (2004)
Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, Adrian R. Krainer
ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 31 (13) (2003)
Theresa Zhang, Michael Q. Zhang
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinform. 17 (12) (2001)
Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang
Identifying the 3'-terminal exon in human DNA. Bioinform. 17 (7) (2001)
Michael Q. Zhang
Discriminant Analysis and Its Application in DNA Sequence Motif Recognition. Briefings Bioinform. 1 (4) (2000)
Jian Zhu, Michael Q. Zhang
SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinform. 15 (7) (1999)
Michael Q. Zhang
Promoter Analysis of Co-regulated Genes in the Yeast Genome. Comput. Chem. 23 (3-4) (1999)
Michael Q. Zhang, T. G. Marr
A weight array method for splicing signal analysis. Comput. Appl. Biosci. 9 (5) (1993)