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2020 – today
- 2024
[j61]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): 1204-1226 (2024)- 2023
- [j60]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: 107550 (2023) - [j59]Michael Q. Zhang:
Dialog between artificial intelligence & natural intelligence. Quant. Biol. 11(4): 359-362 (2023) - 2022
- [j58]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) - 2021
- [j57]Haipeng Xing, Yingru Wu, Michael Q. Zhang, Yong Chen:
Deciphering hierarchical organization of topologically associated domains through change-point testing. BMC Bioinform. 22(1): 183 (2021) - [j56]Michael Q. Zhang:
A personal journey on cracking the genomic codes. Quant. Biol. 9(1): 8 (2021) - 2020
- [j55]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): 159 (2020)
2010 – 2019
- 2019
- [j54]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): 110-121 (2019) - 2018
- [j53]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): 361-373 (2018) - [j52]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): 381-387 (2018) - [j51]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): D308-D314 (2018) - [c7]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: 3399-3404 - 2017
- [j50]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): 2986-2994 (2017) - [j49]Maoxiang Shi, Juntao Gao, Michael Q. Zhang:
Web3DMol: interactive protein structure visualization based on WebGL. Nucleic Acids Res. 45(Webserver-Issue): W523-W527 (2017) - [j48]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): 183-190 (2017) - 2016
- [j47]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): 203-208 (2016) - [j46]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): 129-147 (2016) - [j45]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): 217-225 (2016) - 2015
- [j44]Chao He, Michael Q. Zhang, Xiaowo Wang:
MICC: an R package for identifying chromatin interactions from ChIA-PET data. Bioinform. 31(23): 3832-3834 (2015) - [j43]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): W264-W269 (2015) - [j42]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): 317-330 (2015) - [j41]Yang Wang, Yanjian Li, Juntao Gao, Michael Q. Zhang:
A novel method to identify topological domains using Hi-C data. Quant. Biol. 3(2): 81-89 (2015) - 2013
- [j40]Chengqi Wang, Michael Q. Zhang, Zhihua Zhang:
Computational Identification of Active Enhancers in Model Organisms. Genom. Proteom. Bioinform. 11(3): 142-150 (2013) - [j39]Michael Q. Zhang, Chao Tang:
QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life. Quant. Biol. 1(1): 1-2 (2013) - [j38]Da Zhou, Dingming Wu, Zhe Li, Minping Qian, Michael Q. Zhang:
Population dynamics of cancer cells with cell state conversions. Quant. Biol. 1(3): 201-208 (2013) - 2012
- [j37]Xiaoyue Zhao, Lilia M. Iakoucheva, Michael Q. Zhang:
Prioritizing Disease Genes and Understanding Disease Pathways. Int. J. Knowl. Discov. Bioinform. 3(4): 31-49 (2012) - [j36]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) - [c6]Michael Q. Zhang:
Computational Modeling of Mammalian Promoters - (Invited Keynote Talk). ISBRA 2012: 330 - 2011
- [j35]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): 2972-2978 (2011) - [j34]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): 3010-3016 (2011) - [j33]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: 155 (2011) - [j32]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): S8 (2011) - [j31]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): 430-436 (2011) - [c5]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: 78-82 - [p1]Michael Q. Zhang:
Computational Promoter Prediction in a Vertebrate Genome. Handbook of Statistical Bioinformatics 2011: 73-85 - 2010
- [j30]Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q. Zhang:
SFSSClass: an integrated approach for miRNA based tumor classification. BMC Bioinform. 11(S-1): 22 (2010)
2000 – 2009
- 2009
- [j29]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): 2841-2842 (2009) - [j28]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) - [j27]Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang:
The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinform. 10(S-1) (2009) - [j26]Michael Q. Zhang, Andrew D. Smith:
Challenges in Understanding Genome-Wide DNA Methylation. J. Comput. Sci. Technol. 25(1): 26-34 (2009) - 2008
- [j25]Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li:
Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinform. 24(2): 165-171 (2008) - [j24]Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li:
ZOOM! Zillions of oligos mapped. Bioinform. 24(21): 2431-2437 (2008) - [j23]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) - [j22]Andrew D. Smith, Zhenyu Xuan, Michael Q. Zhang:
Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinform. 9 (2008) - [j21]Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, Josh Dubnau:
Identification of Synaptic Targets of Drosophila Pumilio. PLoS Comput. Biol. 4(2) (2008) - [c4]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: 1536-1543 - 2007
- [j20]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): 21-29 (2007) - [j19]Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang:
Computing exact P-values for DNA motifs. Bioinform. 23(5): 531-537 (2007) - [j18]Bo Jiang, Michael Q. Zhang, Xuegong Zhang:
OSCAR: One-class SVM for accurate recognition of cis-elements. Bioinform. 23(21): 2823-2828 (2007) - [j17]Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang:
Statistical significance of cis-regulatory modules. BMC Bioinform. 8 (2007) - [j16]Michael Q. Zhang:
Computational analyses of eukaryotic promoters. BMC Bioinform. 8(S-6) (2007) - [j15]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): 137-140 (2007) - [j14]Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li:
Neighbor number, valley seeking and clustering. Pattern Recognit. Lett. 28(2): 173-180 (2007) - 2006
- [j13]Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang:
Predicting methylation status of CpG islands in the human brain. Bioinform. 22(18): 2204-2209 (2006) - [j12]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: 202 (2006) - [c3]Nevenka Dimitrova, Yee Him Cheung, Michael Q. Zhang:
Analysis and visualization of DNA spectrograms: open possibilities for the genome research. ACM Multimedia 2006: 1017-1024 - 2005
- [j11]Pavel Sumazin, Gengxin Chen, Naoya Hata, Andrew D. Smith, Theresa Zhang, Michael Q. Zhang:
DWE: Discriminating Word Enumerator. Bioinform. 21(1): 31-38 (2005) - [j10]Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang:
Similarity of position frequency matrices for transcription factor binding sites. Bioinform. 21(3): 307-313 (2005) - [j9]Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang:
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res. 33(Database-Issue): 103-107 (2005) - [c2]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: 403-412 - [c1]Michael Q. Zhang:
Computational Molecular Biology of Genome Expression and Regulation. PReMI 2005: 31-38 - 2004
- [j8]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): 395-410 (2004) - 2003
- [j7]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): 3568-3571 (2003) - 2001
- [j6]Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang:
Identifying the 3'-terminal exon in human DNA. Bioinform. 17(7): 602-607 (2001) - [j5]Theresa Zhang, Michael Q. Zhang:
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinform. 17(12): 1232-1233 (2001) - 2000
- [j4]Michael Q. Zhang:
Discriminant Analysis and Its Application in DNA Sequence Motif Recognition. Briefings Bioinform. 1(4): 331-342 (2000)
1990 – 1999
- 1999
- [j3]Jian Zhu, Michael Q. Zhang:
SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinform. 15(7): 607-611 (1999) - [j2]Michael Q. Zhang:
Promoter Analysis of Co-regulated Genes in the Yeast Genome. Comput. Chem. 23(3-4): 233-250 (1999) - 1993
- [j1]Michael Q. Zhang, T. G. Marr:
A weight array method for splicing signal analysis. Comput. Appl. Biosci. 9(5): 499-509 (1993)
Coauthor Index
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