2010

• Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells.
  Jun Cai, Dan Xie, Zhewen Fan, John Marden, Wing H. Wong, Sheng Zhong.
  PLoS Computational Biology, accepted.

2009

• Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells.
  Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, Wing H. Wong, Huck H. Ng, Sheng Zhong.
  PLoS Computational Biology, 5(12): e1000607. Text
   
• A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data
  Xin He, Chieh-Chun Chen, Feng Hong, Fang Fang, Saurabh Sinha, Huck-Hui Ng, Sheng Zhong.
  PLoS ONE, 4(12): e8155. Text. This paper was presented on RECOMB Regulatory Genomics 09. Software
   
• SeqMapReduce: software and web service for accelerating sequence mapping.
  Yanen Li, Sheng Zhong.
  CAMDA 09, accepted. Software
   
• Transcriptomic Profiling of Central Nervous System Regions in Three Species of Honey Bee during Dance Communication Behavior.
  Moushumi Sen Sarma, Sandra Rodriguez-Zas, Feng Hong, Sheng Zhong, Gene E Robinson.
  PLoS ONE 4(7): e6408. TEXT
   

2008

• Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.
  Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng and Sheng Zhong.
  Genome Research. 18:1325-1335. TEXT. Software
   
• Inferring Gene Regulatory Networks by Thermodynamic Modeling.
  Chieh-Chun Chen, Sheng Zhong.
  BMC Genomics. 9(Suppl 2):S19. TEXT
   
• A core Klf circuitry regulates self-renewal of embryonic stem cells.
  Jianming Jiang, Yun-Shen Chan, Yuin-Han Loh, Jun Cai, Guo-Qing Tong, Ching-Aeng Lim, Paul Robson, Sheng Zhong & Huck-Hui Ng.
  Nature Cell Biology. 10: 353 - 360. Abstract, PDF
   
• Systems Biology and Stem Cell Biology.
  Huck-Hui Ng, Sheng Zhong and Bing Lim.
  Systems Biology, Edison Liu, Garry Nolan and Douglas Lauffenburger (Ed.), Elsevier Inc, in press.
   
• Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells.
  Chieh-Chun Chen, Xinguang Zhu, Sheng Zhong.
  BMC Genomics, 9(Suppl 1):S18. TEXT, PDF
   
• The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.
  Leming Shi, 45 other authors, Sheng Zhong, Russell Wolfinger, Weida Tong.
  BMC Bioinformatics. 9(Suppl 9):S10. TEXT
   

2007

• Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in ageing and Alzheimer’s disease.
  Yue Lu, Xin He and Sheng Zhong. 
  Nucleic Acids Research. 35: W105-W114 Abstract, TEXT, Software
   
• TagSmart: Software for Analysis and Visualization of Yeast Mutant Fitness Data Measured by TAG Microarrays.
  Chulyun Kim, Sangkyum Kim, Russell Dorer, Dan Xie, Jiawei Han, Sheng Zhong.
  BMC Bioinformatics 8:128. Abstract, TEXT, Software
   
• Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework.
  Sheng Zhong and Dan Xie.
  Artificial Intelligence in Medicine. 41:105-115 Abstract, PDF
  This paper is reviewed by Editorial on Artificial Intelligence in Medicine 41:83-86
   
• Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.
  Steven A. Vokes, Hongkai Ji, Scott McCuine, Toyoaki Tenzen, Shane Giles, Sheng Zhong, William J. R. Longabaugh, Eric H. Davidson, Wing H. Wong and Andrew P. McMahon.
  Development. 134: 1977-1989. TEXT
   

2006

• Reproducibility Probability Score - incorporating measurement variability across laboratories for gene selection.
  Guixian Lin, Xuming He, Hanlee Ji, Leming Shi, Ronald Davis, Sheng Zhong.
  Nature Biotechnology, 24(12): 6-7. Software, TEXT, Supplementary Material
   
• The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
  The MAQC Consortium.
  Nature Biotechnology, 24(9): 1151-1161. Abstract, Full paper, Project website
  This article is discussed by News of the week on Science 313: 1559; Analysis on Cell 127: 657-659; Research Highlights on Nature Methods 3: 772; News on Analytical Chemistry 78: 7358-7360
   
• Comparative Genomic Analysis Suggests FOXP3 Facilitates Tumor Evasion against Immunosurveillance by Transcriptionally Up-regulating Proteinase Inhibitor 9.
  Xinguo Jiang, Jun Cai, Sheng Zhong.  Proceedings of the International Conference on Biomedical and Pharmaceutical Engineering (ICBPE) 2006: 447-452. Full paper. Presentation video, by Xinguo Jiang
  This paper was a course project paper on BIOE498 (STAT578): Models and Computations for Functional Genomics

2005

• Reliable identification of transcription factor binding sites using phylogenetic verification.
  Xiaoman Li, Sheng Zhong, Wing H. Wong.
  PNAS 102: 16945-16950 Full paper
   

• mSin3A co-repressor regulates diverse transcriptional networks governing normal and neoplastic growth and survival.
  Jan-Hermen Dannenberg, Gregory David, Sheng Zhong, Jaco van der Torre, Wing H. Wong and Ronald A. DePinho.
  Genes & Development 19: 1581-1595 Abstract, Full paper
  This article is rated as "must read" by Faculty of 1000
   

• A Small Molecule Inhibitor of Mps1 Blocks the Spindle Checkpoint Response to a Lack of Tension on Mitotic Chromosome.
  Russell K. Dorer, Sheng Zhong, John A. Tallarico, Wing H. Wong, Timothy J. Mitchison and Andrew W. Murray.
  Current Biology 15(11): 1070-1076 Abstract, Full paper
  This article is discussed by Research Highlights on Nature Methods (2005) 2:566-567
  This article is rated as "must read" by Faculty of 1000
   

• UBIC²-Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval.
  Pengyu Hong, Sheng Zhong and Wing H. Wong.
  International Journal of Software Engineering and Knowledge Engineering 15(3) 475-485 Abstract, Full paper, Software.
  This paper is an extended version of:
  Proc IEEE Symposium on Bioinformatics and Bioengineering (BIBE) 2004: 57-64. Abstract, Full paper, Software.

2004

• Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework.
  Sheng Zhong, Lu Tian, Cheng Li, Kai-Florian Storch, Wing H. Wong.
  Proc IEEE Computational Systems Bioinformatics (CSB) 3: 425-435. Full paper, Erratum, Software
   

• GoSurfer:  a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.
  Sheng Zhong, Kai-Florian Storch, Ovidiu Lipan, Ming-Chih J. Kao, Charles J. Weitz, Wing H. Wong.
  Applied Bioinformatics 3(4): 1-5. Abstract, Technical report, Software
   

• In silico prediction of transcription factors that interact with the E2F family of transcription factors.
  Zhong S, Zhou Q, Giangrande P, Nevins JR, Wong WH.
  Proc International Conference on Control, Automation, Robotics and Vision (ICARCV) 2004: 1325-1330. Abstract, Full paper. Best Paper Award (Runner up).

2003

• ChipInfo: Software for Extracting Gene Annotation and Gene Ontology Information for Microarray Analysis.
  Sheng Zhong, Cheng Li and Wing H. Wong.
  Nucleic Acids Research, 31(13): 3487-3490. Abstract, Full paper, Software

2001

• DNA Data Mining and Promoter Prediction.
  Sheng Zhong.
  Chinese Journal of Applied Probability and Statistics 17(1):99-102