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发信人: genome (do real science), 信区: Bioinformatics
标题: [讲座]CBI：networks
发信站: 水木社区 (Fri May 16 13:40:53 2008), 站内

Seminar #1:

Time: 2-3pm, Wednesday, May 21
Location: Room 610, new Life Science Building, Peking University
Speaker: Sheng Zhong
Assistant Professor of Bioengineering
University of Illinois
Title: Transcription Networks in Embryonic Stem Cells

Abstract:
Embryonic Stem Cells (ESCs) possess several notable properties that account for their exceptional scientific and medical importance, including development of treatments to degenerative, malignant, or genetic diseases such as diabetes, Parkinson's disease, Alzheimer's and heart failure, as well as injury due to inflammation, infection, and trauma, such as spinal cord injury. Transcriptional control is thought to be a key control mechanism for ESCs to maintain their undifferentiated state. Our group use experimental and computational methods to study the engineering principles built within the transcriptional networks of ESCs.

In this talk, I present genomic data and computational analysis of the dynamic gene expression during the differentiation of mouse and human ESCs. We developed a novel Markov Chain Monte Carlo approach that achieved better accuracy than peer algorithms for detecting transcription regulatory elements in the mammalian genomes. Chromatin immunoprecipitation (ChIP) experiments confirmed that this method could distinguish functional and non-function transcription factor binding sites within a DNA regulatory region [1]. Hybridizing protein-DNA interaction data and gene expression data, specific interaction forms of collaborating transcription factors were identified [2]. With this theoretical development, a larger computational scheme was implemented to incorporate three types of genomic data and multiple datasets to reconstruct transcription networks [3][4]. The identified networks and experimental data served as empirical knowledge and enabled us to develop novel machine learning methods to dissect essential and non-essential components of transcription networks [5]. In particular, a small module of the transcription network that is essential in mouse ESCs but not essential for human ESCs was experimentally characterized [6].

[1] Xie, Cai, Cha, Ng & Zhong. (2008), Genome Research, in press. http://www.genome.org/cgi/content/short/gr.072769.107v1?rss=1
[2] Chen, Zhu & Zhong. (2007), BMC Genomics, 9(Suppl 1):S18.
[3] Lin, He, Ji, Shi, Davis & Zhong. (2006), Nature Biotechnology, 4(12): 6-7.
[4] Chen & Zhong. (2008), BMC Genomics, in press.
[5] Lu, He & Zhong. (2007), Nucleic Acids Research, 35: W105-W114
[6] Jiang, Chan, Loh, Cai, Tong, Lim, Robson, Zhong & Ng. (2008), Nature Cell Biology, 10: 353 – 360

Bio:

Sheng Zhong received BS/BA in Mathematics and Economics from Beijing University, China. He did his Ph.D. research with Professor Wing Wong in Department of Biostatistics at Harvard University, with a Ph.D. minor in Molecular Biology. From 2004 to 2005 he was an exchange student scholar at Department of Statistics and BioX Center at Stanford University. He joined University of Illinois as an Assistant Professor of Bioengineering in 2005. He has since also held affiliate positions in Departments of Statistics, Computer Science, Biophysics and Computational Biology and Institute for Genomic Biology. He became a Faculty Fellow of National Center for Supercomputing Applications in 2007. He received Xerox Award for Faculty Research in 2008.

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Seminar #2:

Time: 3-4pm, Thursday, May 22
Location: Room 610, new Life Science Building, Peking University
Speaker: Hui Ge
Whitehead Fellow (Principal Investigator)
Whitehead Institute for Biomedical Research
Title: Understanding biology in a network

Abstract:
Development is the result of complex events including cascades of transcriptional programs and numerous molecular interactions. Traditionally, research focus has been given to the characterization of individual mutants, regulators or interactions. With the availability of complete genome sequences and high-throughput (HT) experimental techniques, probing biological systems on a global scale has become possible. On the other hand, however, it is not clear how the data emerging from various HT techniques can be effectively integrated and how new insights can be gained for specific biological processes upon such integration. Here we describe our effort of mapping a large fraction of protein-protein interaction (or interactome) network for a metazoan, Caenorhabditis elegans. We develop computational models to integrate the interactome network with other HT datasets such as expression profiles, phenotypic profiles, and genetic interaction networks, and apply them to understanding developmental processes in Caenorhabditis elegans. We confirm the biological hypotheses learned from the computational models by experimental results.

Bio:

EDUCATION
1999-June 2004 Harvard Uniersity Cambridge, MA
Ph.D., Division of Medical Sciences
Research area: systems biology, bioinformatics, and genomics.
Thesis Advisor: Dr. Marc Vidal
Thesis work on integration of various sources of high-throughput biological data.

1995-1999 Beijing University Beijing, China
B.S.,Department of Biochemistry and Molecular Biology
Broad coursework on biochemistry, molecular biology, cell biology, genetics, and immunology.

EXPERIENCE
May 2005-present Whitehead Institute for Biomedical Research Cambridge, MA
Whitehead Fellow (Principal Investigator)

Oct.2004-Apr.2005 Harvard University Cambridge, MA
Visiting Scholar, Department of Molecular and Cellular Biology

Jul.2004-Oct.2004 AstraZeneca USA Waltham, MA
Intern, Cancer Informatics Group

1999-2004 Harvard Medical School/Dana-Farber Cancer Institute Boston, MA
Research assistant, Dr. Marc Vidal’s laboratory

2001-2002 Harvard University Cambridge, MA
Teaching Fellow, Course in Genomics and Computational Biology

AWARDS/HONORS
Stewart Trust Cancer Pilot Research Award (2005-2007); Whitehead Fellowship (2005-present); Fink Fellowship (2005-2007); Fu Fellowship (1999-2004); Honored Graduate Award (1999); Baogang Fellowship (1997); Outstanding Freshman Fellowship (1995)

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biozy 编辑于 2008-05-20 10:41

• 一年又半-深圳入职后

downsea

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嘿嘿，不去了，刚听过两位的讲座~

2008-05-20 20:17

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