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Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks
(20 - 25 November 2008)

Jointly organized with Bioinformatics Institute, Agency for Science, Technology and Research, Singapore



Venue: IMS Auditorium
Institute for Mathematical Sciences, NUS
3 Prince George's Park
Singapore 118402
Tel: +65 6516 1897


Venue: BII Auditorium
Bioinformatics Institute, A-Star
30 Biopolis Street #07-01, Matrix Singapore 138671
Contact person: Lina Tan
Tel: +65 6826 6440 http://www.a-star.edu.sg


Organizing Committee · Visitors and Participants · Overview · Activities · Venue


Thursday, 20 Nov 2008
Venue: IMS Auditorium

08:45am - 09:00am

Registration

Chairs:
Jun Liu, Harvard University, USA
Chris Cannings, University of Sheffield, UK

09:00am - 09:15am

Opening remarks
Louis Chen, Institute for Mathematical Sciences

Vladimir Kuznetsov, Bioinformatics Institute

09:15am - 10:00am

Computational and experimental approaches to modeling gene regulation
Gary Stormo, Washington University School of Medicine, USA

10:00am - 10:30am

--- Coffee Break ---

10:30am - 11:15am

Inference of patterns and associations using dictionary models
Jun Liu, Harvard University, USA

11:15am - 12:00nn

The domain model for protein-protein interaction networks
Chris Cannings, University of Sheffield, UK

12:00nn - 01:15pm

--- Lunch Break ---

01:15pm - 02:00pm

An iterative approach to weighting and expanding protein interaction networks and its impact on complex discovery
Guimei Liu, National University of Singapore

02:00pm - 02:25pm

Data mining in protein interaction networks
Xiao-Li Li, Institute for Infocomm Research

02:25pm - 02:35pm

TBA
Chandra Verma, Bioinformatics Institute

02:35pm - 03:00pm

Computations reveals novel methods of regulation of tumor suppressors
Madhumalar Arumugam, Bioinformatics Institute

03:00pm - 03:35pm

A region based nucleus detector using the mumford-Shah model
Hwee Kuan Lee, Bioinformatics Institute

03:35pm - 04:00pm

--- Coffee Break ---

04:00pm - 04:45pm

Genome-wide identification of differential histone modification sites from ChIP-seq data using HMM
Ken Sung, National University of Singapore

04:45pm - 05:30pm

Weighted gene coexpression network analysis and causality testing for finding complex disease genes (PDF)
Angela Presson, University of California, Los Angeles, USA

End of Day 1

Friday, 21 Nov 2008
Venue: Glycine/Cysteine Room (BII Office, Level 7, Matrix Building)

08:45am - 09:00am

Registration

Chairs:
Michael R. Lieber, USC Norris Comprehensive Cancer Center, USA
Danail Georgiev Bonchev, Virginia Commonwealth University, USA

09:00am - 09:45am

The mechanism of human nonhomologous DNA end joining and its role in chromosomal translocations
Michael R. Lieber, USC Norris Comprehensive Cancer Center, USA

09:45am - 10:30am

Chromosomal instabilities and cancer
Eytan Domany, The Weizmann Institute of Science, Israel

10:30am - 11:00am

--- Coffee Break ---

11:00am - 11:45am

Modeling and analysis of relative avidity, specificity, sensitivity of Transcription Factor-DNA binding in Genome-scale experiments
Vladimir Kuznetsov, Bioinformatics Institute

11:45am - 12:30pm

Chiping the human cistrome
Shirley X Liu, Harvard University, USA

12:30pm - 02:00pm

--- Lunch Break ---

02:00pm - 02:45pm

Tumor marker-encoding genes: a bunch of mysterious diamonds in the pile of evolutionary compost PPT
Ancha Baranova, George Mason University, USA

02:45pm - 03:30pm

Dynamics of DNA methylation
Chih-Lin Hsieh, USC Norris Comprehensive Cancer Center, USA

03:30pm - 04:00pm

--- Coffee Break ---

04:00pm - 04:45pm

Transcriptional and post-transcriptional control of gene expression by actin and myosin
Piergiorgio Percipalle, Karolinska Institute, Sweden

04:45pm - 05:30pm

Functional analysis of OMICs data for cancer and toxicity phenotypes
Yuri Nikolsky, GeneGo Inc, USA

End of Day 2

Saturday, 22 Nov 2008
Venue: IMS Auditorium

08:45am - 09:00am

Registration

Chairs:
Alessandro Giuliani, Istituto Superiore di Sanità, Italia
Piergiorgio Percipalle, Karolinska Institute, Sweden

09:00am - 09:45am

Scalability : a statistical mechanics perspective on gene regulation and expression PPT
Alessandro Giuliani, Istituto Superiore di Sanità, Italia

09:45am - 10:30am

The analysis of organism complexity through functional space of proteome
Alex Kanapin, Cold Spring Harbor Laboratory, USA

10:30am - 11:00am

--- Coffee Break ---

11:00am - 11:45am

In silico search for natural antisense transcripts in human genome and analysis of their expression patterns
Mikhail Skoblov, Russian Academy of Medical Science, Russia

11:45am - 12:30pm

Liquid association for large scale gene expression and network studies
Ker-Chau Li, Academia Sinica , Taiwan

12:30pm - 01:45pm

--- Lunch Break ---

01:45pm - 02:30pm

RNA polymerase, cell growth and proliferation: inhibitory mechanisms by the tumour suppressor glycogen synthase kinase (GSK) 3beta
Piergiorgio Percipalle, Karolinska Institute, Sweden

02:30pm - 03:00pm

Thermodynamic insights based on atomistic computer simulations reveal an intricate coupling between enthalpy and entropy
Shubhra Ghosh Dastidar, Bioinformatics Institute

Chandra Verma, Bioinformatics Institute

03:00pm - 03:30pm

--- Coffee Break ---

03:30pm - 04:15pm

Signal transduction noise in eukaryotic cells: measurements and modeling
Marek Kimmel, Rice University, USA

End of Day 3

Monday, 24 Nov 2008
Venue: Aspiration Theatre (BII, Level 2M, Matrix Building)

08:45am - 09:00am

Registration

Chairs:
Michael Zhang, Cold Spring Harbor Laboratory, USA
Vladimir Kuznetsov, Bioinformatics Institute

09:00am - 09:45am

Defining splicing-regulatory networks of the tissue-specific factors fox-1/2
Michael Zhang, Cold Spring Harbor Laboratory, USA

09:45am - 10:30am

Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome (PDF)
Angela Presson, University of California, Los Angeles, USA

10:30am - 11:00am

--- Coffee Break ---

11:00am - 11:45am

Global and local transcriptome reprogramming in low- and high- aggressive breast cancer sub-types
Vladimir Kuznetsov, Bioinformatics Institute

11:45am - 12:30pm

Outcome prediction in breast and colon cancer: machine learning vs biology
Eytan Domany, The Weizmann Institute of Science, Israel

12:30pm - 02:00pm

--- Lunch Break ---

02:00pm - 02:45pm

The mechanism of lymphoid gene rearrangements and their role in chromosomal translocations
Michael R. Lieber, USC Norris Comprehensive Cancer Center, USA

02:45pm - 03:30pm

Bioinformatic analysis of plant microtubule and cell cycle regulating kinases
Yaroslav Blyum, National Academy of Sciences of Ukraine, Ukraine

03:30pm - 04:00pm

--- Coffee Break ---

04:00pm - 04:45pm

Modeling the evolution of Alu repeats in human genome
Marek Kimmel, Rice University, USA

04:45pm - 05:15pm

Biomolecular network reconstruction reveals mechanisms of immune reaction in colorectal cancer
Zlatko Trajanoski, University Graz, Austria

End of Day 4

Tuesday, 25 Nov 2008
Venue: IMS Auditorium

08:45am - 09:00am

Registration

Chairs:
Eytan Domany, The Weizmann Institute of Science, Israel
Ancha Baranova, George Mason University, USA

09:00am - 09:45am

Network motifs performance and its possible evolutionary importance
Danail Georgiev Bonchev, Virginia Commonwealth University, USA

09:45am - 10:30am

Hypothesis: an ectopic synthesis of the melanin in adipose may help to counteract metabolic syndrome PPT1, PPT2, PPT3
Ancha Baranova, George Mason University, USA

10:30am - 11:00am

--- Coffee Break ---

11:00am - 11:45am

Network-based global inference of human disease genes
Michael Zhang, Cold Spring Harbor Laboratory, USA

11:45am - 12:30pm

The biological implications of regulatory genetic variation and the definition of "normal"
Peter Little, National University of Singapore

12:30pm - 01:45pm

--- Lunch Break ---

01:45pm - 02:30pm

Biological context prediction from gene sequence sets within the ANNOTATOR framework
Frank Eisenhaber, Bioinformatics Institute

02:30pm - 03:00pm

Efficient watershed evolution for cellular image segmentation based on topological analysis
Weimiao Yu, Bioinformatics Institute

03:00pm - 03:30pm

--- Coffee Break ---

03:30pm - 04:00pm

Importance sampling of word patterns in DNA and protein sequences
Hock Peng Chan, National University of Singapore

04:00pm - 04:45pm

Round table discussion
Vladimir Kuznetsov, Bioinformatics Institute

04:45pm - 04:55pm

Closing remarks
Frank Eisenhaber, Bioinformatics Institute

End of Day 5


Organizing Committee · Visitors and Participants · Overview · Activities · Venue


 

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