Computational Biology and Bioinformatics

(Hershey In-House Seminar and Discussion Group)

Coordinated by Michael Q. Zhang (mzhang@cshl.edu). Contact Lincoln Stein (lstein@cshl.edu) in case Michael is not in.

Regular Meetings:

Noon - 1:00 pm, Wednesdays  Bush Fireplace Room

(Unless otherwise indicated)

The duration will be about one hour. The format is flexible with lunch provided. Formally, all regular participants are listed alphabetically. You can choose to present anything that may be "cool" or useful to the field. For example, you could give a talk on a research project or new results, introduce a review article, new paper or an algorithm, present a tutorial on special topics in biology, computer science, statistics, book publication or software licensing, etc. From time to time, we will also have talks from visitors or other CSHL personnel who want to speak to us. You could also give a presentation followed by open discussion. Participants are welcome to make other suggestions on format or topics. Anyone who is not able to speak or who would like to speak on another date should try to switch with another person. If you need more than one session or if we insert a guest speaker, the speaker list will automatically be shifted down. Let Paloma Anderson (anderson@cshl.edu) know of any changes so that she can update the schedule in time.

The Schedule for Fall 2007 and Spring 2008

Please email Paloma Anderson (anderson@cshl.edu) with a topic title as early as you can. If you wish to include a reference for a current paper or background review, you can send it later. Speaker is responsible for making sure the equipment required is in place and is working properly. (Please check the projector before the meeting. If there is a problem, call AV at x8365).

(See below for previous seminars given in this series, suggested topic links and other resources.)

Date

Presenter

Topic/Paper

05/14

 Wang, Haibin

Evolution of song culture in zebra finch

 05/21

Lin, John

 Text Mining and Literature Curation for Human Brain Connectivity Architecture

 

 

 

 

SEMINAR SERIES END - WILL BEGIN AGAIN IN THE FALL

 

 

 

 

 

PREVIOUS SEMINARS IN THIS SERIES

 

Date

Presenter

Topic/Paper

09/12

 Eisen, Michael - Visiting Scientist, Lawrence Berkeley National Lab (LBNL) and the University of California at Berkeley (UCB)

Function and Evolution of Regions Bound by Drosophila Transcription Factors

09/19

 Feng, Xin

Incorporate Geneways into Naive Bayes Classifier for Functional Interaction Predication

09/26

 Xuan, Zhenyu

Hybrid Selection with Solexa Sequencing

10/03

 Gessler, Damian - Visiting Scientist, National Center for Genome Resources, Santa Fe, NM

SSWAP: Simple Semantic Web Architecture and Protocol

10/10

 Wong, Wing Hung - Visiting Scientist, Stanford University

A gene regulatory network in mouse embryonic stem cells

10/10-13

 CSHL Meeting - Functional Genomics and Systems Biology

 

10/11-13

 RECOMB Regulatory Genomics 2007 - Boston/MIT

 

10/17

 Taylor, James - Visiting Member/Instructor, Courant Institute, NYU - McClintock Conference Room

Extracting signals from multi-genome alignments for identification of functional elements

10/17-30

 CSHL Course -  Programming for Biologists

 

10/24

 Heywood, Todd - McClintock Conference Room

BlueHelix (HPCC): Architecture and Applications

10/31

 Kluger, Yuval - Visiting Scientist, Skirball Institute of Biomolecular Medicine, NYU - McClintock Conference Room

State Dependent Gene Regulatory Networks

11/1-5

 CSHL Meeting - Genome Informatics

 

11/07

 Duan, Shenghua - Visiting Postdoc, Mello Lab, UMass Medical School - McClintock Conference Room

Bioinformatics in RNA Interference

11/7-13

 CSHL Course - Computational & Comparative Genomics

 

11/14

 Sumazin, Pavel - Visiting Assoc. Research Scientist, Joint Centers for Systems Biology, Columbia University - McClintock Conference Room

Sequence-Centric Analysis of the Affect of BCL6 and Myc on Burkitt's Lymphoma

11/18-19

 CSHL Course - The Genome Access Course

 

11/21

 Thanksgiving

 

11/28

 Lee, Yoon-Ha Zhang, Michael

 

12/05

 Stark, Alexander - Computational Biology and Bioinformatics, The Broad Institute, MIT

 

12/12

 Zhao, Hongyu - Visiting Scientist, Yale University

 

12/19

 Schones, Dustin - Visiting Postdoc, LMI/NHLBI/NIH

A nucleosome landscape for the human genome

12/26

 Christmas

 

01/02

 New Year

 

01/09

 McCombie, Dick

 

01/14-17

The Sixth Asia Pacific Bioinformatics Conference
Kyoto, Japan

 

01/16

 Pai, Shraddha Zhang, Chaolin

Defining splicing regulatory networks of the tissue-specific splicing factors Fox-1/2 by phylogenetic analysis

01/23

 Pant, Shruv Leotta, Anthony Margolin, Adam - Visiting Gradute Student, Columbia University

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

01/30

 Rosenfeld, Jeffrey - McClintock Conference Room

Determination of Enriched Histone Modifications in Non-genic Parts of the Human Genome

02/06

 Stein, Lincoln Kuznetsov, Vladimir - Visiting Scientist, Genome and Gene Expression Data Analysis Bioinformatics Institute, Singapore

Computational Mapping and Statistical Analysis of Transcriptional Factor Binding Site in ChIP-PET and Chip-seq Experiments

02/13

 Saar, Sigal Tharakaraman, Kannan - Postdoc Candidate

Finding functional motifs in eukaryotic promoters using sequence characteristics and positional preferences

02/20

 Sachidanandam, Ravi Leotta, Anthony

Copy Number Data Analysis and Visualization

02/27

 Wang, Xiaowo

Computational analysis of microRNA promoters

03/05

 Serkhane, Jihene Valente, Dan

Trajectory measures describing the locomotor behavior of Drosophila melanogaster in a circular arena

03/12

 Smith, Andrew Tsigankov, Mitya

Computational modelling of development of neural curcuitry

03/19

 Tsigankov, Mitya Smith, Andrew - Rozen, Steve (Bioinformatics Faculty Candidate) Gerry Conference Room - Marks Building

Part 1: Generating and analyzing metabolic profiles to study CNS disease
Part 2: Human Y variation and its phenotypic consequences

03/26

 Valente, Dan Lin, John Shay, Shay, Tal (Postdoc candidate from Wwezmann Insitute, host Michael Zhang)

A simple way to detect significant local DNA copy number aberrations

Array CGH data is noisy. In addition to the technical measurement noise, many tumors have a large number of different aberrations (DNA amplifications or deletions). An aberration is more likely to have biological significance if it happens in a significant fraction of the patients, and if it is strong. Also, a longer aberration is less likely to be attributable to measurement error.

 

We define V, the “volume” associated with an aberration as the product of three factors: (a) fraction of patients with the aberration, (b) the aberration’s length and (c) its amplitude. Our algorithm compares the volume V derived from the real data to a random model obtained by permutations, and yields the statistical significance (p-value) of the measured value of V. We applied  the method on different aCGH datasets, including Glioblastoma, Medulloblastoma, and Neuroblastoma, and detected genetic locations that were significantly aberrant. Previously observed genomic aberrations as well as new ones were detected. We explored the relationships between whole chromosome events and different local DNA aberrations, trying to refine clinical subgroups.

04/02

 Vaughn, Matthew  Prof. Wang, Jin

http://www.sunysb.edu/chemistry/faculty/jwang.htm

 

Landscape Theory of Cellular Networks

04/09

 Bonneau, Richard - Visiting Scientist, Courant Institute, NYU - James Library

Learning global transcriptional dynamics with the Inferelator and cMonkey

Abstract
Our system for network inference and modeling consists of two major components: cMonkey and the Inferelator. We describe their integration into a functioning integrated system applied to several prokaryotic organisms.

cMonkey groups genes and conditions into biclusters on the basis of 1) coherence in expression data across subsets of experimental conditions, 2) co-occurrence of putative cis-acting regulatory motifs in the regulatory regions of bicluster members and 3) the presence of highly connected sub-graphs in metabolic and functional association networks. We describe the algorithm and the results of extensive tests of several previously described methods, showing that cMonkey has several advantages in the context of regulatory network inference.

The Inferelator is a network inference algorithm that infers regulatory influences for genes and/or gene clusters from mRNA and/or protein expression levels. The procedure can simultaneously model equilibrium and time-course expression levels, such that both kinetic and equilibrium expression levels may be predicted by the resulting models. Through the explicit inclusion of time, and gene-knockout information, the method is capable of learning causal relationships.

It also includes a novel solution to the problem of encoding interactions between predictors.


For Background on our integrated system see:

http://www.cell.com/content/article/abstract?uid=PIIS009286740701416X

http://genomebiology.com/2006/7/5/R36

http://www.biomedcentral.com/1471-2105/7/280

04/16

 Li, Wen-Hsiung - Visiting Scientist, University of Chicago

Protein evolution in terms of structure

04/23

 Wen, Quan Stein, Lincoln Vaughn, Mathew - McClintock Conference Room

Efficient genome methylation profiling using next-generation sequencing

04/30

 Muthuswamy, Lakshmi

Statistical interpretation of copy number variations in genetic diseases

05/07

 Smith Andrew - McClintock Conference Room

Identifying functional domains of diffuse epigenomic marks from ChIP-seq data
     

 

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Last updated September 13, 2006