Computational Biology and Bioinformatics

(In-House Seminar and Discussion Group)

Coordinated by Michael Q. Zhang (mzhang@cshl.edu). Contact Zhenyu Xuan (xuan@cshl.edu) in case Michael is not in.

Regular Meetings:

12:00 - 1:00 p.m., Wednesdays

Samet Conference Room (Koch)
(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 2009 and Spring 2010

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
1/20	McKay, Sheldon	The iPlant tree of life grand challenge
1/27	TBD
2/3	~~Oswald, Michaela~~ Kato, Mamoru	Haplotype inference of copy number variations
2/10	Paradesi, Martin
2/17	Salzberg, Steven - University of Maryland
2/24	QB Seminar Stolovitzky, Gustavo - IBM Research	Systems Biology of small and large scale gene regulatory networks
3/3	Parla, Jennifer
3/10	Kulkarni, Jayant
3/17	QB Seminar Michor, Franziska - MSKCC
3/24	Ware, Doreen
3/31	Liao, Willey
4/7	D'Eustachio, Peter
4/14	Iossifov, Ivan
4/21	Xue, Chenghai
4/28	QB Seminar Wingreen, Ned - Princeton
5/5	Tang, Eric
5/12	Wrzeszczynski, Kaz
5/19	QB Seminar Sander, Chris - MSKCC
5/26	Zhang, Michael

	SUBSTITUTE SPEAKERS
	Bekritsky, Mitchell
	Chia, Jer-Ming
	Zhu, Prof. Wei (Stony Brook)
	Wang, Prof. Jinhua (NYU)
	Akerman, Martin
	Erlich, Yaniv
	Kolterman, Brian
	Wang, Liya

	SEMINAR SERIES END - WILL BEGIN AGAIN IN THE FALL

	PREVIOUS SEMINARS IN THIS SERIES
Date	Presenter	Topic/Paper
9/9	Shringarpure, Suyash	Detecting recent co-selection in human populations
9/16	Atwal, Mickey	Statistical physics of population genetics
9/23	~~Bekritsky, Mitchell~~ Narzisi, Giuseppe (Mishra Lab - NYU)	SUTTA: Scoring-&-unfolding trimmed tree assembler
9/30	Dobin, Alex	Suffix array-based unbiased transcript reconstruction using high throughput sequencing data
10/7	~~Stein, Josh~~ CANCELLED	Evolution of parental subgenomes in the ancient tetraploid Zea mays (maize)
10/14	Eveland, Andrea	Genome-wide digital expression signatures for maize development: an analysis framework using the first assembled reference genome
10/21	Chung, Wen Yu
10/23	QB Seminar Reed, Jason - CNSI/UCLA	Novel applications of nano-metrology in biology and medicine
10/28	Feng, Xin	The landscape of D. melanogaster insulator binding proteins
11/4	~~Erlich, Yaniv~~ Zhang, Zefeng - Visiting Scientist	ZOOM: A fast and accurate short reads mapping and post-analysis software with Graphical User Interface
11/11	Mikkelsen, Tarjei - Broad Institute	Comparative epigenomics of human and murine adipogenesis
11/18	Xuan, Zhenyu	Mutation detection in genome re-sequencing
11/25	No Seminar - Thanksgiving
12/2	Kluger, Yuval & Parisi, Fabio - Skirball Institute, NYU	Copy number analysis in tumor biopsies
12/9	Lewis, Darrin	Genomic structural variation from paired end sequencing
12/16	QB Seminar Wiggins, Chris - Columbia University	Form, function, and information processing in stochastic regulatory networks
12/23	No Seminar - Christmas
12/30	No Seminar - New Year's
1/6	~~Valente, Dan~~ ~~Pasternak, Shiran~~	CANCELLED
1/13	Luo, Weijun	Generally Applicable Gene set Enrichment (GAGE) and pathway analysis

Looking for a topic or paper?

List of suggested topics
List of Computational Biology related journals

PubMed literature search at NCBI

Other Resources: