Program

RECOMB Bioinformatics Education Conference

Saturday, March 14 (CalIT2 Auditorium, Atkinson Hall)

12:15-12:40 Registration, light lunch, and poster setup

Session Chair: Ron Shamir

12:40-12:45 Opening Remarks

12:45-1:00 The Challenges in Bioinformatics Education: preview of the topics that will be discussed during the conference (Pavel Pevzner)

1:00-1:30 Trey Ideker (UCSD). Facebook for Proteins - Mapping Protein Networks in the Cell.

1:30-2:00 Dick Karp (UC Berkeley). Haplotypes, Genotypes and Phenotypes.

2:00-2:10 Steffen Heber (NCSU). The Bioinformatics in Motion Project

2:10-2:55 Discussion Panel I: (Ron Shamir (moderator), Sridhar Hannenhalli, Dick Karp, Manolis Kellis, Mikhail Gelfand, Trey Ideker, Pavel Pevzner)

What is bioinformatics: Science, Engineering or Service? Should it be taught as Science, Engineering or Trade?

What is the right background for a bioinformatics graduate degree? Biology? Computer Science? Mathematics? Bioengineering? Should future applicants to bioinformatics graduate programs master all these skills?

The best bioinformatics education: undergraduate, graduate, or postgraduate? Should we start early or late?

The split personality of bioinformatics: systems biology, bioengineering, computational biology: Why, and what next? What are the implications for bioinformatics education?

2:55-3:15 Coffee Break

Session Chair: Pavel Pevzner

3:15-3:45 Manolis Kellis (MIT). Understanding genomes from their evolutionary signatures

3:45-4:15 Sridhar Hannenhalli (University of Pennsylvania) Survival of the fittest - detecting adaptive evolution

4:15-4:45 Gill Bejerano (Stanford). "All your base are belong to us": Thinking non-conservatively about genome conservation

4:45-5:05 Coffee Break

Session Chair: David Sankoff

5:05-5:35 Terry Gaasterland (UCSD) Deciphering variant splice forms in proteins that control transcription

5:35-6:05 Michael Eisen (UC Berkeley). TBA

6:05-6:40 Discussion panel II: (Trey Ideker (Moderator), Gill Bejerano, David Sankoff, Michel Eisen, Terry Gaasterland, Natasha Przulj, Amos Tanay)

What is the difference between bioinformatics and systems biology? Is systems biology really a new discipline? What are the implications for bioinformatics/systems biology education?

Women in bioinformatics: another gender gap, or a model for other disciplines to follow?

Should we educate bioinformaticians do wet experiments?

Bioinformatics wiki resources: can they be built from various bioinformatics courses?

6:40-7:10 Poster viewing

7:10 - Dinner Reception (poster viewing continues)

Sunday, March 15

8:00-9:00 Breakfast

Session Chair: Terry Gaasterland

9:00-9:30 Martin Vingron (Max Planck Institute, Berlin). Sorting gene expression matrices (linear algebra can be good for something!)

9:30-10:00 Serafim Batzoglou (Stanford). How soon will everyone be sequenced?

10:00-10:30 Vineet Bafna (UCSD). Hunting for the Huntington disease gene

10:30-10:50 Coffee break

Session Chair: Martin Vingron

10:50-11:20 Alexey Kondrashov (U. of Michigan) Detecting selection from sequence data

11:20-11:30 Russell Schwartz (CMU). Tailoring Undergraduate Computational Biology Training to Diverse Student Needs: the Carnegie Mellon Experience

11:30-12:15 Discussion Panel III. (Pavel Pevzner (moderator), Martin Vingron, Serafim Batzoglou, Vineet Bafna, Alexey Kondrashov, Chris Lee, Lior Pachter)

Should Life Sciences undergraduates be required to learn bioinformatics? How to teach bioinformatics to Life Science (and Medicine) students?

How to teach bioinformatics to Life Science (and Medicine) students? Should biology students also cover Algorithms and Statistics 101, or should they be taught "bioinformatics for future presidents" course without any formulas?

If bioinformatics should be a required course in Biology, what courses can be removed from the current Biology curriculum?

Should MD students take bioinformatics? In view of the next-generation sequencing revolution and fast proliferation of the personal genomics companies, should all medical students take a bioinformatics course?

12:15-1:15 Lunch

Session Chair: Natasa Przulj

1:15-1:45 Lior Pachter (UC Berkeley) What is epigenomics?

1:45-2:15 David Sankoff (University of Ottawa) Whole genome duplication and its consequences for genome organization

2:15-2:25 Shuba Gopal (Rochester Institute of Technology). Do you speak genome? Understanding the language(s) of genomes

2:25-3:00 Discussion Panel IV. (Serafim Batzoglou and Terry Gaasterland (moderators), Shuba Gopal, Dick Karp, Natasha Przulj, Ron Shamir, Mikhail Gelfand)

What is the educational core of Bioinformatics? What is the educational core of Systems Biology?

Building a curriculum in a nascent field: What can we learn from the adolescent experience of other fields.

Undergraduate research experience in bioinformatics: learning from past experience.

There are dozens of bioinformatics textbooks: do we need more? There is still no "standard" systems biology textbook – is it a symptom or just a delay?

3:00-3:30 Coffee Break

Session Chair: Alexey Kondrashov

3:30-4:00 Chris Lee (UCLA) How can we fight the scourge of AIDS drug resistance?

4:00 - 4:30 Mikhail Gelfand (Moscow State University). From computer to a lab bench and back. How comparative genomics leads to the discovery of bacterial transporters with a new mode of action.

4:30 – 5:00 Natasa Przulj (UC Irvine) From Network Topology to Biological Function and Disease

5:00 -5:30 Amos Tanay (Weizmann Institute) Evolution: An omnipotent optimizer or a sloppy problem solver? or both?

5:30-6:00 Closing Discussion (Pavel Pevzner and Ron Shamir)