Adam Siepel
Assistant Professor
Biological Statistics & Computational Biology
Cornell University
Area of tremendous growth
Computing plays a central role
Of increasing interest to nonspecialists
Important in the commercial, academic, and
government sectors
Complex concepts, large data sets, lots of noise
The typical molecular biologist is a good proxy for a “citizen
scientist” vis-à-vis computer literacy
Widely used public, web-based resources for researchers
(NCBI Entrez, Genome Browsers, OMIM, PubMed, etc.)
Many academic analysis programs (of highly
variable quality)
Some commercial analysis and visualization packages
Strong online/open-access publication movement
Decent educational resources for lay people: blogs,
wikipedia, etc. (but unconnected)
Rapid growth in resources for personal genomics
Open-access publishing
Public Library of Science (PLoS): seven journals, rigorous review,
high impact factors
BioMed Central (BMC): 190 journals (!), peer review, rapid
turnaround, respectable impact
Both pay-to-publish, free distribution
Personal genomics
Most famous: 23andMe, Navigenics, deCODEMe
Consumer genotyping (500k-1M SNPs) from saliva samples for
$1000 – $2500
Electronic report of disease risk; in some cases geneology,
nondisease phenotypes
Ethical, legal, and political controversy
More information for citizen scientists
Opening up of “black box” of scientific research;
democratization of science
Opportunity to “write” as well as “read”
Increased dependency on electronic resources,
eScience infrastructure
Improved connectivity between resources at different levels:
blogs, textbooks, wikipedia, browsers, research papers
Better access to underlying science from personal
genomics gateways
Genotyping in a clinical setting (for diagnosis, guiding
treatment); requires computational infrastructure!
Progress toward a more dynamic, interactive
publication model
Steady progress in usability and integration of tools
and databases
Use of new genotyping technologies in forensics, paternity
testing, etc.
A much stronger form of personalized medicine (every
genome sequenced)
A completely different publishing model (?)
Analytical power tools in the hands of citizens (association
mapping, ancestry inference, …) (?)
Gene therapy (?)
Attaching funding to community contributions can
be effective
Tool developers need recognition (Bioinformatics
application notes)
Comprehensive databases with simple, general
visualization are catalysts for progress (Genome browsers)
Components and pipelines work
Progress has to be bottom-up as well as top-down
Incentives still not adequate in some cases: improving
annotations, building well-engineered software, ensuring
scientific reproducibility, obeying standards, etc.
Privacy and security are HUGE unresolved issues
Academic world still very focused on papers, but papers are
static, machine nonreadable, incomprehensible to lay
people
Hording of data for attribution or profit
Difficulty of interpreting results (personal genomics,
phylogenetics, etc.)
NCBI gateway: www.ncbi.nlm.nih.gov
UCSC Genome Browser: genome.ucsc.edu
Ensembl Genome Browser: www.ensembl.org
PLoS Gateway: www.plos.org
BMC Gateway: www.biomedcentral.com
Personal genomics: www.23andme.com,
www.navigenics.com, www.decodeme.com
Microsoft Research
Faculty Summit 2008