Saturday, April 23, 2016

Fwd: Abstract for Talk on Personal Genomics

Abstract & Title for talk at Big Data Bioinformatics (May 2016, Boston, MA)

Personal Genomics

My talk will focus on a variety of topics in personal genomics,
principally on how we interpret and prioritize the many variants in a
personal genome. I will concentrate on rare and somatic variants. I
will discuss a number of ways of getting at the impact of rare
variants including looking for cryptic allosteric sites in coding
regions, analyzing the burdening in non-coding regions, finding
allelic elements differentially affected by variants in paternal and
maternal alleles and using at network connectivity (eg hubs).
Throughout the talk I will highlight a number of practical software
tools that we have developed for this purpose, including: , , and .


Saturday, April 9, 2016

Re: ModSTI: Conference Abstract


The emergence of collective creative enterprise such as large
scientific consortia is a unique feature in modern scientific
research, especially in genomic areas. Recent examples include the
ENCyclopedia Of DNA Elements (ENCODE) consortium annotating the human
genome and the 1000 Genomes consortium generating a catalog of
uniformly called variants for the biomedical community. To ensure that
the scientific community can benefit from these efforts, it is
important to understand the connections between consortium members and
researchers outside of the consortium. To address the issue, we
analyzed the temporal co-authorship network structures of ENCODE and
modENCODE consortia. Our analysis revealed their publication
patterns showing that the consortium members work closely as a
community whereas non-members collaborate in the scale of a few
laboratories. We also identified a few brokers playing an important
role to facilitate collaborations with outside researchers, which
suggests that large scientific consortia should set up formal an
outreach group to communicate with outside researchers.

Daifeng Wang, Koon-Kiu Yan, Joel Rozowsky, Eric Pan, Mark
Gerstein, Temporal dynamics of collaborative networks driven by large
scientific consortia, Trends in Genetics, 2016