abstract for talk at 2011 CEGS Symposium 21-Oct-2011 [i0cegsbos]

Integrated Technologies for Genome Characterization

Mark Gerstein

Yale U., New Haven, CT, USA

Over the past few years the Stanford-Yale CEGS has developed a number
of technologies using next generation sequencing for studying human
variation and doing human genome functional annotation. Much of these
technologies have come together in the Test Sample Project. Here, I
will present some of these technologies and then talk a little bit
about the test sample analysis. The technologies presented include
analysis of structural variation in the genome from paired-ends,
read-depth and split-reads. They also include pipelines for the
analysis of RNA-Seq data and ChIP-seq datasets and approaches to
relate these functional genomics data to human genome variation.

abstract for talk at 2011 CRG Symposium 11-Nov-2011 [i0crg]

ANNOTATING NON-CODING REGIONS OF THE GENOME

Mark Gerstein

Yale U., New Haven, CT, USA

A central problem for 21st century science is annotating the human
genome and making this annotation useful for the interpretation of
personal genomes.  My talk will focus on annotating the bulk of the
genome that does not code for canonical genes, concentrating on
intergenic features such as TF binding sites, non-coding RNAs
(ncRNAs), and pseudogenes (protein fossils). I will describe an
overall framework for data integration that brings together different
evidence to annotate features such as binding sites and ncRNAs. Much
of this work has been carried out within the ENCODE and modENCODE
projects, and I will describe my approach interchangeably both in
human and various model organisms (e.g. worm). I will further explain
how many different annotations can be inter-related to characterize
the intergenic space, build regulatory networks, and construct
predictive models of gene expression from chromatin features and the
activity at binding sites.

URLS:

http://pseudogene.org
http://GenomeTECH.Gersteinlab.org