Abstract & Title for talk at Royal Holloway, University of London (July 2016)

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 their impact 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 network connectivity (eg hubs). Throughout the talk I will
highlight a number of practical software tools that we have developed
for prioritization, including: FunSeq.gersteinlab.org ,
AlleleDB.gersteinlab.org, STRESS.gersteinlab.org and
Networks.gersteinlab.org . I will also motivate the talk a bit by
discussing why prioritization is useful in the context of rapidly
increasing amounts of genome sequences.

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i0genc16+rh

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:
FunSeq.gersteinlab.org , AlleleDB.gersteinlab.org ,
STRESS.gersteinlab.org and Networks.gersteinlab.org .

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i0gtcbio

Re: ModSTI: Conference Abstract

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
http://dx.doi.org/10.1016/j.tig.2016.02.006
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i0scisipc

Abstract for seminar at Next Generation Sequencing USA Congress and Single Cell Genomics & Transcriptomics USA Congress, 27-28 October 2015

Title: Human Genome Analysis

I will discuss various aspects of RNA-seq for human genome analysis, including:

- potential privacy implications
- use of these data for the studying disruption of normal regulation
in cancer with a logic gate model
- use of a state-space model and dimensionality reduction to analyze
time courses


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i0ngs15

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Madrid, Spain.
Mr. Benjamin Hook
(Claim Officers)
E-mail: sr_benjamin.hook@consultant.com
Tel: +34 634 031 280
Fax: +34 917 692 656

Abstract for seminar at Tel Aviv University

Title: Comparative Genome Analysis

Abstract:

The ENCODE and modENCODE consortia have generated a resource
containing large amounts of transcriptomic data, extensive mapping of
chromatin states, as well as the binding locations of over 300
transcription-regulatory factors for human, worm and fly. The
consortium performed
extensive data integration on this data set. Here
I will give an overview of the data and some of the key analyses.
In particular:

(1) Conservation & Divergence of Transcription

(1a) A novel cross-species clustering algorithm to
integrate the co-expression networks of the three species, resulting in
conserved modules shared between the organisms. These modules are
enriched in developmental genes and exhibited hourglass behavior.

(1b) The extent of the non-coding, non-canonical
transcription is consistent between worm, fly and human.

(1c) In contrast, analyses of pseudogene (fossil genes) show that they
diverged greatly between the organisms, much more so than genes.
Nevertheless, they had a consistent amount of residual transcription.

(2) Conservation of Regulation

(2a) A global optimization algorithm to examine the
hierarchical organization of the regulatory network.
Despite extensive rewiring of binding targets, high-level organization
principles such as a three-layer hierarchy are conserved across the
three species.

(2b) The gene expression levels in the organisms, both coding
and non-coding, can be predicted consistently based on their upstream
histone marks. In fact, a "universal model" with a single set of
cross-organism parameters can predict expression level for both protein
coding genes and ncRNAs.

encodenets.gersteinlab.org
encodeproject.org/comparative
pseudogene.org/psicube

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i0isgc