Wednesday, April 22, 2015

Re: Abstract for Arrowhead's 7th Annual Precision Medicine Conference [i0pgx]

Thanks so much Mark

---
Mollie Roth, J.D.                                                  
Managing Partner
PGx Consulting

Tel:  202-280-5887
E-mail: mollie.roth@pgxconsulting.com
www.pgxconsulting.com

Save the Date! Arrowhead's 1st Annual Translational Microbiome Conference, May 14-15, in Boston. For more information about our exciting line-up of speakers, 
www.microbiomeconference.com









On Apr 22, 2015, at 6:36 PM, Mark Gerstein <mark@gersteinlab.org> wrote:

Genomic Privacy

With every new exciting development in genomics come the often
underappreciated ethical legal and social concerns.  Particularly with
regard to issues of privacy, there are ultimate tradeoffs as the
technology continues to develop and the real-life applications of
genomics become more of a reality. Numerous technical solutions have
been proposed, but every technical safeguard is accompanied by
increased complications with analyzing and manipulating datasets.
Moreover, technical solutions invite both white-hat and black-hat
efforts of circumvention, making them less useful in the long-run.
Rather we propose a multi-prong approach to dealing with privacy
issues in genomics that includes technical, regulatory and social
advances that will create an environment that both safeguards privacy,
prevents harms associated with a lack of privacy and promotes
innovation in the fields of genomics and medicine.

Abstract for Arrowhead's 7th Annual Precision Medicine Conference [i0pgx]

Genomic Privacy

With every new exciting development in genomics come the often
underappreciated ethical legal and social concerns.  Particularly with
regard to issues of privacy, there are ultimate tradeoffs as the
technology continues to develop and the real-life applications of
genomics become more of a reality. Numerous technical solutions have
been proposed, but every technical safeguard is accompanied by
increased complications with analyzing and manipulating datasets.
Moreover, technical solutions invite both white-hat and black-hat
efforts of circumvention, making them less useful in the long-run.
Rather we propose a multi-prong approach to dealing with privacy
issues in genomics that includes technical, regulatory and social
advances that will create an environment that both safeguards privacy,
prevents harms associated with a lack of privacy and promotes
innovation in the fields of genomics and medicine.

Fwd: Fw: Invitation to ICEBEM 2015

Title & abstract for
ICEBEM 2015
the 8th International
Conference on Ethics in Biology, Engineering & Medicine (ICEBEM 2015 ) that
will be held at Brooklyn, April 24th to 26th , 2015.

Meeting website:
www.downstate.edu/orthopaedics/bioethics/index.html

Genomic Privacy

With every new exciting development in genomics come the often
underappreciated ethical legal and social concerns. Particularly with
regard to issues of privacy, there are ultimate tradeoffs as the
technology continues to develop and the real-life applications of
genomics become more of a reality. Numerous technical solutions have
been proposed, but every technical safeguard is accompanied by
increased complications with analyzing and manipulating datasets.
Moreover, technical solutions invite both white-hat and black-hat
efforts of circumvention, making them less useful in the long-run.
Rather we propose a multi-prong approach to dealing with privacy
issues in genomics that includes technical, regulatory and social
advances that will create an environment that both safeguards privacy,
prevents harms associated with a lack of privacy and promotes
innovation in the fields of genomics and medicine.

==
i0icebem15

Sunday, April 19, 2015

Abstract for Talk at BioIT World 2015

Human Genome Analysis

Identification of noncoding cancer "drivers" from thousands of somatic
alterations is an unsolved problem. Here, we developed a computational
framework to annotate cancer regulatory mutations. The framework
combines an adjustable data context summarizing large-scale genomics
and cancer-relevant datasets with an efficient variant prioritization
pipeline. To prioritize high impact variants, we developed a weighted
scoring scheme to score each mutation's impact.

Session in
http://www.bio-itworldexpo.com/Clinical-Omics/

Podcast
http://www.bio-itworldexpo.com/Bio-It_Expo_Content.aspx?id=146139

Sunday, April 5, 2015

Fwd: Abstract for Structural Genomics Conference in Israel

Abstract for "ISCG2015: Deep Sequencing Meets Structural Biology,"
Weizmann Institute, on June 7th-11th, 2015

Title: Analysis of Protein Networks

Protein-protein interaction (PPI) networks may be studied through the
lens of both 3-dimensional protein structures as well as the
large-scale genome variation data being generated as part of
next-generation sequencing initiatives. In terms of protein structural
data, I will describe how mapping the structures of protein complexes
onto PPI networks enables the classification of hubs into two distinct
types: multi- and singlish-interface. These two categories exhibit
very distinct properties, especially in terms of the well-known
preferential attachment model of network growth. Secondly, I will
discuss how the integration of alternative conformations with PPI
networks further highlights interesting disparities, with the
permanent multi-interface hubs tending to exhibit a greater degree of
conformational plasticity relative to singlish-interface hubs. In
addition, I will briefly discuss how alternative conformations are
being culled from the PDB to study the significance of sequence
variation in the context of allosteric behavior. I will then discuss
the some of the insights gained by integrating variation data with
these networks (especially when using population-scale sequencing data
from the 1000 Genomes Project). Several well-known results are
recapitulated using this data: greater network centralityis associated
with a greater degree of negative selection, and the proclivity of the
network tends to be under positive selection. Finally, I will show how
this type of data further illuminates aspects of the intricacies of
protein structures and motions.

Integration of protein motions with molecular networks reveals
different mechanisms for permanent and transient interactions.
N Bhardwaj, A Abyzov, D Clarke, C Shou, MB Gerstein (2011). Protein
Sci 20:1745-54.

Integrative annotation of variants from 1092 humans: application to
cancer genomics.
E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, L
Lochovsky, J Chen, A Harmanci, J Das, A Abyzov, S Balasubramanian, K
Beal, D Chakravarty, D Challis, Y Chen, D Clarke, L Clarke, F
Cunningham, US Evani, P Flicek, R Fragoza, E Garrison, R Gibbs, ZH
Gumus, J Herrero, N Kitabayashi, Y Kong, K Lage, V Liluashvili, SM
Lipkin, DG MacArthur, G Marth, D Muzny, TH Pers, GR Ritchie, JA
Rosenfeld, C Sisu, X Wei, M Wilson, Y Xue, F Yu, 1000 Genomes Project
Consortium, ET Dermitzakis, H Yu, MA Rubin, C Tyler-Smith, M Gerstein
(2013). Science 342: 1235587


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