Wednesday, January 15, 2020

13/01/2020

Good day to you.

We sent you an email yesterday about foundation project funding.

Do let me know if you received it so further details can be advised.

kindest regards,
Fred Anderson
Email:wbfefft@aim.com

Wednesday, December 4, 2019

Re: REMINDER: Information needed for your talk at UCB Center for Computational Biology - Thurs, Dec 12

Hi Mark,

Many thanks for sending us your abstract.

We are working on scheduling the meetings for you with our faculty and I'll send you the schedule for your visit by next Tuesday.

Best,
Xuan

On Wed, Dec 4, 2019 at 11:40 AM Mark Gerstein <mark@gersteinlab.org> wrote:
Title: Topics in Cancer Genomics

Abstract: My talk will focus on how to leverage thousands of cancer
genomes and functional genomics datasets to discover
disease-associated regulators and variations. First, I will go over
the ENCODE annotation related to the cancer genome. I will show how
extended gene annotation allows us to place oncogenic transformations
in the context of a large cell space; here, many normal-to-tumor
transitions move towards a stem-like state, while oncogene knockdowns
show an opposing trend. Second, I will look at how these can be recast
into a comprehensive regulatory network of both transcription factors
and RNA-binding proteins (TFs and RBPs). I will showcase their value
by highlighting how SUB1, a previously uncharacterized RBP, drives
aberrant tumor expression and amplifies the effect of the well-known
oncogenic TF MYC. Third, I will describe a workflow to prioritize key
elements and variants. I will showcase the application of this
prioritization to somatic burdening, cancer differential expression
and GWAS (LARVA, MOAT & uORF tools). Finally, I will put all these
methods together through application to the PCAWG dataset. In this
analysis, we integrate genomic annotations and predicted functional
impact scores to quantify the overall burdening of various elements in
cancer genomes. We also show how the overall functional burdening of
various genomic elements correlates with patient survival time and
tumor clonality. Finally, we adapted an additive-effects model from
complex-trait studies to show that the aggregated effect of putative
passengers, including undetected weak drivers, provides significant
additional power (~12% additive variance) for predicting cancerous
phenotypes, beyond identified driver mutations. Furthermore, this
framework allowed us to estimate potential weak-driver mutations in
samples lacking any well-characterized driver alterations.

==

i0ucb19


--
Xuan Quach
Executive Director
Center for Computational Biology
108 Stanley Hall, UC Berkeley, 94720-3220
ph:  510.666.3342
fax: 510.666.3399

http://ccb.berkeley.edu 

Re: REMINDER: Information needed for your talk at UCB Center for Computational Biology - Thurs, Dec 12

Title: Topics in Cancer Genomics

Abstract: My talk will focus on how to leverage thousands of cancer
genomes and functional genomics datasets to discover
disease-associated regulators and variations. First, I will go over
the ENCODE annotation related to the cancer genome. I will show how
extended gene annotation allows us to place oncogenic transformations
in the context of a large cell space; here, many normal-to-tumor
transitions move towards a stem-like state, while oncogene knockdowns
show an opposing trend. Second, I will look at how these can be recast
into a comprehensive regulatory network of both transcription factors
and RNA-binding proteins (TFs and RBPs). I will showcase their value
by highlighting how SUB1, a previously uncharacterized RBP, drives
aberrant tumor expression and amplifies the effect of the well-known
oncogenic TF MYC. Third, I will describe a workflow to prioritize key
elements and variants. I will showcase the application of this
prioritization to somatic burdening, cancer differential expression
and GWAS (LARVA, MOAT & uORF tools). Finally, I will put all these
methods together through application to the PCAWG dataset. In this
analysis, we integrate genomic annotations and predicted functional
impact scores to quantify the overall burdening of various elements in
cancer genomes. We also show how the overall functional burdening of
various genomic elements correlates with patient survival time and
tumor clonality. Finally, we adapted an additive-effects model from
complex-trait studies to show that the aggregated effect of putative
passengers, including undetected weak drivers, provides significant
additional power (~12% additive variance) for predicting cancerous
phenotypes, beyond identified driver mutations. Furthermore, this
framework allowed us to estimate potential weak-driver mutations in
samples lacking any well-characterized driver alterations.

==

i0ucb19

Sunday, November 24, 2019

Re: reply

Hello, please confirm if you receive my previous email to you. Thank you. Mrs Lister.

Sunday, October 20, 2019

Fwd: genopri abstract

https://broadinstitute.swoogo.com/ga4gh7thplenary/agenda
then
https://www.genopri.org/program.html

9:30 – 10:15am Presentation Session 3: "Models" (Session Chair: Xiaoqian Jiang)

Enhancing open data sharing for functional genomics experiments:
Measures to quantify genomic information leakage & identify file
formats for privacy preservation

Mark Gerstein, Yale University (USA)

Abstract: Functional genomics experiments on human subjects present a
privacy conundrum. On one hand, many of the conclusions we infer from
these experiments are not tied to the identity of individuals but
represent universal statements about biology and disease. On the other
hand, the raw sequencing reads or the phenotypic information inferred
from these experiments can leak information about patients' variants,
which presents privacy challenges in terms of data sharing. There is a
great desire to share data as broadly as possible. Therefore,
measuring the amount of variant information leaked in a variety of
experiments is a key first step in protecting private information. In
this study, we propose metrics to quantify private information leakage
in functional genomics data, linking attacks to validate the proposed
metrics and file formats that maximize the potential for data sharing
while protecting individuals' private information.

Saturday, September 28, 2019

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Wednesday, September 18, 2019

18/09/2019

Good day to you.

We sent you an email yesterday about foundation project funding.

Do let me know if you received it so further details can be advised.

kindest regards,
fred Anderson
Email:wbfefft@aim.com