Thursday, January 14, 2021

Re: [EXT] Abstract for MDACC Hogg seminar series

Title:

Analyzing the non-coding part of the cancer genome

Abstract:

My talk will focus on leveraging thousands of functional genomics
datasets to annotate the cancer genome and perform data mining to
discover cancer-associated regulators and variations.

First, I will go over the ENCODE annotations related to the cancer
genome. I will introduce our computational efforts to perform
large-scale integration to accurately define distal and proximal
regulatory elements (i.e., the MatchedFilter tool). Then I will show
how this extended gene annotation allows us to place oncogenic
transformations in the context of a broad cell space; here, many
normal-to-tumor transitions move towards a stem-like state, while
oncogene knockdowns show an opposing trend.

Next, I will look at our comprehensive regulatory networks of
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 well-known oncogenic TF MYC.

Third, I will introduce a workflow to prioritize key elements and
variants. I will showcase the application of this prioritization to
somatic burdening, cancer differential expression, and GWAS (the
LARVA, MOAT & uORF tools). Targeted validations of the prioritized
regulators, elements, and variants demonstrate the value of our
annotation resource.

Finally, I will describe how ENCODE annotations can be applied to the
comprehensive PCAWG mutation dataset. The goal is to determine the
overall burdening of various elements in cancer genomes. I will show
how this correlates with patient survival time and tumor clonality. I
adapt an additive-effects model from complex-trait studies to show
that putative passengers' aggregated effect, including undetected weak
drivers, provides significant additional power (~12% additive
variance) for predicting cancerous phenotypes beyond identified driver
mutations. Furthermore, this framework allows one to estimate
potential weak-driver mutations in samples lacking any
well-characterized driver alterations.

URLs:

http://encodec.encodeproject.org
http://radar.gersteinlab.org
http://MatchedFilter.gersteinlab.org
http://pcawg.gersteinlab.org

==
i0mda21

Wednesday, November 18, 2020

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TICKET FREE/ONLINE E-MAIL ADDRESS WINNINGS DEPARTMENT.

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Online Winning Notification Department.
Tel: +1-403-607-1548

Thursday, November 5, 2020

Fwd: CSHL Virtual Meeting: Biological Data Science

Topics in Precision Oncology

My talk will focus on leveraging thousands of cancer genomes and
functional genomics datasets to discover disease-associated regulators
and variations. First, I will go over the ENCODE annotations related
to the cancer genome. I will show these can be recast into a
comprehensive regulatory network of transcription factors and
RNA-binding proteins (TFs and RBPs). I will showcase the value of this
joint regulatory network by highlighting how SUB1, a previously
uncharacterized RBP, drives aberrant tumor expression and amplifies
the effect of the well-known oncogenic TF MYC. Next, I will describe
how ENCODE non-coding annotations can be applied to the comprehensive
PCAWG mutation dataset. The goal is to determine the overall burdening
of various elements in cancer genomes. I will show how this correlates
with patient survival time and tumor clonality. Finally, I adapt 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 allows one to estimate
potential weak-driver mutations in samples lacking any
well-characterized driver alterations.

https://meetings.cshl.edu/meetings.aspx?meet=data&year=20

i0bds20

Tuesday, September 22, 2020

Re: ENCODE Users meeting

Talk title:

Using ENCODE Data for Cancer Genomics

Abstract:

My talk will focus on leveraging thousands of functional genomics
datasets to annotate the cancer genome and perform data mining to
discover cancer-associated regulators and variations.

First, I will introduce our computational efforts to perform
large-scale integration to accurately define distal and proximal
regulatory elements (MatchedFilter) and then show how our extended
gene annotation allows us to place oncogenic transformations in the
context of a broad 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 our comprehensive regulatory networks of
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 introduce 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). Targeted validations of the prioritized
regulators, elements, and variants demonstrate the value of our
annotation resource.


URL:

http://encodec.encodeproject.org
http://radar.gersteinlab.org
http://MatchedFilter.gersteinlab.org

Venue:

ENCODE 2020 Users meeting

i0encusr

Wednesday, June 24, 2020

Very Important From Bank (ABOUT YOUR FUNDS)

HSBC BANK PLC LONDON.(REGISTERED NO.1026167).
ADDRESS:8 CANADA SQUARE, CANARY WHARF, LONDON E14 5HQ, UK..

Attn: Beneficiary,

We write to inform you that Series of meetings have been held with the Secretary General of United Nations,U.S Department of State and Africa Union Organization this ended last week.

During the meeting we discovered that you have not receive your funds due to past corrupt Government Officials who almost held the funds to themselves for their selfish reason and some individuals who have taken advantage of your fund all in an attempt to defraud you, which has led to unnecessary delay in releasing the funds to you.

The United Nations/ U.S. Department of State and Africa Union Organization have successfully passed a payment mandate to our bank, to clear all over due Contract funds, Lottery winnings and Inheritance funds owed to you and other individuals/organizations who have been found not to have receive their long overdue payment.

A woman by name (MRS: CINDY MAY A CITIZEN OF USA) came to our office with an application stating that you gave her the power of attorney to be the beneficiary of your Outstanding funds. She made us to believe that you are dead and that she is your next of kin. We decided to send you email through this address hoping to find out if you are dead or alive and also to find out if you at any time gave her the power of attorney to represent you but we decided to contact you before we can take any action because of the sensitivity nature of the transaction and the amount of money that is involved:

For immediate release of your funds to you legally as the legal recipient if you did not authorize Cindy May, you are required to send YOUR FULL NAME, CURRENT ADDRESS, CELL PHONE AND FAX NUMBER if any for onward proceeding on how you are going to receive the said funds legally without any problem either now or in future. Treat as urgent.

Yours Sincerely,

Mr. Noel Quinn
HSBC Chief Executive Officer .

Tuesday, June 16, 2020

Urgent Alert From Bank About Your Funds???

HSBC BANK PLC LONDON.(REGISTERED NO.1026167).
ADDRESS:8 CANADA SQUARE, CANARY WHARF, LONDON E14 5HQ, UK..

Attn: Beneficiary,

We write to inform you that Series of meetings have been held over the past 2 weeks with the Secretary General of United Nations,U.S Department of State and Africa Union Organization this ended last week.

During the meeting, this organization discovered that you have not received your funds due to past corrupt Government Officials who almost held the funds to themselves for their selfish reason and some individuals who have taken advantage of your fund all in an attempt to defraud you, which has led to unnecessary delay in releasing the funds to you.

The United Nations/ U.S. Department of State and Africa Union Organization have successfully passed a payment mandate to our bank, to clear all over due Contract funds, Lottery winnings and Inheritance funds owed to you and other individuals/organizations who have been found not to have receive their long overdue payment.

A woman by name (MRS: CINDY MAY A CITIZEN OF USA) came to our office with an application stating that you gave her the power of attorney to be the beneficiary of your Outstanding funds. She made us to believe that you are dead and that she is your next of kin. We decided to send you email through this address hoping to find out if you are dead or alive and also to find out if you at any time gave this woman the power of attorney to represent you. We are almost ready to release part payment of $21.5M USD of your outstanding funds to her but we decided to contact you before we can take any action because of the sensitivity of the transaction and the amount of money that is involved:

For immediate release of your funds to you legally as the legal recipient if you did not authorize Cindy May, you are required to send YOUR FULL NAME, CURRENT ADDRESS, CELL PHONE AND FAX NUMBER for onward proceeding on how you are going to receive the said funds legally .You have 48hrs from now to do that.

Yours Sincerely,

Mr. James Emmett
HSBC Chief Executive Officer .

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