Re: [EXTERNAL] Re: Invitation to speak at the MD Anderson Virtual Data Science Forum

Hi Mark,

 

Fine.  We'll add that in the morning to the already-posted calendar version (which included the title) and to the ListServ.

 

Again, best wishes.  Bissan will be introducing you, so she can ask for any additional info if needed.

 

Best,

John and Bissan

 

From: Mark Gerstein <mark@gersteinlab.org>
Date: Tuesday, November 26, 2024 at 9:06 PM
To: Al-Lazikani,Bissan <BOverington@mdanderson.org>
Cc: Weinstein,John N <jweinste@mdanderson.org>, Chavez,Sergio <SChavez1@mdanderson.org>, glabstracts.mbglab@blogger.com <glabstracts.mbglab@blogger.com>
Subject: Re: [EXTERNAL] Re: Invitation to speak at the MD Anderson Virtual Data Science Forum

SLOW DOWN!  - EXTERNAL SENDER: mark@gersteinlab.org Be suspicious of tone, urgency, and formatting. Do not click/open links or attachments on a mobile device. Wait until you are at a computer to confirm you are absolutely certain it is a trusted source. If you are at all uncertain use the Report Phish button and our Cybersecurity team will investigate.

TITLE:

Topics in Cancer Genomics

ABSTRACT:

My talk will cover material from the following papers:

Using sigLASSO to optimize cancer mutation signatures jointly with
sampling likelihood.
S Li, FW Crawford, MB Gerstein (2020). Nat Commun 11: 3575.

Latent Evolutionary Signatures: A General Framework for Analyzing
Music and Cultural Evolution
J Warrell, L Salichos, M Gancz, MB Gerstein (2024). J R Soc Interface
21: 20230647.

Assessing and mitigating privacy risks of sparse, noisy genotypes by
local alignment to haplotype databases.
PS Emani, MN Geradi, G Gursoy, MR Grasty, A Miranker, MB Gerstein
(2023). Genome Res 33: 2156-2173.

Unified views on variant impact across many diseases
S Kumar, M Gerstein (2023). Trends Genet 39: 442-450.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall
Molecular Functional Impact and Consequences.
S Kumar, J Warrell, S Li, PD McGillivray, W Meyerson, L Salichos, A
Harmanci, A Martinez-Fundichely, CWY Chan, MM Nielsen, L Lochovsky, Y
Zhang, X Li, S Lou, JS Pedersen, C Herrmann, G Getz, E Khurana, MB
Gerstein (2020). Cell 180: 915-927e16.

Origins and characterization of variants shared between databases of
somatic and germline human mutations.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC
Bioinformatics 21: 227.

i0md24

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Re: [EXTERNAL] Re: Invitation to speak at the MD Anderson Virtual Data Science Forum

TITLE:

Topics in Cancer Genomics

ABSTRACT:

My talk will cover material from the following papers:

Using sigLASSO to optimize cancer mutation signatures jointly with
sampling likelihood.
S Li, FW Crawford, MB Gerstein (2020). Nat Commun 11: 3575.

Latent Evolutionary Signatures: A General Framework for Analyzing
Music and Cultural Evolution
J Warrell, L Salichos, M Gancz, MB Gerstein (2024). J R Soc Interface
21: 20230647.

Assessing and mitigating privacy risks of sparse, noisy genotypes by
local alignment to haplotype databases.
PS Emani, MN Geradi, G Gursoy, MR Grasty, A Miranker, MB Gerstein
(2023). Genome Res 33: 2156-2173.

Unified views on variant impact across many diseases
S Kumar, M Gerstein (2023). Trends Genet 39: 442-450.

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall
Molecular Functional Impact and Consequences.
S Kumar, J Warrell, S Li, PD McGillivray, W Meyerson, L Salichos, A
Harmanci, A Martinez-Fundichely, CWY Chan, MM Nielsen, L Lochovsky, Y
Zhang, X Li, S Lou, JS Pedersen, C Herrmann, G Getz, E Khurana, MB
Gerstein (2020). Cell 180: 915-927e16.

Origins and characterization of variants shared between databases of
somatic and germline human mutations.
W Meyerson, J Leisman, FCP Navarro, M Gerstein (2020). BMC
Bioinformatics 21: 227.

i0md24

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Re: Abstract Required | From Genetic Discoveries to Gene Function in Human Diseases Conference, 13 - 16 July 2024, Portugal

Title: Single-cell genomics and regulatory networks for 388 human brains

Speaker: Mark Gerstein

Abstract:

Single-cell genomics is a powerful tool for studying heterogeneous
tissues such as the brain. Yet little is understood about how genetic
variants influence cell-level gene expression. Addressing this, we
uniformly processed single-nuclei, multiomics datasets into a resource
comprising >2.8 million nuclei from the prefrontal cortex across 388
individuals with various brain-related disorders and controls. For 28
harmonized neuronal and non-neuronal cell types, we assessed
population-level variation in expression and chromatin across gene
families and drug targets. Integration of expression and genotype data
revealed >1.4 million single-cell expression quantitative trait loci
(eQTLs), many of which were not seen in bulk gene-expression datasets.
The chromatin datasets allowed for the identification of >550,000
single-cell cis-regulatory elements enriched at loci linked to
brain-related traits. Combining expression, chromatin, and eQTL
datasets, we built cell type–specific gene regulatory and cell-to-cell
communication networks, which manifest cellular changes in aging and
neuropsychiatric disorders, including altered Wnt signaling in
schizophrenia and bipolar disorder. We further constructed an
integrative deep-learning model that accurately imputes single-cell
expression and simulates perturbations. The model prioritized ~250
disease-risk genes and drug targets with associated cell types,
suggesting potential precision-medicine approaches for
neuropsychiatric disorders.

==
i0lis24, eur24


On Wed, Jun 12, 2024 at 5:41 AM Rosie Johnson
<Rosie@fusion-conferences.com> wrote:
>
> Dear Speakers,
>
>
>
> Please submit your abstract for the 'From Genetic Discoveries to Gene Function in Human Diseases' conference by Friday 21st June 2024 for inclusion in the conference abstract book.
>
>
>
> We are looking forward to welcoming you to Portugal very soon!
>
>
>
> Thank you in advance for your cooperation.
>
>
>
> Best wishes,
>
>
>
> Rosie Johnson | Conference Manager
>
>
>
> T: +44 (0) 1638 555057
>
> DD: +44 (0) 1638 599351
>
> E: rosie@fusion-conferences.com
>
> Twitter: @Fusion_Conf
>
>
>
> Please note the Fusion office is open Mon - Thurs (08.30 – 17:00).
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>
> *SCAM EMAILS* Please be vigilant on email and phone, we have been made aware that our speakers are being approached by several scam companies (Travel Hosting, Traveller Point, E Hotel Services or similar) regarding accommodation for Fusion meetings. Communications relating to our meetings will always come from a named Fusion team member and our email domain will always end in '@fusion-conferences.com'. For peace of mind, you can visit our website at any time to familiarise yourself with the Fusion team.
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Talk at EMBL in July '24 [eur24embl]

Title: Topics in Neurogenomics & Genomic Privacy

Speaker: Mark Gerstein

Abstract:

My talk will focus on neurogenomics and how this has inspired my group
to become interested in genomic privacy and security. I'll first
discuss our work within the PsychENCODE consortium, where we created a
single-cell multiomics resource of the human prefrontal cortex. This
resource encompasses over 2.8 million nuclei from 388 individuals,
enabling the identification of expression quantitative trait loci and
cell type-specific regulatory elements. Our neurogenomics work has
encouraged us to develop computational tools, particularly expression
clustering algorithms. We used these to construct cell-type regulatory
networks and cell-to-cell communication networks, which change
substantially in aging and neuropsychiatric disorders. Furthermore, we
developed an integrative model to impute single-cell expression and
prioritize disease-risk genes and drug targets. Finally, I'll talk
about how important it is to keep large-scale cohort data,
particularly for mental illness, both private and secure. I'll
highlight some techniques that we have developed for security,
particularly in relation to assessing and mitigating privacy leakage
from genomic datasets.

Talk at UCL in July '24 [eur24ucl]

Title: Topics in Neurogenomics & Genomic Privacy

Speaker: Mark Gerstein

Abstract:

My talk will focus on neurogenomics and how this has inspired my group
to become interested in genomic privacy and security. I'll first
discuss our work within the PsychENCODE consortium, where we created a
single-cell multiomics resource of the human prefrontal cortex. This
resource encompasses over 2.8 million nuclei from 388 individuals,
enabling the identification of expression quantitative trait loci and
cell type-specific regulatory elements. Our neurogenomics work has
encouraged us to develop computational tools, particularly expression
clustering algorithms. We used these to construct cell-type regulatory
networks and cell-to-cell communication networks, which change
substantially in aging and neuropsychiatric disorders. Furthermore, we
developed an integrative model to impute single-cell expression and
prioritize disease-risk genes and drug targets. Finally, I'll talk
about how important it is to keep large-scale cohort data,
particularly for mental illness, both private and secure. I'll
highlight some techniques that we have developed for security,
particularly in relation to assessing and mitigating privacy leakage
from genomic datasets.

Talk at NEC Labs America [i0nec24]

Title: Topics in Neurogenomics & Genomic Privacy

Speaker: Mark Gerstein

Abstract:

My talk will focus on neurogenomics and how this has inspired my group
to become interested in genomic privacy and security. I'll first
discuss our work within the PsychENCODE consortium, where we created a
single-cell multiomics resource of the human prefrontal cortex. This
resource encompasses over 2.8 million nuclei from 388 individuals,
enabling the identification of expression quantitative trait loci and
cell type-specific regulatory elements. Our neurogenomics work has
encouraged us to develop computational tools, particularly expression
clustering algorithms. We used these to construct cell-type regulatory
networks and cell-to-cell communication networks, which change
substantially in aging and neuropsychiatric disorders. Furthermore, we
developed an integrative model to impute single-cell expression and
prioritize disease-risk genes and drug targets. Finally, I'll talk
about how important it is to keep large-scale cohort data,
particularly for mental illness, both private and secure. I'll
highlight some techniques that we have developed for security,
particularly in relation to assessing and mitigating privacy leakage
from genomic datasets.

The Festival of Genomics & BioData, June 2024, Boston [i0fog24]

Title: Topics in Neurogenomics

Bullets:

* Single cell analysis of almost 400 brain transcriptomes, including
single-cell eQTLs
* Cell type specific regulatory networks
* Integrative deep-learning model for data imputation and to predict
disease risk