Saturday, October 27, 2018
Fwd: Request for Information and Travel to the Sigma Xi Annual Meeting
October 26–28, 2018
Hyatt Regency San Francisco Airport, California
Posted & "tweeted" my talk, viz:
(I'd use the ppt.)
Talk title and abstract
"Personal Genomics & Data Science"
In this seminar, I will discuss issues in transcriptome analysis. I
will first talk about some core aspects - how we analyze the activity
patterns of genes in human disease. In particular, I will focus on
disorders of the brain, which affect nearly a fifth of the world's
population. Robust phenotype-genotype associations have been
established for a number of brain disorders including psychiatric
diseases (e.g., schizophrenia, bipolar disorder). However,
understanding the molecular causes of brain disorders is still a
challenge. To address this, the PsychENCODE consortium generated
thousands of transcriptome (bulk and single-cell) datasets from 1,866
individuals. Using these data, we have developed a set of
interpretable machine learning approaches for deciphering functional
genomic elements and linkages in the brain and psychiatric disorders.
In particular, we deconvolved the bulk tissue expression across
individuals using single-cell data via non-negative matrix
factorization and non-negative least squares and found that
differences in the proportions of cell types explain >85% of the
cross-population variation observed. Additionally, we developed an
interpretable deep-learning model embedding the physical regulatory
network to predict phenotype from genotype. Our model uses a
conditional Deep Boltzmann Machine architecture and introduces lateral
connectivity at the visible layer to embed the biological structure
learned from the regulatory network and QTL linkages. Our model
improves disease prediction (by 6-fold compared to additive polygenic
risk scores), highlights key genes for disorders, and allows
imputation of missing transcriptome information from genotype data
alone. In the second half of the talk, I will look at the "data
exhaust" from transcriptome analysis - that is, how one can find
additional things from this data than what is necessarily intended.
First, I will focus on genomic privacy: How looking at the
quantifications of expression levels can potentially reveal something
about the subjects studied, and how one can take steps to protect
patient anonymity. Next, I will look at how the social activity of
researchers generating transcriptome datasets in itself creates
revealing patterns in the scientific literature.
Monday, July 16, 2018
Sunday, March 18, 2018
Abstract for talk at McGill University, Human Genetics Seminar Series (*i0mcg18*)
Prioritizing Variants in Personal Genomes, with particular application to cancer
My talk will focus on prioritizing genetic variants associated with
cancer, to identify key variants driving cancer progression. First, I
will look at the overall functional impact of the variants in cancer
genomes, ranking them in terms of impact, for both coding and
non-coding regions. For the coding analysis, we use the ALoFT and
frustration tools, and for the noncoding analysis, we use FunSeq.
Then, I will look at the recurrence of variants within cancer cohorts.
Here we develop two approaches: one parametric (LARVA) and the other
non-parametric (MOAT). These both depend on background
mutation rate, which, in turn, is linked to genomic features such
as replication timing and TADs. I will discuss tools for analyzing these.
Finally, I will put all these methods together
through application to kidney and prostate cancers.
Tuesday, March 6, 2018
Indian Country Books / Native Media Network
Dear Educator / Communicator :
For the past several months Indian Country Books www.indiancountrybooks.com has been morphing into an interactive platform on Facebook and our web www.nativemedianetwork.com platform to produce, publish and distribute cultural and topical programs to our audience that is tethered to their cell phones.
Please take a look at some of the programming that we have posted on Facebook and archives on our platform at www.nativemedianetwork.com/social .
Our editorial policy is simple to show and illustrate the positive side and diversity of being Native.
We have experienced an exponential growth over the past several months, into the millions of views and viewers and look forward to serving Indian Country with high quality content accessible 24/7 on any web enabled device.
Please take a look at our broadcast channel: www.ndn1.com,
Our Archives: www.nativemedianetwork.com/videos-on-demand/
And most of all our catalog of close to 10,000 titles for of and about Native America:
The sole support for our platform comes from the sale of books, so I would like to encourage you to purchase your books from us. "Rather than the other guys".
Harmon Houghton, Director of Programming
Native Media Network
Your $$$$ support means a lot to produce and publish authentic content
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Compliment of the day, I got your contact information from a
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You can contact me on my email:
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please see the link below:
priest Nunzio Scarano
Sunday, January 21, 2018
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