[tags scilit,jclub,GG,fromjclub,conferences,psb18]

Cell-specific prediction and application of drug-induced gene expression Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencodersFunctional network community detection can disaggregate and filter multiple underlying pathways in enrichment analysesA heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methodsCoalitional game theory as a promising approach to identify candidate autism genesNetwork analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentialsAn ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data

Mount Sinai is organizing a symposium in Pamela’s memory that will take place on April 16. Please see attached flyer for more information

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Quantum Computing

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QC call minutes 1/11/18:

· Somatic Mosaicism in Brain project: consequences for SCZ (others in Consortium for ASD, Tourette’s and Epilepsy); specifically, CNVs in single cells; 300 cells per individual, 5 SCZ, 5 CTRLs, 4000 data points per cell, seeking SVM for data classification, or significant features such as genes relevant to SCZ; reduce the resolution and coarse-grain to meet current size limitations of IBM Qubit system – 50 qubits.

· Kanix Wang, U of Chicago (Andrey Rezesky’s lab) Classification of common human determinants: separate genotypic influence from environment and combine to produce phenotypes; define “Disease Liability” that accounts for the genotypic influence (Gaussian distributed); correlation between disease pairs; issues with large sample size (data on 129K families), reduced through filtering, as well as large numbers of disease, reduced as well; model involves decomposition of variance using genetic + several environmental factors, variance among couples, siblings and families; determine heritability; lower size to meet limitations

· Mike Gandal (UCLA) integrative models of psychiatric disease genomic regulation: integration of genotypes, RNA-seq, QTLs into single network and connect this with phenotype; current approach WGCNA; QC could help with non-linearity aspect, small-size + high complexity is sort of problem to deal with;

· Dimension of available space 4^(N-1), N = number of qubits, so lots of problem space, but there are other bottlenecks to large-scale tasks: T1 energy leak (weaker) < quantum coherence < measurement fidelity (environmental noise, precision of acquisition) < gate fidelity (bad control over phase) are issues, need better control; max 100-200 gates, this limits complexity of feature space; cannot debug as this causes wavefunction collapse

· Gerstein lab to come up with proposal presentation for next call

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Notes from P2 Brain

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****** ABSTRACT ******

[[see word doc emailed as a separate file]]

****** Abstract figures ******

– No double line on figure

– Colorization

– Recolorize fn & sl relative to JW/JP subfi

****** JW updates ******

– For main Many schematics going across incl. DW’s network growth

– For abs. Use JP ex. With simplification

****** FN – RCA ******

– Flip graneen v yellow

– Ellipsiods a little faint

****** XS – single cell updates ******

– Brainspan single-cell?

– think about the cell types – collapse cell types + discuss w/ Jim

– add fetal, embryo to brainspan

– make the batch effect suppl. Figure which is diffe.

– determine optimal 100 biomarker, 10 biomarker genes to get the best R^2 [see board pic]

– what about the opc result for the gender disparities – ask Jim

– make a schematic for the 85%

– Cell type QTL – vs all variants like transQTL

****** MG’s suggestions for main text ******

– did we really detect brain-specific? Or brain-active?

– “mega” analysis — remove

– with respect to eTWAS: change if possible

– 1945 — put real number in text (for individuals)

– with respect to MG’s note “more” — elaborate and be sure to remain consistent across different tissues.

– “JW” — JW agrees with the “three-times” improvement remark

****** Quick updates/notes from meeting ******

– Fri website call Geetha

– SL – Fri. at noon or 1:30

– Jeff Lichtman

– SCREEN – reprocessing of roadmap brain samples

On Wed, Jan 10, 2018 at 8:32 PM, Shi, Xu <xu.shi> wrote:

abstract__brain_mtg_Jan_10.docx