Posts Tagged ‘mynotes0mg’

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

February 24, 2018

Genic Intolerance to Functional Variation & the Interpretation of Personal Genomes
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003709 Nice plot of the number of rare v common variants in each gene to find outliers particularly tolerant to impactful (eg #LOF) mutations

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003709

Petrovski et al ’13

JClub by BW on “3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets”, Genome Medicine

February 4, 2018

3D clusters of somatic mutations…reveal numerous rare mutations as functional targets
https://GenomeMedicine.BiomedCentral.com/articles/10.1186/s13073-016-0393-x Introduces 3DHotSpots, which is one of a number of recent approaches (incl. CLUMPS, Hotspot3D, Mutation3D & HotMAPS) for finding groupings of somatic SNVs via structure

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

January 6, 2018

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in #eQTL Studies http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000770 Early discussion & development of PEER factors

Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating – ScienceDirect

November 30, 2017

QT:{{”
• Find 3.8 Å resolution cryo-EM structure of the ∼200 kDa magnesium channel CorA • Mg2+-free CorA exhibits dramatic loss of symmetry in the cytoplasmic domain …
• Inter-subunit Mg2+ is important for stabilizing the closed state of CorA “}}

#CryoEM Structures of the Mg++ Channel CorA Reveal Symmetry Break upon Gating https://www.ScienceDirect.com/science/article/pii/S0092867415017195 In closed conformation: 5 identical subunits arranged tightly around 5-fold axis & pore. In open: they lose bridging ions & open to differing degrees with helix-hinging motions.

Matthies D1, Dalmas O2, Borgnia MJ1, Dominik PK2, Merk A1, Rao P1, Reddy BG2, Islam S2, Bartesaghi A1, Perozo E3, Subramaniam S4. Cell. 2016 Feb 11;164(4):747-56. doi: 10.1016/j.cell.2015.12.055.

My public notes from #RSGDream17, #ERCC9 and other misc. events in late Nov. ’17 (i0isg,i0rsg17,i0exrna17)

November 21, 2017

Links

https://linkstream2.gerstein.info/tag/i0rsg17

Tweets

https://storify.com/markgerstein/favorite-tweets-from-late-nov-17-meetings-ercc9-rs

Talks

http://lectures.gersteinlab.org/summary/Genomics-n-DataSci–20171108-i0isg/

More “Private” Notes

http://meetings.gersteinlab.org/2017/11.19/i0rsg17+i0exrna17/ http://meetings.gersteinlab.org/2017/11.12/i0isg-slides-green-talk/

Genome Informatics meeting

November 5, 2017

LINKS

https://linkstream2.gerstein.info/tag/i0gi2017/

TWEETS

https://storify.com/markgerstein/favorite-tweets-from-genome-informatics-17-gi2017-

TALK

http://lectures.gersteinlab.org/summary/Mutations-in-2500-cancer-genomes–20171104-i0gi2017/

OTHER materials (passwd access) in
http://meetings.gersteinlab.org/2017/10.28/i0gi2017/

My public notes from #ASHG17 & its Satellites (#GenoPri17, #GA4GH2017, #HGVS17, idash, i0hgvs)

October 21, 2017

Links

https://linkstream2.gerstein.info/tag/i0hgvs

Tweets

https://storify.com/markgerstein/favorite-tweets-from-ashg17-ga4gh2017-genopri17-hg

Talks

http://lectures.gersteinlab.org/summary/Mutations-in-2500-cancer-genomes–20171018-i0hgvs+ashg/

http://lectures.gersteinlab.org/summary/Prioritizing-somatic-variants–20171017-i0hgvs+main/

http://lectures.gersteinlab.org/summary/Genomic-Privacy-n-RNAseq-Quantifying-Leakage–20171014-i0hgvs+idash/

Pics

https://www.flickr.com/photos/tags/seriesi0hgvs

Multistep nucleation of nanocrystals in aqueous solution : Nature Chemistry : Nature Research

October 1, 2017

Multistep nucleation of nanocrystals in…solution
http://www.Nature.com/nchem/journal/v9/n1/full/nchem.2618.html Creation of Au-Au pair, expelling water, drives cluster formation

QT:{{”
To explain how the gold-rich aqueous phase forms and breaks down in Figures 1A and 2A, we
performed ab-initio calculations of a hydrated gold atom pair (Figure 4). This hydrated atom pair
becomes ionized when brought closer together: the left gold atom plus two nearby water molecules
form a linear cationic coordination complex, [Au(H2O)2]+1, while the right gold atom becomes an
anion surrounded by a simple hydration shell. Other (square planar and linear) complexes involving
chloride and hydroxide ligands may also participate, depending on pH (26, 33) (Section SI2). For
nanoclusters to form inside the gold-rich aqueous phase, pairs of gold atoms within it must be partially
dehydrated. In our calculations (Figure 4), this dehydration is delayed by a 7.6 kcal/mol (12.9 kBT)
energy barrier required to breakdown the linear cationic complex (close to the gold anion).
“}}

also:
https://arxiv.org/abs/1605.04632

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer | Bioinformatics | Oxford Academic

September 30, 2017

Assembly-based inference of Bcell receptor repertoires from..RNAseq w/
V’DJer https://academic.OUP.com/bioinformatics/article/32/24/3729/2525640/Assembly-based-inference-of-B-cell-receptor Less diversity assoc w/ long survival

Network propagation: a universal amplifier of genetic associations : Nature Reviews Genetics : Nature Research

September 11, 2017

#Network propagation [by Markov walks, heat flow, diffusion, &c]: a universal amplifier of genetic associations
http://www.Nature.com/nrg/journal/v18/n9/abs/nrg.2017.38.html

Lenore Cowen,
Trey Ideker,
Benjamin J. Raphael
& Roded Sharan

http://www.nature.com/nrg/journal/v18/n9/abs/nrg.2017.38.html?foxtrotcallback=true