Posts Tagged ‘mynotes0mg’

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data | Nature Genetics

March 18, 2018

Fast, scalable prediction of deleterious #noncoding variants from functional & population genomic data LINSIGHT, by @ASiepel et al., combines DNAse & conservation information

Yi-Fei Huang, Brad Gulko & Adam Siepel
Nature Genetics 49, 618–624 (2017)
Published online:
13 March 2017

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

February 24, 2018

Genic Intolerance to Functional Variation & the Interpretation of Personal Genomes Nice plot of the number of rare v common variants in each gene to find outliers particularly tolerant to impactful (eg #LOF) mutations

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 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 Early discussion & development of PEER factors

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

November 30, 2017

• 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 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




More “Private” Notes

Genome Informatics meeting

November 5, 2017




OTHER materials (passwd access) in

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

October 21, 2017





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

October 1, 2017

Multistep nucleation of nanocrystals in…solution Creation of Au-Au pair, expelling water, drives cluster formation

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).


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 Less diversity assoc w/ long survival