Posts Tagged ‘mynotes0mg’

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

Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates – Journal of Chemical Theory and Computation (ACS Publications)

September 4, 2017

Structural Memory Influences Ligand-Binding Mode http://pubs.ACS.org/doi/abs/10.1021/acs.jctc.5b01052 Rearrangement of #solvation layer is ~100x slower than unbinding

J Chem Theory Comput. 2016 Mar 8;12(3):1393-9. doi:
10.1021/acs.jctc.5b01052. Epub 2016 Feb 3.

Xu M, Caflisch A, Hamm P.

Whole-genome landscapes of major melanoma subtypes : Nature : Nature Research

September 4, 2017

Hayward, Nicholas K., et al. "Whole-genome landscapes of major melanoma subtypes." Nature 545.7653 (2017): 175-180.

Whole-genome landscapes of…#melanoma subtypes http://www.Nature.com/nature/journal/vaop/ncurrent/full/nature22071.html Sun-exposed cutaneous w. many C>T SNVs v acral/mucosal w. many SVs

Genome sequence-independent identification of RNA editing sites : Nature Methods : Nature Research

August 27, 2017

http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html

Genome seq–independent Identification of #RNAediting http://www.Nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html Accurate sites from uncorrelated SNV pair, spanned by reads

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

August 14, 2017

Naldi, A. et al. Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PLOS Computational Biology 13, e1005432 (2017).

Reconstruction & signal propagation analysis of the Syk signaling #network http://journals.PLoS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005432 Inferring potential targets of the kinase