Posts Tagged ‘i0ismb14’

Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Asso ciation” Principle

August 7, 2014

Inheritance Modes in… #Network Challenges… Guilt-by-Association http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710751 #Diseases of recessive interface SNVs predictable

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710751/

surprisingly, no positional effects on LOF mutations … significant proportion of truncation alleles give rise to functional products

“guilt by assoc works”

signif. number dom mut give rise to func products

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My “public” notes from ISMB 2014

July 19, 2014

I took lots of notes at ISMB 2014. I saved “public” versions of these as a storified tweet-stream, viz:

https://storify.com/markgerstein/tweet-related-to-ismb-2014-i0imsb14-i0afpsig-ismb

I also tagged lots of sites & papers that I discovered at the meeting, viz:

https://linkstream2.gerstein.info/tag/i0ismb14
https://linkstream2.gerstein.info/tag/i0afpsig

http://www.iscb.org/ismb2014 [Main meeting]

http://biofunctionprediction.org/node/7 [AFP SIG]

mRNA surveillance mitigates genetic dominance … Mol Gen Genet. 1998 – PubMed – NCBI

July 19, 2014

Below is key ref.

## From Brenner talk at ISMB:

Argues that domain trunc prot have a dom. neg pheno.
(ex binding domain for reg & tf or sox10)

NMD fixes this; truncated case now looks like hemizyg.

## Related twitter dialogue:

Brenner: expl. how premature truncation is often a dominant neg. (ex SOX10), providing a rationalization for the purpose of NMD #ISMB #LBR01

@rtraborn · Jul 13
Why would cells generate mRNA that are then immediately degraded by NMD? Brenner suggests that this process has a regulatory function #ISMB

@raarjr · Jul 13
Brenner: 50 nt rule accurately predicts NMD, and is prevalent in auto regulation.so what’s our ruler? #ismb

## REF

http://www.ncbi.nlm.nih.gov/pubmed/9862469

Mol Gen Genet. 1998 Nov;260(2-3):176-84.

mRNA surveillance mitigates genetic dominance in Caenorhabditis elegans.

Cali BM, Anderson P.

NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes

July 19, 2014

Linial: ClanTox (www.clantox.cs.huji.ac.il) to classify short peptides as toxins. #ismb #kn1

TOLIPS relevant to brain, neuropeptides

Linial mentions NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
http://bioinformatics.oxfordjournals.org/content/early/2014/03/05/bioinformatics.btt725.abstract #ismb #kn1

ThinkGeek :: Shrinter

July 19, 2014

ThinkGeek :: Shrinter
http://www.thinkgeek.com/stuff/looflirpa/shrinter.shtml

The SeaMonkey(R) Project

July 19, 2014

contains HTML editor + thunderbird + firefox

http://www.seamonkey-project.org/

Tools & Resources : Waldron Lab

July 19, 2014

survHD Bioconductor package: Synthesis of high-dimensional survival analysis.

http://waldronlab.org/tools-resources/

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkan e and n‐Alkane Molecules

July 19, 2014

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules http://scitation.aip.org/content/aip/journal/jcp/49/11/10.1063/1.1670007

Lifson & Warshel
CFF

Bicycle-pedal model for the first step in the vision process

July 19, 2014

http://www.nature.com/nature/journal/v260/n5553/abs/260679a0.html

Warshel_JMB76_Enzymic_reactions.pdf

July 19, 2014

Theoretical Studies of Enzymic Reactions :
Dielectric, Electrostatic and Steric Stabilization of
Reaction of Lysozyme
the Carbonium Ion in the
A. WARSHEL AND M. LEVITT

http://csb.stanford.edu/levitt/Warshel_JMB76_Enzymic_reactions.pdf