Archive for the 'SciLit' Category

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whole genome assembly from Hi-C data

April 2, 2017

De novo assembly of the A aegypti genome using #HiC, by @erezaterez et al http://science.ScienceMag.org/content/early/2017/03/22/science.aal3327.full Works on human too, w. promise for #SVs

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

Olga Dudchenko1,2,3,4,
Sanjit S. Batra1,2,3,*,
Arina D. Omer1,2,3,*,
Sarah K. Nyquist1,3,
Marie Hoeger1,3,
Neva C. Durand1,2,3,
Muhammad S. Shamim1,2,3,
Ido Machol1,2,3,
Eric S. Lander5,6,7,
Aviva Presser Aiden1,2,8,9,
Erez Lieberman Aiden1,2,3,4,5,†

Science 23 Mar 2017:
eaal3327
DOI: 10.1126/science.aal3327

on whole genome assembly from Hi-C reads. There is also some info on chromosomal rearrangement from Hi-C.

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Mechanisms underlying structural variant formation in genomic disorders : Nature Reviews Genetics : Nature Publishing Group

April 1, 2017

Mechanisms underlying #SV formation in…disorders
http://www.Nature.com/nrg/journal/v17/n4/abs/nrg.2015.25.html Highlights importance of repeats in creating genomic plasticity

Nat Rev Genet. 2016 Apr;17(4):224-38. doi: 10.1038/nrg.2015.25. Epub 2016 Feb 29.
Mechanisms underlying structural variant formation in genomic disorders. Carvalho CM, Lupski JR

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Phys. Rev. E 92, 032810 (2015) – Thermodynamic characterization of networks using graph polynomials

March 31, 2017

Thermodynamic characterization of #networks using graph polynomials https://journals.APS.org/pre/abstract/10.1103/PhysRevE.92.032810 Application to the stockmarket & biological data

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Genes, environment, and “bad luck” | Science

March 26, 2017

Genes, environment & bad luck
http://science.ScienceMag.org/content/355/6331/1266 To what degree are #cancer mutations due to replication error (3rd factor), not 1st 2?

discusses R v D correlation

Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention Cristian Tomasetti1,2,*, Lu Li2, Bert Vogelstein3,*
Science 24 Mar 2017:
Vol. 355, Issue 6331, pp. 1330-1334
DOI: 10.1126/science.aaf9011
http://science.sciencemag.org/content/355/6331/1330

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Education in Computational Biology Today and Tomorrow

March 25, 2017

Education in #CompBio, by @bffo & @joannealisonfox
http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003391 Keeping up in a rapidly changing field. Will implement some @Yale

QT:{{”
“These initiatives help to extend computational biology beyond the domain of specialized laboratories. Researchers, at all levels, need to keep themselves up-to-date with the quickly changing world of computational biology, and trainees need programs where bioinformatics skills are embedded so they can have comprehensive training. New bioinformatics workflows can be adopted more widely if education efforts keep pace. As previously pointed out , starting early is also very important. There is still room for programs that capture the excitement and enthusiasm of secondary school students and convey the potential of computational biology to the public. We welcome additions to the PLOS Computational Biology “Bioinformatics: Starting Early” collection (www.ploscollections.org/cbstartingearly).

We would like to involve the community in this endeavor. With this editorial, we are calling out to educators and researchers who have experience in teaching, specifically, those keen to raise the expectations and the inquisitiveness of the next generation of biologists. The Education collection will continue to publish leading edge education materials in the form of tutorials that can be used in a “classroom” setting (whatever that may mean nowadays: stated more generically, “the places where people learn”). We will continue to encourage articles set in the context of addressing a particular biological question and, as mentioned above, we welcome new “primers” and “quick guides.” We will also be inviting tutorials from the various computational meetings. A new category of papers that is in the pipeline for the Education collection is the “Quick Tips” format, the first of which was just published . The “Quick Tips” articles address specific tools or databases that are in wide use in the community.
“}}

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Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin C, Cooney J, Anderson H, King M, Stottmann RW, Ha S, Drummond I, Paw BH, North T, Beier D, Goessling W, Sunyaev S. Mutation mapping and identification by whole genome sequencing. Genome Research (…

March 24, 2017

Mutation mapping & identification by WGS
http://Genome.CSHLP.org/content/22/8/1541 SNPtrack server, for uploading reads, does #SNP calls & prioritization

This is a novel method for genetic mapping of mutations.
It accomplishes (1) SNP discovery, (2) mutation localization (including
enumerating allele distribution, assessing recombination breakpoint), and
(3) identifying potential causal variants.
In contrast to previous approaches, this method implemented a HMM model
which does not rely on prior knowledge of SNP variation. The HMM model
predicts the recombination events/breakpoints in increasing distance from
the homozygous SNP sites over whole genome.

Software available: SNPtrack
http://genetics.bwh.harvard.edu/snptrack

Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin C, Cooney J, Anderson H, King M, Stottmann RW, Ha S, Drummond I, Paw BH, North T, Beier D, Goessling W, Sunyaev S. Mutation mapping and identification by whole genome sequencing. Genome Research (2012) 22: 1541-1548.

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Pseudogene derived chimeric CEL-HYB protein

March 14, 2017

Recombined allele of..lipase gene CEL & its #pseudogene CELP confers susceptibility to..pancreatitis
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3249.html CEL-HYB chimera

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Is American Pet Health Care (Also) Uniquely Inefficient?

March 11, 2017

Is American Pet Health Care (Also) Uniquely Inefficient?
http://www.NBER.org/papers/w22669 High correlation betw. #healthcare costs for people & pets

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uri alon’s coherent/incoherent ffls

March 9, 2017

Function of the FFL network motif
http://www.PNAS.org/content/100/21/11980.abstract Decade-old work defining coherent & incoherent ones based on activation/repression

http://sites.fas.harvard.edu/~mcb195/lectures/Networks-II/Literature/pnas_Mangan03.pdf

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New Brain Insights from Cochlear Implants » American Scientist

March 5, 2017

#Brain Insights from Cochlear Implants
http://www.americanscientist.org/blog/pub/new-brain-insights-from-cochlear-implants Soundtracks simulating the voice of implant based on 1 sided deaf patients

QT:{{”
An additional insight provided by single-sided deaf patients is that they allow us, for the first time, to objectively determine the “voice” of an implant. That’s because these patients can compare how speech sounds through their cochlear implant with what they hear in their normal-hearing ear.”
“}}

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