Archive for the 'SciLit' Category

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.

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

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

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

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.”
“}}

Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage | Science

March 4, 2017

Transmissible Dog Cancer Genome Reveals…History of an Ancient Cell Lineage http://science.sciencemag.org/content/343/6169/437.full After 11k yrs 2M SNVs & 646 genes KO’ed

Elizabeth P. Murchison1,2,*,†,
David C. Wedge1,*,
Ludmil B. Alexandrov1,
Beiyuan Fu1,
Inigo Martincorena1,
Zemin Ning1,
Jose M. C. Tubio1,
Emma I. Werner1,
Jan Allen3,
Andrigo Barboza De Nardi4,
Edward M. Donelan3,
Gabriele Marino5,
Ariberto Fassati6,
Peter J. Campbell1,
Fengtang Yang1,
Austin Burt7,
Robin A. Weiss6,
Michael R. Stratton1,†

+ See all authors and affiliations

Science 24 Jan 2014:
Vol. 343, Issue 6169, pp. 437-440
DOI: 10.1126/science.1247167

TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants | eLife

March 4, 2017

TP53 copy number expansion is associated w…enhanced DNA damage response in elephants https://elifesciences.org/content/5/e11994 18 p53 retro- & pseudo- genes

Big Data: Astronomical or Genomical?

March 3, 2017

#BigData: Astronomical or Genomical?
http://journals.PLOS.org/plosbiology/article?id=10.1371/journal.pbio.1002195 Est. current storage in EB/yr: Astro .1, omics .1, Twitter .001, YouTube .1-1

QT:{{”
“Data storage requirements for all four domains are projected to be enormous. Today, the largest astronomy data center devotes ~100 petabytes to storage, and the completion of the Square Kilometre Array (SKA) project is expected to lead to a storage demand of 1 exabyte per year. YouTube currently requires from 100 petabytes to 1 exabyte for storage and may be projected to require between 1 and 2 exabytes additional storage per year by 2025. Twitter’s storage needs today are estimated at 0.5 petabytes per year, which may increase to 1.5 petabytes in the next ten years. (Our estimates here ignore the “replication factor” that multiplies storage needs by ~4, for redundancy.) For genomics, we have determined more than 100 petabytes of storage are currently used by only 20 of the largest institutions ().”
“}}

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data | BMC Bioinformatics | Full Text

March 2, 2017

FastProject: A Tool for Low-Dimensional Analysis of #ScRNASeq https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1176-5 Software for many reductions to 2D scatterplots

* FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data/ D. DeTomaso, N. Yosef. BMC Bioinformatics
2016.17(1):315. doi: 10.1186/s12859-016-1176-5

FastProject, developed by DeTomaso and Yosef, is a software tool for analyzing and interpreting single-cell RNA-Seq(scRNA-Seq) data. This pipeline utilizes a plethora of dimensionality reduction methods to project the high-dimensional scRNA-Seq data (i.e. the gene expression matrix) to dozens of two-dimensional scatter-plots. By incorporating the signature-based analysis, the biological significance of these two-dimensional representations can be systematically investigated. FastProject was designed using a modular architecture with the aim of serving as a general platform for the development and evaluation of new scRNA-Seq analysis methods.

Inferring chromatin-bound protein complexes from genome-wide binding assays – Genome Research

February 26, 2017

Inferring [w. NMF] chromatin-bound protein complexes [of TFs] from [ENCODE ChIP-seq] binding assays, by @ElementoLab
http://genome.cshlp.org/content/23/8/1295.full

Giannopoulou E, Elemento O. 2013. Inferring chromatin-bound
protein complexes from genome-wide binding assays. Genome Research, Published in Advance April 3, 2013, doi: 10.1101/gr.149419.112.

This study uses nonnegative matrix factorization (NMF) of ENCODE CHIP-seq data (transcription
factors and histone modifications) to predict complexes of
transcription factors that bind DNA
together; it then assesses how these predicted complexes regulate gene expression. It goes beyond
previous studies in that it attempts to treat the TFs as complexes rather than individuals. A handful of
the predicted complexes correspond to known regulatory complexes, e.g. PRC2, and overall, the
complexes were enriched for known protein-protein interactions. Linear regression and random forest
models were then used to predict the effects of the complexes on the expression of adjacent genes. In
both models, the complexes performed better than those predicted from a scrambled TF read count
matrix. Overall, this study provides a large set of hypotheses for combinations of TFs that may
function together, as well as potential new components of known complexes.