Posts Tagged ‘jclub’

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors : Nature Genetics : Nature Research

May 6, 2017

http://www.nature.com/ng/journal/v49/n5/full/ng.3818.html

Ref component analysis..of transcriptomes, by @Robson_Paul &co http://www.Nature.com/ng/journal/v49/n5/full/ng.3818.html Clustering similarity of samples to tissue references

Aging increases cell-to-cell transcriptional variability upon immune stimulation | Science

April 21, 2017

#Aging increases cell-to-cell transcriptional variability upon immune stimulation, but just for 225 up-reg. genes http://science.ScienceMag.org/content/355/6332/1433

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression: Cell

April 16, 2017

"Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression"

(http://www.sciencedirect.com/science/article/pii/S0092867417301289)

#Neanderthal-Introgressed Sequences [&]…Gene Expression http://www.Cell.com/cell/abstract/S0092-8674(17)30128-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867417301289%3Fshowall%3Dtrue ASE for Hn SNPs shows lower #brain expression vs reference

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

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

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

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human: Cell

February 24, 2017

FissionNet: Proteome-wide [pombe] Interactome Reveals #Network Evolution Principles
http://www.Cell.com/cell/abstract/S0092-8674(15)01556-1 Involving ~1300 soluble proteins

JClub papers

February 16, 2017

A #circadian gene-expr atlas in mammals by @jbhclock lab
http://www.PNAS.org/content/111/45/16219.abstract 43% of genes have a daily rhythm in at least 1 tissue [1/2]

.@jbhclock Fewest circadian genes in brain; most in liver. Perhaps this more reflects daily feeding cycle than true light-dark cycle? [2/2]

A circadian gene expression atlas in mammals: Implications for biology and medicine

Ray Zhanga,1,
Nicholas F. Lahensa,1,
Heather I. Ballancea,
Michael E. Hughesb,2, and
John B. Hogenescha,2

* Interestingly brain regions have the fewest circ genes(only ~3%), liver has most

* Diseases assoc with circadian genes correlate with NIH funding

* Genes can have up to a 6-hour phase diff. Between diff. organs (eg Vegfa betw. Heart & fat)

* 56 of the top 100 drugs incl. Top 7, targeted the product of a circadian gene. Related to the half-life of drugs.

* Could the liver genes be more reflective of feeding rhythm rather than true circadian clock.

Jclub Paper

January 28, 2017

#RNA Struc. Determinants of Optimal Codons…by MAGESeq
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4 Probing effect of synonymous changes; towards a better dN/dS

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4