Adam D Ewing, Tracy J Ballinger, Dent Earl, Broad Institute Genome Sequencing and Analysis Program, Christopher C Harris, Li Ding, Richard K Wilson and David Haussler
Archive for the 'SciLit' Category
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
March 17, 2013Absolute quantification of somatic DNA alterations in human cancer
March 17, 2013Nat Biotechnol. 2012 May;30(5):413-21. doi: 10.1038/nbt.2203. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G.
Facebook ‘likes’ can predict gender, ethnicity etc….
March 17, 2013http://www.pnas.org/content/early/2013/03/06/1218772110.abstract Private traits and attributes are predictable from digital records of human behavior
Michal Kosinskia
David Stillwella, and
Thore Graepelb
regulatory cancer drivers
March 11, 2013http://www.nytimes.com/2013/01/25/science/new-mutations-discovered-in-melanomas.html
Two papers in Science talking about recurrent mutations in TERT promoter in melanoma.
1) http://www.sciencemag.org/content/339/6122/957.full
Highly Recurrent TERT Promoter Mutations in Human Melanoma
Franklin W. Huang1,2,3,* Eran Hodis1,3,4,*,Mary Jue Xu1,3,4,Gregory V. Kryukov1,Lynda Chin5,6,Levi A. Garraway1,2,3,†
2) http://www.sciencemag.org/content/339/6122/959.full
TERT Promoter Mutations in Familial and Sporadic Melanoma
Susanne Horn1,2,Adina Figl1,2,P. Sivaramakrishna Rachakonda1,Christine Fischer3,Antje Sucker2,Andreas Gast1,2,Stephanie Kadel1,2,Iris Moll2,Eduardo Nagore4,Kari Hemminki1,5,Dirk Schadendorf2,*,†,Rajiv Kumar1,*,†
bio v tech rep
March 11, 2013http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1910.html
discusses (at a very basic level) the issue of tech versus bio reps related class:
correlated noise in TF co-association / FFLs
March 9, 2013http://dx.doi.org/10.1016/j.bpj.2013.01.033
Cross Talk and Interference Enhance Information Capacity of a Signaling Pathway Sahand Hormoz
QT:”
A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we suggest that this motif maximizes information flow in a noisy network. Gene expression is an inherently noisy process due to thermal fluctuations and the small number of molecules involved. A consequence of multiple TFs interacting at overlapping binding sites is that their binding noise becomes correlated. Using concepts from information theory, we show that in general a signaling pathway transmits more information if 1), noise of one input is correlated with that of the other; and 2), input signals are not chosen independently.
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Cell – Identifying Recent Adaptations in Large-Scale Genomic Data
March 9, 2013pos. sel. from 1000G phase 1
http://www.cell.com/retrieve/pii/S0092867413000871
Cell, Volume 152, Issue 4, 703-713, 14 February 2013
Copyright © 2013 Elsevier Inc. All rights reserved.
10.1016/j.cell.2013.01.035
Sharon R. Grossman,Kristian G. Andersen,Ilya Shlyakhter,Shervin Tabrizi,Sarah Winnicki,Angela Yen,Daniel J. Park,Dustin
Griesemer,Elinor K. Karlsson,Sunny H. Wong,Moran Cabili,Richard A. Adegbola,Rameshwar N.K. Bamezai,Adrian V.S. Hill,Fredrik O.
Vannberg,John L. Rinn,1000 Genomes Project,Eric S. Lander,Stephen F. Schaffner,Pardis C. Sabeti
The epidemic of allergy and asthma : Nature
March 4, 2013~15 year old review but still interesting
http://www.nature.com/nature/journal/v402/n6760supp/full/402b002a0.html
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