Posts Tagged ‘jclub’

Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma (ATS Journals)

May 30, 2015

Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma http://www.atsjournals.org/doi/abs/10.1164/rccm.201408-1440OC Consistent blood expression patterns

Noninvasive Analysis of the Sputum Transcriptome Discriminates
Clinical Phenotypes of Asthma (ATS Journals)

Yan, X., Chu, J.-H., Gomez, J., Koenigs, M., Holm, C., He, X., Perez,
M. F., Zhao, H., Mane, S., Martinez, F. D., Ober, C., Nicolae, D. L.,
Barnes, K. C., London, S. J., Gilliland, F., Weiss, S. T., Raby, B.
A., Cohn, L., and Chupp, G. L. “Non-Invasive Analysis of the Sputum
Transcriptome Discriminates Clinical Phenotypes of Asthma” American
Journal of Respiratory and Critical Care Medicine (2015):
doi:10.1164/rccm.201408-1440OC,

QT:{{"
Conclusions: There are common patterns of gene expression in the
sputum and blood of children and adults that are associated with near
fatal, severe and milder asthma.
"}}

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

April 5, 2015

Circadian #Enhancers Coordinate… Rhythmic… Transcription http://www.cell.com/cell/abstract/S0092-8674%2814%2901310-5
Periodicity helps find #eRNAs/enhancers & their targets

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance : Nature Genetics : Nature Publishing Group

March 29, 2015

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3222.html

Nat Genet. 2015 Mar 2. doi: 10.1038/ng.3222. [Epub ahead of print]

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.

Crowley JJ1, Zhabotynsky V1, Sun W2, Huang S3, Pakatci IK3, Kim Y1, Wang JR3, Morgan AP4, Calaway JD4, Aylor DL1, Yun Z1, Bell TA4, Buus RJ4, Calaway ME4, Didion JP4, Gooch TJ4, Hansen SD4, Robinson NN4, Shaw GD4, Spence JS1, Quackenbush CR1, Barrick CJ1, Nonneman RJ1, Kim K5, Xenakis J5, Xie Y1,Valdar W6, Lenarcic AB1, Wang W3, Welsh CE3, Fu CP3, Zhang Z3, Holt J3, Guo Z3, Threadgill DW7, Tarantino LM8, Miller DR4, Zou F5, McMillan L3, Sullivan PF9, Pardo-Manuel de Villena F4.

http://www.nature.com/ng/journal/v47/n4/full/ng.3222.html

Carefully controlled allele expt – hets midway in expr betw homs for parents for 76pct (additive model) but 25pct hets diff. from parents

ASE in…divergent mouse crosses identifies pervasive allelic imbalance, 80%, w/ 60% closely following additive model
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3222.html

Genotype to phenotype relationships in autism spectrum disorders : Nature Neuroscience : Nature Publishing Group

February 26, 2015

Genotype to phenotype relationships in ASD http://www.nature.com/neuro/journal/v18/n2/abs/nn.3907.html Expression differences in #brain development for LOF-containing, M v F, &c

Also, netbag finds subnets assoc w autism

A load driver device for engineering modularity in biological networks : Nature Biotechnology : Nature Publishing Group

December 9, 2014

A load driver device for engineering modularity in…#networks http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3044.html Allows joining components w/o downstream retroactivity

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study : Nature Biotechnology : Nature Publishing Group

October 10, 2014

Multiplatform assessment of #transcriptome profiling [w.] RNAseq http://www.nature.com/nbt/journal/v32/n9/full/nbt.2972.html Nice plots showing great effect of poly-A selection

Constructing structural networks of signaling pathways on the proteome scale

September 6, 2014

Structural networks of signaling pathways
http://www.sciencedirect.com/science/article/pii/S0959440X1200070X Prism on IL10 #networks, mapping on Cosmic, disrupting mutations as drivers

Genome-scale functional characterization of Drosophila developmental enhancers in vivo : Nature : Nature Publishing Group

August 13, 2014

Functional characterization of… developmental #enhancers in vivo: 3.5k of 7.7k tested active in fly embryo stages
http://www.nature.com/nature/journal/v512/n7512/abs/nature13395.html

“An information-theoretic framework for resolving community structure in complex networks.” Proceedings of the National Academy of Sciences

June 12, 2014

Rosvall, Martin, and Carl T. Bergstrom. “An information-theoretic framework for resolving community structure in complex networks.” Proceedings of the National Academy of Sciences 104.18 (2007): 7327-7331.

Info-theoretic framework for… community structure in complex #networks. Compression v modularity, former better?
http://www.pnas.org/content/104/18/7327.short

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

June 1, 2014

Massive Genomic Decay in… a Recently Evolved #Symbiont of Aphids. Creation of #pseudogenes in many COG categories
http://gbe.oxfordjournals.org/content/3/195.long

Gaelen R. Burke & Nancy A. Moran