Expanded seq. context model…explains variability in polymorphism[s] http://www.nature.com/NG/journal/vaop/ncurrent/full/ng.3511.html Reminiscent of GOR sec. structure prediction
Posts Tagged ‘jclub’
AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms
March 19, 2016http://dx.doi.org/10.1093/bioinformatics/btw120
http://AlgoRun.org, #Docker-based packaging [w/ web GUI & workflow mgt] for platform-agnostic implement[ations]
http://Bioinformatics.Oxfordjournals.org/content/early/2016/03/02/bioinformatics.btw120
Hosny, A. et al. AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics Advance Access, Mar 2, 2016.
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription: Cell
March 4, 2016CTCF-Mediated…3D Genome Architecture
http://www.cell.com/cell/abstract/S0092-8674(15)01504-4 SNPs give different #chromatin topologies, including strong #allelic effects
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins : Nature Genetics : Nature Publishing Group
March 3, 2016Gene-gene & gene-env interactions…by #transcriptome…in twins by @dermitzakis lab
http://www.nature.com/ng/journal/v47/n1/full/ng.3162.html Nice model for ASE HT @cjieming
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Hou-Feng Zheng, J Brent Richards, Daniel Glass, Kerrin S Small, Richard Durbin, Timothy D Spector & Emmanouil T Dermitzakis
Similarity network fusion for aggregating data types on a genomic scale : Nature Methods : Nature Publishing Group
February 9, 2016Similarity #network fusion for aggregating data types
http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2810.html Combines mRNA, miRNA & gene fusions to classify cancer subtypes http://compbio.cs.toronto.edu/SNF/SNF
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution : Nature : Nature Publishing Group
January 23, 2016Dynamics of genomic clones in breast #cancer PDX at #singlecell resolution http://www.nature.com/nature/journal/v518/n7539/full/nature13952.html Extensive trees of samples & some WGS
Peter Eirew,
Adi Steif,
Jaswinder Khattra,
Gavin Ha,
…
Jazmine Brimhall,
Arusha Oloumi,
Tomo Osako
et al.
Nature 518, 422–426 (19 February 2015) doi:10.1038/nature13952
Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells | Science
January 13, 2016#SingleCell #RNASeq Reveals Dynamic, Random Monoallelic Gene Expression, occurring in ~20% of genes in mice cells
http://science.sciencemag.org/content/343/6167/193.abstract
PLOS Computational Biology: Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations
December 18, 2015Folding by Chaperones Accelerates Evolutionary Dynamics
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003269 Multiscale models link NT mutations, PPIs & cell populations
Cell type- and brain region-resolved mouse brain proteome : Nature Neuroscience : Nature Publishing Group
December 13, 2015Celltype & region–resolved mouse brain proteome
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html proteins enriched there v liver & in specific regions (eg NCX v STR)
http://www.nature.com/neuro/journal/v18/n12/full/nn.4160.html
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells : Nature Biotechnology : Nature Publishing Group
November 14, 2015Heterogeneity in #singlecell RNAseq…hidden subpopulations by @OliverStegle lab http://www.nature.com/nbt/journal/v33/n2/full/nbt.3102.html scLVM corrects for cell cycle phase
Buettner, Florian, Kedar N. Natarajan, F. Paolo Casale, Valentina
Proserpio, Antonio Scialdone, Fabian J. Theis, Sarah A. Teichmann,
John C. Marioni, and Oliver Stegle. "Computational analysis of
cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals
hidden subpopulations of cells." Nature biotechnology 33, no. 2
(2015): 155-160.
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