Mirsynergy: detecting synergistic #miRNA regulatory modules by… neighborhood expansion
http://www.ncbi.nlm.nih.gov/pubmed/24894504 creates overlapping clusters
Posts Tagged ‘rnaseq’
Mirsynergy: detecting synergistic miRNA regul… Bioinformatics. 2014 – PubMed – NCBI
July 19, 2014Pseudogene expression in TCGA data
July 11, 2014http://www.nature.com/ncomms/2014/140707/ncomms4963/full/ncomms4963.html
The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes
Leng Han
Yuan Yuan
Siyuan Zheng
Yang Yang
Jun Li
Mary E. Edgerton
Lixia Diao
Yanxun Xu
Roeland G. W. Verhaak
Han Liang
Looking for a tool to find fusion transcript — use Grep :)
June 28, 2014The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099439
Characterization of the human ESC transcriptome by hybrid sequencing
May 27, 2014Characterization of the… #transcriptome by hybrid sequencing, using Illumina reads to error-correct #PacBio ones
http://www.pnas.org/content/110/50/E4821.long
Developmental dynamics and disease potential of random monoallelic gene expression.
April 6, 2014Developmental dynamics… of random monoallelic gene expression. #RNAseq on 100s of instances without causative SNPs
An analysis of differentiated cell lines.
http://www.cell.com/developmental-cell/abstract/S1534-5807(14)00057-4
number of transcription factor molecules per cell
March 6, 2014System-wide analyses have underestimated #protein abundances… Corrected protein conc. better correlated w/ #mRNA
https://peerj.com/articles/270
…once a non linear bias in mass spec. data is corrected, the concentration of the factor expressed at the median level is present at 70,000 molecules per cell. ….
Li, J, Bickel, P.J. and Biggin M.D. (2014) System Wide Analyses have Underestimated Protein Abundances and the Importance of Transcription in Mammals. PeerJ DOI10.7717/peerj.270
Detection and replication of epistasis influencing transcription in humans : Nature : Nature Publishing Group
March 2, 2014NA12878 high confidence calls
February 20, 2014Integrating genotype from many callers & indication of where they differ. Might be useful for the personal diploid genome.
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2835.html
Singled out for sequencing : Nature Methods : Nature Publishing Group
January 27, 2014Nice piece on #SingleCell Seq w/ implications for #cancer, neurosci, &c. Singled out for #sequencing
http://www.nature.com/nmeth/journal/v11/n1/full/nmeth.2768.html HT @naivelocus
Lots on brain, cancer & prenatal sequencing, viz:
QT:{{”
For example, as part of the Single Cell Analysis Program supported by the US National Institutes of Health Common Fund, Kun Zhang’s team will generate full transcriptomes from 10,000 cells in three areas of the human cortex. They will group the transcripts into cell
types—perhaps redefining those cell types in the process—and map the transcripts back to cortical slices of the brain. Single-cell RNA-seq itself is no longer a barrier. “If you have a good cell, and you want to get a measure of the transcriptome, there is more than one option that can lead you to that goal,” Zhang says. In general, however, extracting the neurons posthumously, minimizing RNA degradation and preserving some of the neuronal spatial information is challenging, and the group is evaluating several approaches, Zhang says.
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The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species
January 27, 2014Quite relevant to #transcriptome changes over #development: Earliest Transcribed… Genes Are Short, Newly Evolved…
http://www.cell.com/cell-reports/fulltext/S2211-1247(13)00788-2
linkstream2 microblog 