linkstream2 microblog

BLOG:
http://blog.pacificbiosciences.com/2013/12/data-release-human-mcf-7-transcriptome.html

DATASETS:
http://datasets.pacb.com.s3.amazonaws.com/2013/IsoSeqHumanMCF7Transcriptome/list.html

Mirsynergy: detecting synergistic #miRNA regulatory modules by… neighborhood expansion
http://www.ncbi.nlm.nih.gov/pubmed/24894504 creates overlapping clusters

http://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

The “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… #transcriptome by hybrid sequencing, using Illumina reads to error-correct #PacBio ones
http://www.pnas.org/content/110/50/E4821.long

Developmental 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

System-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

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13005.html

Integrating 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

Nice 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.
“}}