Posts Tagged ‘rnaseq’

Pacbio MCF-7 transscriptome dataset

Wednesday, July 30th, 2014



Mirsynergy: detecting synergistic miRNA regul… Bioinformatics. 2014 – PubMed – NCBI

Saturday, July 19th, 2014

Mirsynergy: detecting synergistic #miRNA regulatory modules by… neighborhood expansion creates overlapping clusters

Pseudogene expression in TCGA data

Friday, July 11th, 2014

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 :)

Saturday, June 28th, 2014

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)

Characterization of the human ESC transcriptome by hybrid sequencing

Tuesday, May 27th, 2014

Characterization of the… #transcriptome by hybrid sequencing, using Illumina reads to error-correct #PacBio ones

Developmental dynamics and disease potential of random monoallelic gene expression.

Sunday, April 6th, 2014

Developmental dynamics… of random monoallelic gene expression. #RNAseq on 100s of instances without causative SNPs

An analysis of differentiated cell lines.

number of transcription factor molecules per cell

Thursday, March 6th, 2014

System-wide analyses have underestimated #protein abundances… Corrected protein conc. better correlated w/ #mRNA

…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

Sunday, March 2nd, 2014

NA12878 high confidence calls

Thursday, February 20th, 2014

Integrating genotype from many callers & indication of where they differ. Might be useful for the personal diploid genome.

Singled out for sequencing : Nature Methods : Nature Publishing Group

Monday, January 27th, 2014

Nice piece on #SingleCell Seq w/ implications for #cancer, neurosci, &c. Singled out for #sequencing HT @naivelocus

Lots on brain, cancer & prenatal sequencing, viz:

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.