Posts Tagged ‘transcriptome’

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins : Nature Genetics : Nature Publishing Group

March 3, 2016

Gene-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

http://www.nature.com/ng/journal/v47/n1/full/ng.3162.html

seasonal effects on gene expression

August 9, 2015

Widespread [25% genes] seasonal…expression reveals [circ]annual differences in…immunity, relevant for vaccination http://www.nature.com/ncomms/2015/150512/ncomms8000/full/ncomms8000.html

In addition to circadian rhythms, batch effects, now consider seasonal effects on gene expression

Single cell Genome + Transcriptome Sequencing

July 28, 2015

G&T-seq: parallel…#singlecell genomes & transcriptomes by @CGATist
lab & others http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3370.html low cov. matched data on 130+ cells

https://twitter.com/CGATist/status/604271101678587904

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Iain C Macaulay,
Wilfried Haerty,
Parveen Kumar,
Yang I Li,
Tim Xiaoming Hu,
Mabel J Teng,
Mubeen Goolam,
Nathalie Saurat,
Paul Coupland,
Lesley M Shirley,
Miriam Smith,
Niels Van der Aa,
Ruby Banerjee,
Peter D Ellis,
Michael A Quail,
Harold P Swerdlow,
Magdalena Zernicka-Goetz,
Frederick J Livesey,
Chris P Ponting
& Thierry Voet

Nature Methods 12, 519–522 (2015) doi:10.1038/nmeth.3370Received 18 November 2014 Accepted 27 March 2015 Published online 27 April 2015

Identification of Asthma Phenotypes Using Cluster Analysis in the Severe Asthma Research Program (ATS Journals)

May 30, 2015

Identification of #Asthma Phenotypes Using Cluster Analysis
http://www.atsjournals.org/doi/abs/10.1164/rccm.200906-0896OC#.VWk-gFxViko 5 canonical groups based on lung function, meds usage, &c

Canonical clustering of asthmatic patients into different groups

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.
"}}

The landscape of long noncoding RNAs in the human transcriptome : Nature Genetics : Nature Publishing Group

January 28, 2015

Landscape of lncRNAs in the human #transcriptome
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3192.html Derived from RNAseq read assembly; not much overlap w/ @GencodeGenes

Matthew K Iyer,
Yashar S Niknafs,
Rohit Malik,
Udit Singhal,
Anirban Sahu,
Yasuyuki Hosono,
Terrence R Barrette,
John R Prensner,
Joseph R Evans,
Shuang Zhao,
Anton Poliakov,
Xuhong Cao,
Saravana M Dhanasekaran,
Yi-Mi Wu,
Dan R Robinson,
David G Beer,
Felix Y Feng,
Hariharan K Iyer
& Arul M Chinnaiyan

Nature Genetics (2015) doi:10.1038/ng.3192Received 20 June 2014 Accepted 18 December 2014

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

Blood transciptome paper

September 28, 2014

Splicing changes along the blood lineage, good ex. of the
state-of-the-art in human transcriptomics
http://www.sciencemag.org/content/345/6204/1251033.abstract

Science 26 September 2014:
Vol. 345 no. 6204
DOI: 10.1126/science.1251033

Transcriptional diversity during lineage commitment of human blood progenitors

Chen et al.

Pseudogene expression in TCGA data

July 11, 2014

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

Characterization of the human ESC transcriptome by hybrid sequencing

May 27, 2014

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