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CAARS: comparative assembly and annotation of RNA-Seq data

Carine Rey, Philippe Veber, Bastien Boussau, Marie Sémon, Janet Kelso
2018 Bioinformatics  
We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis.  ...  However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction.  ...  Allio for their contributions to testing and releasing of CAARS.  ... 
doi:10.1093/bioinformatics/bty903 pmid:30452539 pmcid:PMC6596894 fatcat:6zgu2kwjpzf7jncddtotwlcwy4

Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver

Cristian A Alvarez Rojas, Brendan RE Ansell, Ross S Hall, Robin B Gasser, Neil D Young, Aaron R Jex, Jean-Pierre Y Scheerlinck
2015 Parasites & Vectors  
duct, we used RNA sequencing (RNA-seq) to investigate livers from sheep infected for eight weeks compared with those from uninfected controls.  ...  Our molecular findings provide significant new insights into the mechanisms linked to metabolism, fibrosis and tissue-repair in sheep, and highlight the relative importance of specific components of immune  ...  RNA-seq pre-processing, mapping and differential transcription analysis After trimming and correction, a total of 82,557,944 RNA-seq paired-end reads were generated from all cDNA libraries (mean of 13.2  ... 
doi:10.1186/s13071-015-0715-7 pmid:25885344 pmcid:PMC4382932 fatcat:bqneezqgnbat3f6iovnwwkg4gm

Identification of Androgen Receptor Modulators in a Prostate Cancer Cell Line Microarray Compendium

John P Rooney, Brian Chorley, Nicole Kleinstreuer, J Christopher Corton
2018 Toxicological Sciences  
of AR, (2) decreases in availability of androgens by castration or removal from media, and (3) exposure to chemical modulators that work through indirect mechanisms including suppression of AR expression  ...  The biomarker correctly classified 16 out of the 17 AR reference antagonists including those that are "weak" and "very weak".  ...  Department of Energy and EPA.  ... 
doi:10.1093/toxsci/kfy187 pmid:30085300 pmcid:PMC6454424 fatcat:tvciwk3yyreyndkgg54htyjhbu

Single-cell immune repertoire tracing identifies rituximab refractory B cells that emerge during relapse [article]

Roy Jiang, Miriam L. Fichtner, Kenneth B. Hoehn, Panos Stathopoulos, Richard J. Nowak, Steven Kleinstein, Kevin C. OConnor
2019 bioRxiv   pre-print
Computational analysis of these data identified individual B cells that were refractory to rituximab depletion by linking them to clones that were present prior to therapy and continued to persist after  ...  Here we show that rituximab (RTX) therapy is not fully effective at eliminating disease-associated B cells and provide a mechanistic understanding of relapse.  ...  We thank Karen Boss and Abeer Obaid for helpful feedback for the manuscript. We thank Eileen Dimalanta and Chen Song for providing reagents used for the preparation of bulk BCR libraries.  ... 
doi:10.1101/840389 fatcat:hpoa72ll4za7rfs6i6dfk75hwy

Heterochromatin-Driven Nuclear Softening Protects the Genome against Mechanical Stress-Induced Damage

Michele M Nava, Yekaterina A Miroshnikova, Leah C Biggs, Daniel B Whitefield, Franziska Metge, Jorge Boucas, Helena Vihinen, Eija Jokitalo, Xinping Li, Juan Manuel García Arcos, Bernd Hoffmann, Rudolf Merkel (+3 others)
2020 Cell  
A central source of stress is mechanical force that acts on cells, their nuclei, and chromatin, but how the genome is protected against mechanical stress is unclear.  ...  Tissue homeostasis requires maintenance of functional integrity under stress.  ...  ., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550.  ... 
doi:10.1016/j.cell.2020.03.052 pmid:32302590 pmcid:PMC7237863 fatcat:rwpwyhbigbftrbtwpl4v2d47re

Poster Session II

2010 Neuropsychopharmacology  
Results: Genome-wide, RNA-Seq changes associated with alcohol and cocaine addiction were extensive, and included both up-and down-regulation.  ...  In this study we undertook whole genome sequencing of mRNA transcripts in the body of the hippocampus (dentate gyrus and Ammon's horn) using RNA-Seq, a methodology that provides precise, accurate measurements  ...  Compared to the effects on MMP and ATP-levels, effects on mitochondrial morphology were much more pronounced.  ... 
doi:10.1038/npp.2010.217 fatcat:gbcgyi35jbdndlwhlgwio7ts7y