Thompson et al. model gene expression as a binary trait to examine transcriptome turnover across Drosophila species, inferring gains and losses of organ-specific expression.

🔗 doi.org/10.1093/molbev/msaf106

#molbio #evobio #transcriptomic #drosophila

Understanding scale #insect #phylogenetics is critical to combating these #agricultural pests. Song et al. use #genomic and #transcriptomic data to construct a phylogenetic analysis of Hemiptera: Coccoidea.
https://doi.org/10.1111/jse.13141
@WileyEcolEvol
#evolution #CropSci #JSE

First-of-its-kind integrated dataset enables #genes-to-#ecosystems research.

#g2e #microbiome #soil #biome_omics #metagenomic #metabolomic #transcriptomic

https://phys.org/news/2024-04-kind-dataset-enables-genes-ecosystems.html

Being queen is all in this #termite's head, finds #gene expression study.

#queen_central_module #transcriptomic #upregulation #totipotent

https://phys.org/news/2024-03-queen-termite-gene.html

#Bamboo sp. Dendrocalamus brandisii is a valuable source of both #food and #wood. Jiang et al. combine #genomic, #transcriptomic, and #metabolomic analyses to help further the #development of this valuable resource.🔓⬇️🎍
https://doi.org/10.1111/jipb.13592
@wileyplantsci
#JIPB #PlantSci #botany

Researchers Create Comprehensive Map of Mouse Brain
https://www.sci.news/biology/mouse-brain-atlas-12542.html #Transcriptomic #cellーtype #taxonomy #whole #mouse #brain #atlas #epigenome

Using #transcriptomic and population #genomic analyses, map-based #cloning, and functional characterizations, Ren et al. explore post-transcriptional #regulation of #grain weight and shape by the RBP-A-J-K complex in #rice
https://doi.org/10.1111/jipb.13583
@wileyplantsci
#JIPB #PlantSci #PlantScience #botany

`Investigations..ascertain that the motors are non-toxic..#transcriptomic analysis affirms that the motors are not genotoxic..#Toxicity studies in mice reveal that the motors show no signs of toxicity up to a dose of 55 mg/ kg body weight..biodistribution studies show that they remain in the blood circulation after injection and..possibly adhere to the walls of the blood vessel..we demonstrate the #biocompatibility of #nanomotors in live cellular and organismal systems`

https://www.sciencedirect.com/science/article/abs/pii/S2772950822003259

Now Golnaz Vahedi from UPenn
https://vahedilab.com/
speaking on
"Modeling Type 1 #Diabetes progression from single-cell #transcriptomic measurements in #human #islets

Vision is to do #SingleCell profiling of #pancreatic cells and peripheral blood, simultaneously, to identify patients who can benefit from early interventions

https://www.nature.com/articles/s42255-022-00531-x

#CSSingleCells23

Large-scale across species #transcriptomic analysis identifies genetic selection signatures associated with #longevity in mammals

Organ-specific expression patterns of #methionine restriction and translation fidelity genes correlate with longevity in 103 #mammalian species

https://www.embopress.org/doi/full/10.15252/embj.2022112740

🔓⬇️#OpenAccess #PlantScience for your weekend!
#Genomic, #transcriptomic, and #metabolomic analysis of Oldenlandia corymbosa reveals the #biosynthesis and mode of action of anti-#cancer metabolites.
https://doi.org/10.1111/jipb.13469
@wileyplantsci
#JIPB #PlantSci #medicine #PlantScience

#Cochlea #cell atlas built from single-cell sequencing discovers new cell types, uncovers hidden molecular features.

#genomics #transcriptomic #Emilin2 #mRNA

https://phys.org/news/2023-06-cochlea-cell-atlas-built-single-cell.html

And this simulation #rstats code, shows why one must use use very short seeds when using #blast to map #nanopore #transcriptomic #RNAseq data (Q10 quality scores are not unheard of, in such datasets).

Take home message, one has got to work for their database searches for long read platforms
(R code in the alt description)

High-resolution #transcriptomic and #epigenetic profiling identifies novel regulators of chronic obstructive pulmonary disease #COPD
Multi-omics resource of primary human lung #fibroblasts across COPD stages by Renata Jurkowska and coworkers at Cardiff University

https://www.embopress.org/doi/10.15252/embj.2022111272

New method developed to infer #gene #regulatory networks from single-#cell #transcriptomic data.

https://phys.org/news/2023-04-method-infer-gene-regulatory-networks.html

Alright, #bioinformatics folk, which multiple sequence #alignment and #clustering packages should I add to my #transcriptomic @nanopore workflow?
Linclust, uclust/ cd-hit are candidates for clustering.
Candidates for MSA: clustal/kalign/hmmalign.
Other suggestions? #nanopore #sequencing

Another Atlassing talk 😆, from Kimberly Siletti: #transcriptomic cell-type diversity across the human #brain.

Don't miss this great #OpenAccess #review in @Non_Coding_RNA about #MicroRNA resources- it has a wonderful section about the contributions and use of the #GeneOntology for examining #transcriptomic data: DOI: 10.3390/ncrna9020018
---
RT @UCLgene
Fantastic to see my previous student, Diana Luna Buitrago, writing this great review of microRNA analysis tools: Insights into Online microRNA Bioinformatics Tools https://www.mdpi.com/2311-553X/9/…
https://twitter.com/UCLgene/status/1632682509069680641

12 #PhD positions in the LongTREC #European #MarieCurie Network - a programme that will develop methods and tools for the analysis of #transcriptomic data obtained with the most recent single-molecule, long-reads #sequencing technologies.

https://career.longtrec.eu/#section-jobs

Absolutely fantastic new paper from Marie Brasseur & @leeselab in @BioMedCentral featuring Gammarus fossarum - a wonderful demonstration of the #geneontology in use (thanks for the citation!) @VascoElbrecht @rksalis @weiss_martina @Daniel_G1978 #goannotation
---
RT @leeselab
New study by our @unidue team & @Leibniz_LIB on #multiplestressor impacts lead by Marie Brasseur 🎉. We herein focused on #transcriptomic analysis of the #freshwater k…
https://twitter.com/leeselab/status/1601184358370459648