My son, Ronan, who is double-majoring in #biochemistry and #physics, is working at Georgetown University in DC this summer, on a #cancer research internship. His work focuses on #cell-type #deconvolution in spatial #transcriptomics.
I know nothing about biology, but I am assisting him with deconvolution. My MathsTodon friends, have you any guidance to offer, either in mathematics or in biology?
"Scalable image-based visualization and alignment of spatial transcriptomics datasets", by Preibisch et al. 2025 @preibischs
https://www.sciencedirect.com/science/article/pii/S2405471225000973
#transcriptomics #BioimageInformatics
SciTech Chronicles. . . . . . . . .April 2nd, 2025
Landscape #transcriptomics may give insight into what #stresses wild #bees.
#RNA #conservation #AI #genomics #conservation #bumblebees #Bombus #funded_by_USDA #funded_by_us
https://phys.org/news/2025-03-landscape-transcriptomics-insight-stresses-wild.html
Last time teaching Applied Plant Transcriptomics at TU Braunschweig 
Slides & resources: https://github.com/bpucker/AppliedPlantTranscriptomics
#Bioinformatics #Transcriptomics
@PuckerLab
Pipeline release! nf-core/molkart v1.1.0 - 1.1.0 - Resolution Road!
Please see the changelog: https://github.com/nf-core/molkart/releases/tag/1.1.0
Key #genes for #corn #architecture revealed, identifying future #breeding targets.
#agriculture #food-security #genomics #gene_regulation #pleiotropy #transcription_factors #transcriptomics #funded_by_NSF #funded_by_us
https://phys.org/news/2025-03-key-genes-corn-architecture-revealed.html
The #eye is famously a well-accessible extension of the brain. So why not looking into eyes to find out about brain disorders? For #schizophrenia this may become possible as retinal cells are affected. #genomics #transcriptomics https://jamanetwork.com/journals/jamapsychiatry/fullarticle/2829092
Aujourd'hui, Gwenaelle nous partage l'histoire des technologies de transcriptomique : comment faisait-on avant l'ère bénie du séquençage haut débit 
https://bioinfo-fr.net/expression-de-gene-evolution
#bioinfofr #transcriptomics
Interesting opportunity!
A permanent position as an Associate Professor in #Zoology is available
at the #NaturalHistoryMuseum #University of Oslo. #MuseumJobs #EvolutionaryBiology, #comparativegenomics #Transcriptomics #Systematics #populationgenomics
https://www.jobbnorge.no/en/available-jobs/job/268410/associate-professor-in-zoology
deadline February 23rd 2025
A genetic barcoding system lets scientists tag and track cells, making it easier than ever to map gene expression (#transcriptomics) and decode behaviour.
https://elifesciences.org/reviewed-preprints/88334?utm_source=mastodon&utm_medium=social&utm_campaign=organic
Casey Brown was a great scientist and an amazing person. He could always make time to catch up with junior people, give encouragement or just joke about pretty much everything.
Now in his honour some of the leading scientist in #genomics and #complextraits have joint to record the Casey Brown #lectures.
From the basics of human #genetics, to #transcriptomics #epigenetics or #machinelearning for genomics. All free to watch.
https://m.youtube.com/playlist?list=PLlV97eYP56rATGyRK4SSHVXyJjVxPGth_
Cancer cells may change their mechanical properties and thus become able to invade other tissues, i.e. to metastasize. This paper identifies a small network of key genes that tune cell mechanics. https://elifesciences.org/reviewed-preprints/87930 #machinelearning #transcriptomics #cancer
Greetings to i3L students and all life sciences enthusiasts!
i3L proudly presents another episode of Power Talk!
Special in December 2024 Power Talk, i3L proudly invites an expert: Rizky Nurdiansyah .,M.Si (PhD Candidate at Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT))
Register Here: link : https://lnkd.in/gVxJ7v5c
We're looking forward to seeing you! 
metagenomics #i3L #biotechnology #biomedicine #genomics #transcriptomics
Open-ST: High-resolution spatial transcriptomics in 3D #spatial #transcriptomics #python #newtool
https://www.sciencedirect.com/science/article/pii/S0092867424006366
I am very happy to announce that our work on hemichordate gene expression and chromatin accessibility dynamics is now published on Nature Ecology and Evolution! https://www.nature.com/articles/s41559-024-02562-x
Do you know gget by the Pachter lab? You should! It now includes efficient querying of Bgee in Python. Get high quality curated gene expression data directly in Python or command line. https://pachterlab.github.io/gget/en/bgee.html #RNAseq #biocuration #Python #scRNAseq @SIB @marcrr @fbastian @dee_unil
Surprising #hormone-related #gene activity discovered in the early #larval stage of the Malabar #grouper.
#Epinephelus #metamorphosis #transcriptomics
https://phys.org/news/2024-09-hormone-gene-early-larval-stage.html
"Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis", by Wan et al. 2024
https://www.biorxiv.org/content/10.1101/2024.08.27.609868v1
Know your neighbours…
Spatial positioning determines tissue-resident memory T cell fate in the gut.
Marina Schernthanner covers work from Miguel Reina-Campos & colleagues. #preprint
