Sinan U. Umu
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sinanugur.github.io
Sinan U. Umu
@sinanugur.github.io
11 followers 15 following 1 posts
Physicist, I do (Computational Biology, Bioinformatics, Biostatistics)
Researcher @ Department of Pathology (UiO)

Available on Bioconda:
MirMachine, cellsnake

On PyPi:
Easydecon
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sinanugur.github.io
Sinan U. Umu @sinanugur.github.io · Apr 25
Our new spatial analysis tool is out: Easydecon: A Lightweight Workflow for Cell Type Analysis in High-Definition Spatial Transcriptomics Assays www.biorxiv.org/content/10.1...
Easydecon: A Lightweight Workflow for Cell Type Analysis in High-Definition Spatial Transcriptomics Assays
Spatial transcriptomics enables mapping gene expression within tissue structures. The VisiumHD platform by 10x Genomics advances this further, offering near-single-cell resolution across tissue sectio...
www.biorxiv.org
sinanugur.github.io
Our new spatial analysis tool is out: Easydecon: A Lightweight Workflow for Cell Type Analysis in High-Definition Spatial Transcriptomics Assays www.biorxiv.org/content/10.1...
Easydecon: A Lightweight Workflow for Cell Type Analysis in High-Definition Spatial Transcriptomics Assays
Spatial transcriptomics enables mapping gene expression within tissue structures. The VisiumHD platform by 10x Genomics advances this further, offering near-single-cell resolution across tissue sectio...
www.biorxiv.org
April 25, 2025 at 7:46 AM
Reposted by Sinan U. Umu
marcfriedlander.bsky.social
We are extremely grateful to receive an ERC proof-of-concept grant! The funding will go into developing and testing methods to apply RNA profiling to detect food fraud. 🥳🥦🥩🇪🇺

The research will be conducted at @stockholmuni.bsky.social and @scilifelab.se

erc.europa.eu/news-events/...
134 researchers supported to turn their science into practice
In the final round of the 2024 European Research Council (ERC) Proof of Concept grant competition, 134 projects will receive support, bringing the total number of grants awarded under the 2024 work pr...
erc.europa.eu
January 24, 2025 at 7:51 AM
Reposted by Sinan U. Umu
phylogenomics.bsky.social
An important read for all microbiome researchers #microbiomania www.theguardian.com/science/2024...
There’s little evidence of a ‘brain microbiome’ | Letter
Letters: Prof Mark Pallen, Dr Aimee Parker, Prof Nick Loman and Prof Alan Walker take issue with an article that discussed the existence of a brain microbiome and its impact on diseases
www.theguardian.com
December 20, 2024 at 3:28 PM
Reposted by Sinan U. Umu
erictopol.bsky.social
MicroRNAs
From their role in cancer
jci.org/articles/vie...
to
Rejuvenating aged mice, w/ enhanced physical and cognitive function, and longevity
sciencedirect.com/science/arti...
+ explainer
nature.com/articles/d41...
January 17, 2025 at 9:08 PM
Reposted by Sinan U. Umu
frommlab.bsky.social
MirGeneDB 3.0 is published.
Great teamwork and substantial improvement of database, Taxon sampling and we took over nomenclature of novel genes and families, too

academic.oup.com/nar/advance-...
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models
Abstract. We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation
academic.oup.com
November 30, 2024 at 11:46 AM