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
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#Transcriptomics
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Does anyone know where the @bioconductor {estrogen} dataset is derived from?
https://www.bioconductor.org/packages/release/data/experiment/html/estrogen.html
The vignette doesn't really give any details on what the time component is, for example. And I'm sure these are probably sub-samples from an actual experiment that was published somewhere, but I'd love to know where from if it's actually published.
BioconductorestrogenData from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level).
Doing QC-QA on a new multi-omics dataset (bulk rna-seq, and then three metabolomics), and it's weird to see different analytes having different correlations amongst samples, where there will be a possible outlier for one type but not another.
It is paired though, cancer with adjacent "normal", so it will be interesting to see if I still get any odd-balls after doing cancer / normal ratios and calculating patient - patient correlations.
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@SIB @alfonsovalencia such an important part / responsibility of bioinformatics is to make your raw data available for others to re-use for their own means. No better way also to increasee value for money for the sizeable investment of generating such data! #bioinformatics #genomics #Transcriptomics
Very happy that our review paper "A primer on #correlation-based #dimension #reduction methods for #multi-omics analysis" is out. Thanks to the reviewers & journal too for their help.
https://royalsocietypublishing.org/doi/10.1098/rsif.2023.0344
#genomics #omics #systems #data #model #modelling #biology #transcriptomics
Dear All,
The Workshop on Genomics, and the Workshop on Phylogenomics are now open for applications for 2024!
Workshop on Genomics - 7th - 20th January 2024 - https://evomics.org/2024-workshop-on-genomics/
Workshop on Phylogenomics - 21st - 2nd February 2024 - https://evomics.org/2024-workshop-on-phylogenomics-cesky-krumlov/
There is also some limited Equal Opportunities funding available.
#bioinformatics #genomics #phylogenomics
#transcriptomics #evomics24 #evomics2024
Image-seq - cool tech for #spatial #transcriptomics though looks like it needs a fancy laser micro-dissection microscope. Need to read more about it...#Science #immunology
https://www.nature.com/articles/s41577-023-00912-7?utm_source=nri_etoc&utm_medium=email&utm_campaign=toc_41577_23_8&utm_content=20230727
NatureImage-seq: image-guided cell isolation for spatially resolved transcriptomic analysis - Nature Reviews ImmunologyIn this Tools of the Trade article, Christa Haase (at the Charles Lin lab) describes a technique called Image-seq that enables image-guided cell isolation from a specific, intact tissue location for subsequent single-cell gene expression analysis.
Hey there!
I'm a French researcher in developmental biology, focusing on mammalian sex determination and gonadal development at the genetic level. I have a PhD in bioinformatics but I do wet and dry lab.
I am a free (as in freedom) and open source software advocate, formerly actively involved in FOSS groups.
I love dataviz, photography, classic rock music, and playing video games.
I moved from another Mastodon instance.
#introductions #stem #DevBio #genetics #genomics #transcriptomics #SexDet
If you've ever felt like you are in over your head trying to define #RStats linear models for your -omics experiments, this paper does an excellent job of showing the reasoning why the model is defined that way, what contrasts you want to define, and what is actually being tested.
A guide to creating design matrices for gene expression experiments
https://f1000research.com/articles/9-1444/v1
These apply to more than just gene expression #transcriptomics. Work for #proteomics and #metabolomcs too. 
f1000research.comF1000Research Article: A guide to creating design matrices for gene expression experiments.Read the latest article version by Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie, at F1000Research.
Yet another violation of the 'central dogma' of molecular biology thinking a single gene (ORF) makes a single #transcriptomics of #connectomics of a #covid protein https://pubmed.ncbi.nlm.nih.gov/33774510/
PubMedConflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution - PubMedAt least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and func …
Epigenomes & transcriptomes are clearly related, and merit co-analysis.
If we're going to do spatial analyses, no reason (other than technical & financial!) that we shouldn't consider both transcriptomic & epigenetic assessments concurrently in these experiments too.
#Science #ScienceMastodon #academia #transcriptomics #spatial #epigenetics
I forgot to do this, so here it is:
Hello #mastodon! I'm Luca, a #PhD student in #complexsystems at the University of Turin (#unito).
I mainly work in #genomics and #transcriptomics. My project involves the study of the #cancer #transportome, and its role in the overall #cellbiology.
I code in #python and #R, but i'm trying to (slowly) learn about #rustlang. I use #archlinux, btw.
I also play a ton of #boardgames and #videogames. I love #mechanicalkeyboard (s) and own a #corne myself.
Includes my interview with 10xGenomics! #neuroscience #transcriptomics #spatialtranscriptomics #datascience #bioinformatics #developmentalbiology #SfN22 #SfN2022
Where neuroscientists go to connect: Recapping Society for Neuroscience 2022
https://www.10xgenomics.com/blog/where-neuroscientists-go-to-connect-recapping-society-for-neuroscience-2022
10x GenomicsWhere neuroscientists go to connect: Recapping Society for Neuroscience 2022 - 10x GenomicsFind highlights from SfN 2022, including new single cell and spatial research, and our poster contest winners!
An #introduction of sorts:
My name is Ron! I’m a senior undergraduate student in Florida studying Biology with an emphasis on Molecular Biology. I’m mainly interested in the #microbiome #metabolomics #transcriptomics #bioinformatics #bacteria and #fungi secondary metabolites (along with tons of other random stuff). Excited to wander around the Fediverse!
Hello everyone! Here is my #introduction.
I'm a #bioinformatics manager at the Canadian Centre for Computational Genomics (C3G), based in #McGill University.
Most recently, I helped coordinate the bioinformatics analysis for the #COVID19 sequencing effort in the province of Quebec. Additionally, I have experience in #transcriptomics, #GenomeAssembly and #OxfordNanopore, among other things.
Excited to give this new platform a try, so far, so good!
#introduction
Heyo, I'm a #bioinformatician nearing the end of my PhD at #OsloMet , working with #transcriptomics and microRNA in Salmon, though my secret love is for #syntheticbiology .
Other interests include #gaming #dnd #polyamory #philosophy #transhumanism (the egalitarian European kind, libertarians beware), #maker and #Hacker culture, sci-fi and #fantasy (particularly Clarke and Pratchett), #cryptography (fuck cryptocurrency and web3), #art and #theatre .
Currently listening to #mika
I guess it might be time for an #introduction on this site.
I am a research analyst in academic #bioinformatics. I'm interested in new computational #metabolomics methods, #transcriptomics, data integration, etc.
I know just enough #statistics to be useful / dangerous, depending on your POV.
I use #rstats heavily (in a lab that mostly uses #python), and believe in the value of graphing your data, as well as making work reproducible and as open as possible.