#transcriptomics — Public Fediverse posts

https://www.europesays.com/uk/989281/ Gene-expression patterns can be used to estimate mortality risk and chronological age – Nature #Ageing #ComputationalBiologyAndBioinformatics #Health #HumanitiesAndSocialSciences #multidisciplinary #Science #Transcriptomics #UK #UnitedKingdom

Our paper (with Julie Cartier, Johanna Lagoas, Youmna Ayadi, Adeline Fermanian and @flomass) on the use of statistical knockoffs for the differential analysis of transcriptomics data just came out, very appropriately as it nicely illustrates my point:
https://academic.oup.com/bib/article/27/3/bbag148/8687371

Using simulated outcomes on real transcriptomics data, we've shown that KOs (and in particular, the KOPI approach) do retrieve important variables with better power than classical approaches (Wilcoxon, Lasso), while controlling FDR.

However, all methods perform poorly when the relationship between gene expressions and outcome is nonlinear.

On real outcomes, the method is overly conservative (having no discoveries is a surefire way of controlling your number of false discoveries), and we had to turn the false discovery rate threshold to 50% to select any gene at all.

#machineLearning #genomics #featureSelection #biomarkerDiscovery #transcriptomics

Our paper (with Julie Cartier, Johanna Lagoas, Youmna Ayadi, Adeline Fermanian and @flomass) on the use of statistical knockoffs for the differential analysis of transcriptomics data just came out, very appropriately as it nicely illustrates my point:
https://academic.oup.com/bib/article/27/3/bbag148/8687371

Using simulated outcomes on real transcriptomics data, we've shown that KOs (and in particular, the KOPI approach) do retrieve important variables with better power than classical approaches (Wilcoxon, Lasso), while controlling FDR.

However, all methods perform poorly when the relationship between gene expressions and outcome is nonlinear.

On real outcomes, the method is overly conservative (having no discoveries is a surefire way of controlling your number of false discoveries), and we had to turn the false discovery rate threshold to 50% to select any gene at all.

#machineLearning #genomics #featureSelection #biomarkerDiscovery #transcriptomics

Our paper (with Julie Cartier, Johanna Lagoas, Youmna Ayadi, Adeline Fermanian and @flomass) on the use of statistical knockoffs for the differential analysis of transcriptomics data just came out, very appropriately as it nicely illustrates my point:
https://academic.oup.com/bib/article/27/3/bbag148/8687371

Using simulated outcomes on real transcriptomics data, we've shown that KOs (and in particular, the KOPI approach) do retrieve important variables with better power than classical approaches (Wilcoxon, Lasso), while controlling FDR.

However, all methods perform poorly when the relationship between gene expressions and outcome is nonlinear.

On real outcomes, the method is overly conservative (having no discoveries is a surefire way of controlling your number of false discoveries), and we had to turn the false discovery rate threshold to 50% to select any gene at all.

#machineLearning #genomics #featureSelection #biomarkerDiscovery #transcriptomics

Our paper (with Julie Cartier, Johanna Lagoas, Youmna Ayadi, Adeline Fermanian and @flomass) on the use of statistical knockoffs for the differential analysis of transcriptomics data just came out, very appropriately as it nicely illustrates my point:
https://academic.oup.com/bib/article/27/3/bbag148/8687371

Using simulated outcomes on real transcriptomics data, we've shown that KOs (and in particular, the KOPI approach) do retrieve important variables with better power than classical approaches (Wilcoxon, Lasso), while controlling FDR.

However, all methods perform poorly when the relationship between gene expressions and outcome is nonlinear.

On real outcomes, the method is overly conservative (having no discoveries is a surefire way of controlling your number of false discoveries), and we had to turn the false discovery rate threshold to 50% to select any gene at all.

#machineLearning #genomics #featureSelection #biomarkerDiscovery #transcriptomics

Our paper (with Julie Cartier, Johanna Lagoas, Youmna Ayadi, Adeline Fermanian and @flomass) on the use of statistical knockoffs for the differential analysis of transcriptomics data just came out, very appropriately as it nicely illustrates my point:
https://academic.oup.com/bib/article/27/3/bbag148/8687371

Using simulated outcomes on real transcriptomics data, we've shown that KOs (and in particular, the KOPI approach) do retrieve important variables with better power than classical approaches (Wilcoxon, Lasso), while controlling FDR.

However, all methods perform poorly when the relationship between gene expressions and outcome is nonlinear.

On real outcomes, the method is overly conservative (having no discoveries is a surefire way of controlling your number of false discoveries), and we had to turn the false discovery rate threshold to 50% to select any gene at all.

#machineLearning #genomics #featureSelection #biomarkerDiscovery #transcriptomics

Curious about the dark side of plant biology?

Check out our latest preprint on the secrets of black pigmentation in Rubus:

https://doi.org/10.64898/2026.05.05.723051

#Anthocyanins #Transcriptomics #PlantScience #Fruits
@PuckerLab

Curious about the dark side of plant biology?

Check out our latest preprint on the secrets of black pigmentation in Rubus:

https://doi.org/10.64898/2026.05.05.723051

#Anthocyanins #Transcriptomics #PlantScience #Fruits
@PuckerLab

Curious about the dark side of plant biology?

Check out our latest preprint on the secrets of black pigmentation in Rubus:

https://doi.org/10.64898/2026.05.05.723051

#Anthocyanins #Transcriptomics #PlantScience #Fruits
@PuckerLab

Curious about the dark side of plant biology?

Check out our latest preprint on the secrets of black pigmentation in Rubus:

https://doi.org/10.64898/2026.05.05.723051

#Anthocyanins #Transcriptomics #PlantScience #Fruits
@PuckerLab

Curious about the dark side of plant biology?

Check out our latest preprint on the secrets of black pigmentation in Rubus:

https://doi.org/10.64898/2026.05.05.723051

#Anthocyanins #Transcriptomics #PlantScience #Fruits
@PuckerLab

🧬 Could a single metric decode how genes are regulated across cells?

🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics

🧬 Could a single metric decode how genes are regulated across cells?

🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics

🧬 Could a single metric decode how genes are regulated across cells?

🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics

🧬 Could a single metric decode how genes are regulated across cells?

🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics

🧬 Could a single metric decode how genes are regulated across cells?

🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics

🧬 What if disease isn’t written in DNA, but in how RNA is edited and spliced?

🔗 Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0052

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#RNASequencing #Genomics #Transcriptomics #PrecisionMedicine #MolecularBiology #Bioinformatics #NextGenSequencing #RNA #DNA

🧬 What if disease isn’t written in DNA, but in how RNA is edited and spliced?

🔗 Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0052

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#RNASequencing #Genomics #Transcriptomics #PrecisionMedicine #MolecularBiology #Bioinformatics #NextGenSequencing #RNA #DNA

🧬 What if disease isn’t written in DNA, but in how RNA is edited and spliced?

🔗 Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0052

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#RNASequencing #Genomics #Transcriptomics #PrecisionMedicine #MolecularBiology #Bioinformatics #NextGenSequencing #RNA #DNA

🧬 What if disease isn’t written in DNA, but in how RNA is edited and spliced?

🔗 Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0052

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#RNASequencing #Genomics #Transcriptomics #PrecisionMedicine #MolecularBiology #Bioinformatics #NextGenSequencing #RNA #DNA

🧬 What if disease isn’t written in DNA, but in how RNA is edited and spliced?

🔗 Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0052

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#RNASequencing #Genomics #Transcriptomics #PrecisionMedicine #MolecularBiology #Bioinformatics #NextGenSequencing #RNA #DNA

How could bisphenol A raise depression risk? Study identifies six key molecular targets

Researchers combined genetic epidemiology, transcriptomics, molecular docking, and mous…
#NewsBeep #News #Health #AU #Australia #Blood #Cell #Chemicals #depression #depressivedisorder #ELISA #Endocrine #epidemiology #estrogen #Gene #GeneExpression #Genetic #Kinase #majordepressivedisorder #Mentalhealth #protein #psychiatry #publichealth #Receptor #research #Transcriptomics
https://www.newsbeep.com/au/577535/

How could bisphenol A raise depression risk? Study identifies six key molecular targets

Researchers combined genetic epidemiology, transcriptomics, molecular docking, and mous…
#NewsBeep #News #Health #AU #Australia #Blood #Cell #Chemicals #depression #depressivedisorder #ELISA #Endocrine #epidemiology #estrogen #Gene #GeneExpression #Genetic #Kinase #majordepressivedisorder #Mentalhealth #protein #psychiatry #publichealth #Receptor #research #Transcriptomics
https://www.newsbeep.com/au/577535/

https://www.europesays.com/ie/414176/ How could bisphenol A raise depression risk? Study identifies six key molecular targets #blood #Cell #chemicals #Depression #DepressiveDisorder #Éire #ELISA #Endocrine #Epidemiology #estrogen #Gene #GeneExpression #Genetic #Health #IE #Ireland #Kinase #MajorDepressiveDisorder #MentalHealth #Protein #Psychiatry #PublicHealth #Receptor #Research #Transcriptomics

"Cellular morphology emerges from polygenic, distributed transcriptional variation", Paylakhi et al. 2026
https://www.biorxiv.org/content/10.64898/2026.03.12.711281v1

#CellBiology #transcriptomics #CellPainting #RNAseq

"Cellular morphology emerges from polygenic, distributed transcriptional variation", Paylakhi et al. 2026
https://www.biorxiv.org/content/10.64898/2026.03.12.711281v1

#CellBiology #transcriptomics #CellPainting #RNAseq

"Cellular morphology emerges from polygenic, distributed transcriptional variation", Paylakhi et al. 2026
https://www.biorxiv.org/content/10.64898/2026.03.12.711281v1

#CellBiology #transcriptomics #CellPainting #RNAseq

"Cellular morphology emerges from polygenic, distributed transcriptional variation", Paylakhi et al. 2026
https://www.biorxiv.org/content/10.64898/2026.03.12.711281v1

#CellBiology #transcriptomics #CellPainting #RNAseq

"Cellular morphology emerges from polygenic, distributed transcriptional variation", Paylakhi et al. 2026
https://www.biorxiv.org/content/10.64898/2026.03.12.711281v1

#CellBiology #transcriptomics #CellPainting #RNAseq

Is spatial transcriptomics data preprocessing giving you a headache? You're not alone! 🤯
Join our webinar designed for new researchers to simplify the complex world of image-based spatial omics. We'll walk through the practical workflow step-by-step, from initial cell segmentation to cleaning up your data.
Get the foundational skills you need. 📅 Sign up here: https://t1p.de/lqbg1

#Transcriptomics #SpatialTranscriptomics #Omics #DataScience #ResearchWebinar #GHGA #ELIXIR #deNBI

The Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025.
https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/

@galaxyfreiburg
#UseGalaxy #GalaxyProject #EOSC #SingleCell #SpatialOmics #Omics #Transcriptomics #Bioinformatics #Genomics #ComputationalBiology #EuroScienceGateway #OpenScience #ReproducibleResearch #GalaxyCommunity #SPOC (1/2)

The Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025.
https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/

@galaxyproject
#UseGalaxy #GalaxyProject #EOSC #UniFreiburg #SingleCell #SpatialOmics #Omics #Transcriptomics #Bioinformatics #Genomics #ComputationalBiology #EuroScienceGateway #OpenScience #ReproducibleResearch (1/2)

Bioinformatician @lgatto

UCLouvain

UCLouvain is hiring a #bioinformatician for the e-OMIX project

See the full job description on jobRxiv: https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

#cross_platform #data_analyses #Data_Science #FHIR #genomics #proteomics #transcriptomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

Bioinformatician @lgatto

UCLouvain

UCLouvain is hiring a #bioinformatician for the e-OMIX project

See the full job description on jobRxiv: https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

#cross_platform #data_analyses #Data_Science #FHIR #genomics #proteomics #transcriptomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

Bioinformatician @lgatto

UCLouvain

UCLouvain is hiring a #bioinformatician for the e-OMIX project

See the full job description on jobRxiv: https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

#cross_platform #data_analyses #Data_Science #FHIR #genomics #proteomics #transcriptomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

Bioinformatician @lgatto

UCLouvain

UCLouvain is hiring a #bioinformatician for the e-OMIX project

See the full job description on jobRxiv: https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

#cross_platform #data_analyses #Data_Science #FHIR #genomics #proteomics #transcriptomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

Bioinformatician @lgatto

UCLouvain

UCLouvain is hiring a #bioinformatician for the e-OMIX project

See the full job description on jobRxiv: https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

#cross_platform #data_analyses #Data_Science #FHIR #genomics #proteomics #transcriptomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/uclouvain-27778-bioinformatician/?feed_id=68846

https://www.europesays.com/uk/754232/ New spatial omics platform advances biomedical research in Spain #Bioinformatics #Cancer #CLARITY #EU #Europe #Gene #Genes #Genomic #Genomics #Histopathology #ImmuneSystem #Medicine #Microscopy #Neurodegeneration #NextGeneration #PrecisionMedicine #Protein #ProteinAnalysis #proteomics #Research #SamplePreparation #Spain #Technology #TopDown #Transcriptomics

https://www.europesays.com/ie/329335/ New spatial omics platform advances biomedical research in Spain #Bioinformatics #cancer #CLARITY #Éire #Gene #Genes #Genomic #genomics #Histopathology #IE #ImmuneSystem #Ireland #medicine #Microscopy #Neurodegeneration #NextGeneration #PrecisionMedicine #Protein #ProteinAnalysis #Proteomics #Research #SamplePreparation #Science #Technology #TopDown #Transcriptomics

New spatial omics platform advances biomedical research in Spain https://www.byteseu.com/1788012/ #Bioinformatics #Cancer #clarity #GENE #Genes #Genomic #genomics #Histopathology #ImmuneSystem #Medicine #Microscopy #Neurodegeneration #NextGeneration #PrecisionMedicine #Protein #ProteinAnalysis #Proteomics #Research #SamplePreparation #Spain #Technology #TopDown #Transcriptomics

CDKN2A-p16 Deletion and Activated KRASG12D Drive Barrett’s-Like Gland Hyperplasia-Metaplasia and Synergize in the Development of Dysplasia Precancer Lesions. https://doi.org/10.1016/j.jcmgh.2024.01.014 #Dysplasia #EsophagealAdenocarcinoma #3dOrganoids #Transcriptomics

At #PAG33? Stop by the Galaxy booth to get snacks and talk with us about how we can help you get FREE, reproduceable, publishable high performance computing workflows. #Assembly, #Transcriptomics, #Epigenetics, and much more!

Research Associate
University of Ottawa

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-ottawa-27778-research-associate-2/

#cellbiology #molecularbiology #transcriptomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-of-ottawa-27778-research-associate-2/?fsp_sid=4260

Our review article got published in 'Biotechnology Advances':

"Decoding bioprocesses with transcriptomics: current status and future potential"
https://doi.org/10.1016/j.biotechadv.2025.108736

#Biotech #ScaleUp #ScaleDown #Transcriptomics
@PuckerLab

🧬 Can a single method balance sensitivity and specificity in small RNA annotation across the tree of life?

🔗 Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.05.045

📚 CSBJ: https://www.csbj.org/

#RNA #Bioinformatics #Genomics #SmallRNAs #ComputationalBiology #Transcriptomics #MolecularBiology #Epigenetics

Postdoc Position: Evolution and Organization of Ant Olfactory Systems
Johannes Gutenberg University Mainz

PostDoc position @uni Mainz (Germany)
#genomics #transcriptomics to investigate the olfactory system of ants

See the full job description on jobRxiv: https://jobrxiv.org/job/johannes-gutenberg-university-mainz-27778-postdoc-position-evolu...
https://jobrxiv.org/job/johannes-gutenberg-university-mainz-27778-postdoc-position-evolution-and-organization-of-ant-olfactory-systems/?fsp_sid=550

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

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