home.social

#transcriptomics — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #transcriptomics, aggregated by home.social.

  1. 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:
    academic.oup.com/bib/article/2

    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

  2. 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:
    academic.oup.com/bib/article/2

    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

  3. 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:
    academic.oup.com/bib/article/2

    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

  4. 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:
    academic.oup.com/bib/article/2

    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

  5. 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:
    academic.oup.com/bib/article/2

    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

  6. Curious about the dark side of plant biology?

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

    doi.org/10.64898/2026.05.05.72

    #Anthocyanins #Transcriptomics #PlantScience #Fruits
    @PuckerLab

  7. Curious about the dark side of plant biology?

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

    doi.org/10.64898/2026.05.05.72

    #Anthocyanins #Transcriptomics #PlantScience #Fruits
    @PuckerLab

  8. Curious about the dark side of plant biology?

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

    doi.org/10.64898/2026.05.05.72

    #Anthocyanins #Transcriptomics #PlantScience #Fruits
    @PuckerLab

  9. Curious about the dark side of plant biology?

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

    doi.org/10.64898/2026.05.05.72

    #Anthocyanins #Transcriptomics #PlantScience #Fruits
    @PuckerLab

  10. Curious about the dark side of plant biology?

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

    doi.org/10.64898/2026.05.05.72

    #Anthocyanins #Transcriptomics #PlantScience #Fruits
    @PuckerLab

  11. 🧬 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: doi.org/10.34133/csbj.0044

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

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

  12. 🧬 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: doi.org/10.34133/csbj.0044

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

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

  13. 🧬 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: doi.org/10.34133/csbj.0044

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

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

  14. 🧬 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: doi.org/10.34133/csbj.0044

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

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

  15. 🧬 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: doi.org/10.34133/csbj.0044

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

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

  16. 🧬 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: doi.org/10.34133/csbj.0052

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

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

  17. 🧬 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: doi.org/10.34133/csbj.0052

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

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

  18. 🧬 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: doi.org/10.34133/csbj.0052

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

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

  19. 🧬 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: doi.org/10.34133/csbj.0052

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

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

  20. 🧬 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: doi.org/10.34133/csbj.0052

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

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

  21. 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: t1p.de/lqbg1

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

  22. 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.
    galaxyproject.org/news/2025-10

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

  23. 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.
    galaxyproject.org/news/2025-10

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

  24. CW: Long Hashtag List for the Life Sciences

    Life Sciences Hashtags

    • Animal Behaviour
    #AnimalBehavior #AnimalBehaviour #AnimalCognition #AnimalPsychology #AnimalResearch #AnimalSocieties #AnimalStudies #BehavioralEcology #BehaviouralEcology #BehavioralScience #BehaviouralScience #CameraTraps #ComparativeCognition #CriticalAnimalStudies #Learning #Memory #PositiveReinforcement #Sociobiology #TrailCam

    • Astrobiology
    #AlienLife #Astrobiology #Biosignatures #Cryosphere DeepIce #EarthScience #Exoplanets #GeoScience #Habitability #Karst #MicroHabitats #OceanWorlds #OriginOfLife #PlanetaryCaves #PlanetaryScience

    • Behaviour Science
    #AnthroZoology #Behavior #Behaviour #Behaviour2023 #BehavioralScience #BehaviouralScience #Biopsychology #CognitiveDevelopment #ComparativeCognition #DevelopmentalPsychology #Ethology #Learning #Memory #Neuroethology #PhilosophyOfMind #PleasureActivism #Psychology #SelfOrganisation #SelfOrganization #SocialNetwork

    • Biochemistry | Group: @biochemistry
    #Actin #AminoAcids #Biochemical #Biochemistry #Catalyst #Catalysis #DNA #Enzyme #Enzymes #Hormones #IonChannels #Kinetics #Metabolism #Metabolomics #mRNA #Peptides #Polymer #Protein #Proteins #RNA

    • Bioinformatics | Group: @bioinformatics
    #BigData #Bioinformatics #RStats

    • Biology | Group: [email protected]
    #Biochemistry #Biology #Biomes #Botany #Ecology #Ecosystem #Evolution #Genetics #Habitat #LifeCycle #MarineBiology #Microbiology #Zoology

    • Biomaterial Science
    #Biofilm #Biofilms #Biologics #Biomaterials #Biotechnology #MaterialsScience #Nanotechnology #SustainableDesign #SyntheticBiology

    • Biomedical Science
    #Biomedical #BiomedicalEngineering #BiomedicalScience #NetworkMedicine #SystemsBiology

    • Botany
    #Botany #Botanical #Botanist #FloraIncognita #Florespondence IAmABotanist #Phenology #PlantBiology #PlantCells #PlantID #PlantIdentification

    • Cell Biology | Group: @cellbiology
    #CellBiology #CellDivision #CellMigration #Chloroplast #Cilium #Cytoskeleton #EndoplasmicReticulum #Eukaryotes #Golgi #Lipids #Macrophages #Membrane #Membranes #Microtubules #Mitochondria #Nucleus #Organelle #Organoids #Ribosome #SingleCell

    • Developmental Biology
    #ChildDevelopment #Connectome #Connectomics #DevelopmentalBiology #Embryology #Embryos #EvoDevo #GeneRegulation #Pregnancy #Proteomics #ReproSci #SexDet #StemCells #Transcriptomics

    • Ecology | Group: @ecology
    #AgroEcology #BehavioralEcology #BehaviouralEcology #Biodiversity #BiodiversityCrisis #BiodiversityLoss #Biogeography #ConservationBiology #Ecocide #EcoGrief #Ecological #EcologicalMonitoring #EcologicalSurvey #Ecology #Ecosystem #ForestEcology #Habitat #InvasionEcology #InvasiveSpecies #MassExtinction #OldGrowth #Riparian #WildCounts

    • Entomology | Group: @entomology
    #Beetles #Bugs #Coleoptera #Crustaceans #Entomologia #Entomology #Hemiptera #Hymenoptera #iNaturalist #Insect #Insects #InsectPhotography #Invertebrates #Isopods #Lepidoptera #Metamorphosis #Orthoptera #Pupa #Taxonomy

    • Genetics
    #BasePair #CellDivision #Chromosome #Chromosomes #Clone #Epigenetics #DNA #Gene #GeneExpression #GeneRegulation #GeneticallyModified #Genetics #Genome #Genomics #GMO #Meiosis #Mitosis #Mutation #RNAseq #Telomeres #Variants

    • Immunology
    #Antibodies #Antibody #Antigen #AutoImmune #BCells #Immune #ImmuneSystem #Immunity #ImmunoCompromised #Immunology #ImmunoTherapy #Interferon #Macrophages #Monoclonal #MonoclonalAntibodies (#mAbs) #Neutrophils #TCell #Vaccinated #Vaccine #Viralimmunology

    • Marine Science
    #Acidification #Algae #Aquatic #Cetaceans #Coral #CoralBleaching #CoralReefs #DeepSea #Diatoms #Estuary #Eutrophication #Kelp #KelpForest #MarineBiology #MarineLife #MarineMammals #MarineScience #MarineTaxonomy #Oceanography #Oceans #OceanWarming #Phytoplankton #Reefs #SeaBed #SeaFloor #SeaGrass #Seaweed #ScubaDiving #Snorkeling #UnderWaterPhotography #Zooplankton

    • Microbiology | Group: @microbiology
    #Antibiotics #AntiMicrobial #AntiMicrobialResistance (#AMR) #Bacteria #Bacterial #Bacteriophage #Bacteriology #Cilia #Microbes #Microbial #MicrobialEcology #Microbiology #Microbiome #Microbiota #MicroOrganisms #Phage #Protists

    #EColi #Legionella #Pseudomonas #Salmonella #Streptomyces

    • Molecular Biology | Group: @molecularbiology
    #Biophysics #CellBiology #MolecularBiology #MolecularEvolution #ProteinEngineering #ProteinStructure #Proteomics #StructuralBiology

    • Mycology | Group: @mycology
    #Fungi #Fungiverse #Mushrooms #Mycelium #Mycologists #Mycology #Mycophile #Spores #Sporespondence

    • Ornithology | Group: @ornithology
    #BirdID #Birding #BirdMigration #BirdPhotography #BirdResearch #BirdsOfMastodon #Corvid #eBird #Migration #Nesting #Oology #Ornithology #Raptor #SeaBirds #ShoreBirds

    • Virology | Group: @virology
    #AntiViral #AvianFlu #Bacteriophage #BirdFlu #CoronaVirus #COVID #COVID19 #GiantViruses #HIV #InfectiousDisease #Ebola #Measles #Phage #SARS #SARSCoV2 #Vaccine #Vaccines #ViralLoad #Viralimmunology #ViralPersistence #Variants #Virology #Virome #Virus #Viruses

    • Zoology
    #Animals #Biology #Zoologist #Zoology

    (Click to access Scientists in the Formal, Natural & Social Sciences)

    (See Index for More Hashtags)

    #SciFedi #LifeSciences

  25. CDKN2A-p16 Deletion and Activated KRASG12D Drive Barrett’s-Like Gland Hyperplasia-Metaplasia and Synergize in the Development of Dysplasia Precancer Lesions. doi.org/10.1016/j.jcmgh.2024.0

  26. 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!

  27. Our review article got published in 'Biotechnology Advances':

    "Decoding bioprocesses with transcriptomics: current status and future potential"
    doi.org/10.1016/j.biotechadv.2

    #Biotech #ScaleUp #ScaleDown #Transcriptomics
    @PuckerLab

  28. 🧬 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: doi.org/10.1016/j.csbj.2025.05

    📚 CSBJ: csbj.org/

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

  29. 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: jobrxiv.org/job/johannes-guten...
    jobrxiv.org/job/johannes-guten

  30. 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?