Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Integrative Transcriptomic Analysis and Co-Expression Network Characterization of Soybean Developmental Tissues.

  PMID 41977661 · PMC13075193 · Plants (Basel, Switzerland) · 2026 · 8 claims · 6 setups

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  Tissue identity (seed vs. non-seed) is the dominant driver of transcriptomic variation, as shown by clear separation on PC1

  glycine same seed-upregulated bulk principal differential

• Comparing time series transcriptome data between plants using a network module finding algorithm.

  PMID 31164912 · PMC6544932 · Plant methods · 2019 · 8 claims · 6 setups

  Has reproduction · 59

  Converting gene expression patterns into co-expression networks and applying a cross-species network module finding algorithm (OrthoClust with simulated annealing) solves the problem of matching developmental stages between two species without requiring one-to-one stage mapping.

  soybean arabidopsis cross-species module reciprocal bulk co-expression

• Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

  PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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  Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

  acropora millepora bulk differential pca

• Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

  PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 57

  t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes

  calanus same 11k degs bulk dimensionality differential

• Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

  PMID 42064353 · PMC13126010 · Wellcome open research · 2026 · 7 claims · 7 setups

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  Deformable gametocytes are immediately infectious upon release from the bone marrow into circulation.

  synchronized falciparum blood microsphere bulk exflagellation

• Gene Expression Patterns Regulating Peanut Reproductive Phenology.

  PMID 42099581 · PMC13147162 · Plant direct · 2026 · 8 claims · 6 setups

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  Overall gene expression was distinct between Tifrunner and GT-C20 in both leaf and shoot tip tissues

  leaf deseq2 shoot gene bulk differential principal

• Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

  PMID 41571647 · PMC12905319 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a high-resolution single-cell transcriptomic atlas of 104,671 cells from male and female S. japonicum across four developmental stages, identifying 76 distinct cell populations

  dissociated japonicum reproductive gscs single-cell fluorescence-activated whole-mount

• Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths.

  PMID 41802886 · PMC13014123 · Molecular biology and evolution · 2026 · 8 claims · 8 setups

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  Genomic structural variations and gene family expansions contributed little to morphological (mimicry) evolution in Epicopeiidae

  epicopeiidae mencia ancestral chromosome-level whole-genome hi-c comparative

• Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

  PMID 41649260 · PMC12880807 · eLife · 2026 · 8 claims · 8 setups

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  13LGS cone photoreceptors arise from both early-stage and late-stage neurogenic progenitors, unlike mice where cones arise only from early-stage progenitors

  13-lined retina 13lgs retinal single-cell scrna-seq chromvar

• Trisomy 21 Drives ADARB1 Overexpression and Premature RNA Recoding in the Developing Fetal Brain.

  PMID 41917044 · PMC13039865 · Nature communications · 2026 · 8 claims · 8 setups

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  T21 causes widespread fetal brain gene expression dysregulation with significant enrichment for chromosome 21 genes and perturbation of neurodevelopmental, synaptic, and immune-related pathways

  fetal independent brain bulk editing type

• Modular genetic architecture underlies human hand and foot evolution.

  PMID 42118837 · PMC13187773 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

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  Gene expression and regulatory modules strongly separate metapodials from phalanges, and separate tissues to a lesser extent along the anterior-posterior axis or between limb types

  developing e15.5 chimpanzee developmental rna-seq atac-seq skeletal

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells represent largely distinct, non-overlapping populations across murine and human aging tissues

  hippocampus brain skeletal bone scrna-seq cytof velocity

• A comparison of programmed cell death between species.

  PMID 11178240 · PMC138857 · Genome biology · 2000 · 8 claims · 8 setups

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  The core apoptotic pathway (CED-3/caspases, CED-4/Apaf-1, CED-9/Bcl-2, EGL-1) is conserved across C. elegans, Drosophila, and mammals.

  elegans mammalian drosophila transgenic whole-genome kinetic ectopic

• Oxidative stress and GPX2 control pancreatic vs. non-pancreatic cell fate in human endoderm.

  PMID 41484137 · PMC12881361 · Nature communications · 2026 · 8 claims · 8 setups

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  GPX2 is a critical regulator of human posterior foregut differentiation, with oxidative stress acting as a key determinant of pancreatic vs. non-pancreatic cell fate

  hpsc-derived hpsc fetal bulk immunofluorescence flow

• A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling.

  PMID 41512864 · PMC12903091 · Stem cell reports · 2026 · 7 claims · 8 setups

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  HBC-derived regeneration proceeds via three distinct lineages (rHBC, Sus, mOSN) marked by sequential, lineage-specific transcription factor (TF) expression cascades.

  lineage-traced hbcs* icam1+ scrna-seq trajectory-based seurat