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).

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 8 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific transcriptome signatures in cord blood, with a significant sex-by-exposure interaction for many genes.

  cord maternal pm2.5-associated blood whole-genome spatial-temporal overrepresentation

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups

  Has reproduction · 86

  TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR

  tnbc unique 719-gene gene term machine

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

  PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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  3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

  bovine cow coding blast-based ensembl gene

• 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

• scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

  PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups

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  scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.

  pbmcs epithelial liver glioblastoma scrna-seq gene dimensionality

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

  PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 62

  Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.

  day mature bulk qrt-pcr gene

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• The role of positive selection in determining the molecular cause of species differences in disease.

  PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

  orthologous omim meta-database panther comparative disease protein-protein

• TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

  PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

  fischer computational transcriptomic same bulk gan-based autoencoder

• Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq.

  PMID 41904529 · PMC13217986 · Cell communication and signaling : CCS · 2026 · 8 claims · 7 setups

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  MITF knockdown and IFNγ stimulation each produce substantial but distinct changes in chromatin accessibility in 624Mel melanoma cells

  624mel melanoma atac-seq western motif

• TGFβ induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis.

  PMID 41492090 · PMC12858408 · Nature cancer · 2026 · 7 claims · 8 setups

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  TGFβ initially induces a full, typical EMT (stress fibers, loss of epithelial markers, motility) in dormancy-competent LUAD progenitors that subsequently transitions into an atypical spheroidal mesenchymal state lacking actin stress fibers.

  h2087-lcc m802t4-lcc reconstructed immunofluorescence antibody-mediated