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).

• Sex-biased evolutionary forces shape genomic patterns of human diversity.

  PMID 18818765 · PMC2538571 · PLoS genetics · 2008 · 7 claims · 5 setups

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  X-linked diversity is higher than the neutral expectation (0.75) relative to autosomal diversity in all six sampled human populations

  humans population simulated computational resequencing coalescent-based coalescent

• Transcriptomics Reveal Molecular Signatures of a Resolved Sexual Conflict and Potential Association With Colour Polymorphism in Tawny Owls.

  PMID 41964128 · PMC13069001 · Molecular ecology · 2026 · 8 claims · 8 setups

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  Substantial sex-specific variation exists in differentially expressed genes, SNPs and alternative exon usage in genes involved in life history traits (ZGRF1, VLDLR), behaviour (GSK3B, SLC12A) and growth (GHR, EGF, EPS8L2)

  feather tawny sex individual bulk genome read

• Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

  PMID 35794110 · PMC9258765 · Nature communications · 2022 · 8 claims · 5 setups

  Has reproduction · 94

  Deep learning (FFNN-SS and CNN-CBLV) enables accurate and fast likelihood-free estimation of epidemiological parameters and model selection from phylogenies

  simulated same hiv-1 simulation-based bayesian maximum-likelihood

• Simple models of genomic variation in human SNP density.

  PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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  Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

  genome observed simulated genome hierarchical coalescent

• Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group.

  PMID 35883324 · PMC9312300 · Animals : an open access journal from MDPI · 2022 · 7 claims · 6 setups

  Has reproduction · 84

  Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.

  fresh fecal 16s alpha-diversity beta-diversity

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• GeMI: interactive interface for transformer-based Genomic Metadata Integration.

  PMID 35657113 · PMC9216561 · Database : the journal of biological databases and curation · 2022 · 8 claims · 5 setups

  Has reproduction · 64

  GeMI is a web tool that uses a fine-tuned GPT2 model to extract 15 structured key-value attributes from free-text GEO sample metadata.

  cistrome encode geo fine-tuned manual batch transformer-based

• Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

  PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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  High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

  genomic normalized simulated tiling-resolution snp oligonucleotide

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

  PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 8 setups

  Has reproduction · 88

  Among annotated HM450K GEO samples, about two-thirds were from blood, one-quarter from brain, and about one-third were from cancer patients.

  hm450k geo seven dnam beadarray regular-expression-based

• 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

• Metabolic syndrome: from epidemiology to systems biology.

  PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups

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  MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions

  populations rats adipose four genome-wide linkage gene

• Androgen activity in the male embryonic hindbrain drives lethal PFA ependymoma.

  PMID 41882358 · PMC13083265 · Nature · 2026 · 8 claims · 8 setups

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  The cellular hierarchy of PFA ependymoma is less differentiated in male than in female patients

  pfa pfa-epn normal hindbrain single-cell kaplan-meier literature

• Long non-coding RNA profiling of hypertrophic cardiomyopathy in mice.

  PMID 41942516 · PMC13230700 · Scientific data · 2026 · 6 claims · 8 setups

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  This study presents a transcriptome-wide RNA-Seq dataset delineating differentially expressed lncRNAs in left ventricle of the TNNT2 ∆160 HCM mouse model (n=31 TG, n=33 nTG).

  left fastq rna-seq lncrna bulk fastqc read

• Genetic association study and meta-analysis of the HTR2C Cys23Ser polymorphism and migraine.

  PMID 17901921 · PMC3451673 · The journal of headache and pain · 2007 · 8 claims · 3 setups

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  The HTR2C Cys23Ser polymorphism is not significantly associated with migraine or migraine with aura in the case-control study

  blood-derived migraine pooled allelic case-control meta-analysis

• 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

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• Adaptation, aging, and genomic information.

  PMID 20157529 · PMC2806027 · Aging · 2009 · 8 claims · 6 setups

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  Aging is caused primarily by the absence of adaptive genomic information for later-age survival and function, due to declining forces of natural selection with adult age; this absence secondarily produces misallocation and damage at every level of biological organization.

  drosophila large animal unspecified experimental demographic hormone

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular