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).

• Species-specific protein sequence and fold optimizations.

  PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

  Full-text index only

  Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

  predicted mean over orf principal hierarchical domain-based

• A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

  PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups

  Has reproduction · 90

  A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.

  kidney gene combined microarray machine sequential

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups

  Has reproduction · 59

  TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene

  cd8+ tce manual gene principal

• Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

  PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

  Has reproduction · 68

  200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

  african lion crater simulated genome principal admixture

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

  Full-text index only

  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.

  PMID 33193602 · PMC7541957 · Frontiers in genetics · 2020 · 7 claims · 4 setups

  Has reproduction · 80

  GenomeChronicler is the first pipeline able to run offline or in the cloud to generate personal genomics reports (not limited to disease) from whole genome or whole exome sequencing data.

  wgs na12878 pgp-uk1 genomes ancestry germline genome

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

  Full-text index only

  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 8 claims · 8 setups

  Has reproduction · 83

  Metabolite-centric reporter pathway analysis (RPAm) computes reporter metabolites and reporter pathways from transcriptome P-values by aggregating Z-scores of neighboring genes in a genome-scale metabolic network

  arabidopsis gene-metabolite-pathway tripartite microarray metabolite-centric reporter

• A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

  PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

  pigs sscrofa11.1 pig domestic whole-genome tandem repeat

• Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

  PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

  Has reproduction · 64

  L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

  elegans small small sequencing lifespan

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

  Full-text index only

  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

  PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

  Full-text index only

  A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

  bidirectional across high-quality nascent comparative eqtl

• Multimodal learning reveals plants' hidden sensory integration logic.

  PMID 41714925 · PMC13032346 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  CoMM-BIP (Contrastive Multi-Modal learning with Biologically Informed Priors) integrates transcriptomic, metabolomic, and phenomic data using pathway-guided attention, information-theoretic disentanglement, and domain-aware augmentations

  tomato multimodal transcriptomics metabolomics

• ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

  PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 9 setups

  Has reproduction · 87

  Italian brown trout populations are genetically differentiated but show strong admixture from stocking practices, especially with the Atlantic lineage.

  brown snp subset salmo ddrad-seq admixture newhybrids

• Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.

  PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

  Full-text index only

  Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.

  dart-possessing same land cantareus 28s shimodaira-hasegawa principal

• HUPO Highlights.

  PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing

  liver subcellular models fetal mass antibody-based quantitative