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).
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Species-specific protein sequence and fold optimizations.
PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups
Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes
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GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update.
PMID 17986454 · PMC2238933 · Nucleic acids research · 2008 · 7 claims · 5 setups
GLIDA is a public relational database integrating biological information on GPCRs with chemical information on their ligands and their binding interactions.
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Measurement reproducibility in the early stages of biomarker development.
PMID 15665389 · PMC3839328 · Disease markers · 2004 · 6 claims · 3 setups
Functional PCA can be used as the basis for gauge R&R (repeatability and reproducibility) assessment of mass spectra without prior identification of which spectral features are biomarkers
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Has reproduction · 84
randPedPCA: rapid approximation of principal components from large pedigrees.
PMID 40877802 · PMC12392600 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 2 setups
Matrix-vector multiplication with the dense additive relationship matrix A can be performed implicitly and efficiently via forward/backward substitution using the sparse inverse relationship (Cholesky) factor L^-1, avoiding explicit construction of A.
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Interpretable trajectory inference with single-cell linear adaptive negative-binomial expression (scLANE) testing.
PMID 41533563 · PMC12802912 · Nucleic acids research · 2026 · 8 claims · 3 setups
scLANE models gene expression as a piecewise negative-binomial GLM using truncated power basis (hinge) functions with adaptively chosen knots, yielding directly interpretable multiplicative effect sizes for trajectory differential expression
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Gene expression and isoform variation analysis using Affymetrix Exon Arrays.
PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups
The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 68
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
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
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Directing stem cell differentiation by chromatin state approximation.
PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups
Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols
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Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.
PMID 41528819 · PMC12958807 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups
Differential gene expression caused by disruption of daf-2/InsR during L1 starvation is daf-16-dependent.
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Genetic Surveillance Reveals Differential Evolutionary Dynamic of Anopheles gambiae Under Contrasting Insecticidal Tools Used in Malaria Control.
PMID 41773559 · PMC12954828 · Molecular ecology · 2026 · 6 claims · 8 setups
Despite substantial reductions in indoor mosquito densities, nucleotide diversity and linkage-disequilibrium-based estimates showed no significant decline in effective population size after intervention
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Has reproduction · 100
Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry.
PMID 36670351 · PMC9854048 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups
Dutch traditional chicken breeds show a complex and admixed subdivided population structure that partly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).
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Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.
PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups
QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies
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Reconstructing Indian population history.
PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups
Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).
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Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.
PMID 36093739 · PMC9828440 · The New phytologist · 2022 · 8 claims · 8 setups
Natural selection contributed to the establishment and maintenance of the Scandinavian contact zone between the NFE and CSE genetic clusters.
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Pathway-specific canalization and plasticity of gene expression during C. elegans dauer development.
PMID 41890963 · PMC13014971 · iScience · 2026 · 8 claims · 7 setups
Dauers induced by different environmental (starvation, pheromone, heat) or genetic (daf-2, daf-7, ilc-17.1, cep-1 OE) stimuli are transcriptionally distinct from each other and from continuously developing WT L2/L3 and adults
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Has reproduction · 52
Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.
PMID 31980607 · PMC6981202 · Nature communications · 2020 · 8 claims · 8 setups
MetaMEx integrates transcriptomic data from 66 published human skeletal muscle studies (>1100 individuals) into an online meta-analysis resource (www.metamex.eu)
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups
Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs
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Has reproduction · 55
Natural clines and human management impact the genetic structure of Algerian honey bee populations.
PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups
Algerian honey bees show no significant admixture from European reference honey bee populations
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Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.
PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups
Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.