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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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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Has reproduction · 52
Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.
PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups
A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity
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Physiology engages with functional genomics - at last.
PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups
Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic
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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.
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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
CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling
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Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.
PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups
560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space
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Has reproduction · 71
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 · 7 claims · 6 setups
Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.
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Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups
An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.
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Has reproduction · 71
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.
PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups
TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.
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Has reproduction · 88
Age Deceleration and Reversal Gene Patterns in Dauer Diapause.
PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups
Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption
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Has reproduction · 84
Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.
PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups
Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups
A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).
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Has reproduction · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)
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Has reproduction · 75
The formation of avian montane diversity across barriers and along elevational gradients.
PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups
Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.
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Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.
PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups
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.
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Bayesian survival analysis in genetic association studies.
PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups
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.
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Has reproduction · 75
FEM: mining biological meaning from cell level in single-cell RNA sequencing data.
PMID 34909283 · PMC8641482 · PeerJ · 2021 · 7 claims · 5 setups
The FEM algorithm converts each cell's gene expression matrix (GEM) into a functional expression matrix by applying Fisher's exact test enrichment per cell and per gene set, then encoding adjusted p-values as information content.
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Has reproduction · 88
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.
PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups
Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.
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Has reproduction · 87
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 · 8 setups
Italian brown trout populations are genetically differentiated but show strong admixture introduced by stocking, especially with the Atlantic lineage.