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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Has reproduction · 59
From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.
PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups
382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.
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Application of functional genomics to primate endometrium: insights into biological processes.
PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups
Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.
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An integrative genomic and epigenomic approach for the study of transcriptional regulation.
PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups
Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone
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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 display a complex, admixed, subdivided population structure that broadly matches historical management-based clustering (past-productive, ornamental, country fowl, Lakenvelder).
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Has reproduction · 23
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.
PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations
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Has reproduction · 93
The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees.
PMID 31932598 · PMC6957680 · Nature communications · 2020 · 8 claims · 6 setups
E. dilemma and E. viridissima are reproductively isolated genetically distinct lineages despite low genome-wide differentiation.
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Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
The 196 R. leguminosarum sv. trifolii strains constitute a five-species complex (genospecies gsA-gsE) that occur in sympatry but show little recent between-species gene transfer in core or accessory genomes, except for a few highly mobile regions.
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.
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Has reproduction · 64
Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes.
PMID 38566006 · PMC10985947 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 7 setups
Significant genetic introgression from commercial European pigs (EP) into the Lijiang pig (LJP) and other domestic Chinese pig breeds was detected.
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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 · 23
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.
PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups
The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies
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Analysis of chimpanzee history based on genome sequence alignments.
PMID 18421364 · PMC2278377 · PLoS genetics · 2008 · 8 claims · 6 setups
Bonobos and common chimpanzees separated approximately 1.29 million years ago
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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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Geographical genomics of human leukocyte gene expression variation in southern Morocco.
PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups
Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.
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Has reproduction · 50
Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.
PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups
BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).
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Has reproduction · 85
High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.
PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups
SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.
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Has reproduction · 44
Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data.
PMID 34839581 · PMC9300093 · Pest management science · 2022 · 6 claims · 8 setups
Generated the first chromosome-level genome assembly (AH1) of B. xylophilus using PacBio, Illumina, BioNano, and Hi-C data
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Has reproduction · 59
Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.
PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups
PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation
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Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.
PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups
Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.