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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SVC: structured visualization of evolutionary sequence conservation.
PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups
SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.
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Has reproduction · 100
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.
PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups
44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.
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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 · 100
Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.
PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups
French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.
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Has reproduction · 92
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.
PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups
Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.
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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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Identifying repeat domains in large genomes.
PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups
A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.
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Predicting failure rate of PCR in large genomes.
PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups
The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.
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Non-linear mapping for exploratory data analysis in functional genomics.
PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.