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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Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups
Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods
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Has reproduction · 65
Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.
PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups
eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.
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Has reproduction · 91
Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.
PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups
An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.
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Charting the map of life.
PMID 11171541 · PMC1242061 · Environmental health perspectives · 2001 · 8 claims · 8 setups
Only 3-5% of the human genome, corresponding to 30,000-100,000 genes, is thought to be biologically functional
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Has reproduction · 99
A platinum standard pan-genome resource that represents the population structure of Asian rice.
PMID 32265447 · PMC7138821 · Scientific data · 2020 · 6 claims · 6 setups
The 3,000 Rice Genomes (3K-RG) dataset can be subdivided into 15 subpopulations (K=15), refining the previous K=9 population structure.
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Has reproduction · 75
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.
PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 4 setups
geneshot is a gene-level metagenomic bioinformatics tool that clusters de novo assembled protein-coding genes into co-abundant gene groups (CAGs) to reduce dimensionality and generate testable hypotheses from WGS microbiome data
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Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.
PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups
A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence
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TAC3 and TACR3 mutations in familial hypogonadotropic hypogonadism reveal a key role for Neurokinin B in the central control of reproduction.
PMID 19079066 · PMC4312696 · Nature genetics · 2009 · 8 claims · 5 setups
Homozygous loss-of-function mutations in TAC3 or TACR3 cause congenital hypogonadotropic hypogonadism in four consanguineous families
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Has reproduction · 84
Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome.
PMID 33294007 · PMC7691466 · Evolutionary applications · 2020 · 7 claims · 8 setups
Lingcod comprise two distinct genetic clusters separated latitudinally at a break near Point Reyes off Northern California, with a high frequency of admixed individuals near the break.
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Has reproduction · 54
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.
PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups
EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology
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Personalized copy number and segmental duplication maps using next-generation sequencing.
PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups
mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.
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Has reproduction · 90
The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.
PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups
The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application
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Has reproduction · 93
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.
PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups
Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.
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Evolutionary toggling of the MAPT 17q21.31 inversion region.
PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups
The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31
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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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SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.
PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups
A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.
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The diploid genome sequence of an individual human.
PMID 17803354 · PMC1964779 · PLoS biology · 2007 · 7 claims · 6 setups
Generated an independently assembled diploid human genome sequence (HuRef) from both chromosome sets of a single individual using whole-genome shotgun Sanger sequencing
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Comparative genomics of the neglected human malaria parasite Plasmodium vivax.
PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups
P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential
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Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.
PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups
Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.
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Has reproduction · 94
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.
PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups
The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.