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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Visualization of shared genomic regions and meiotic recombination in high-density SNP data.
PMID 19696932 · PMC2725774 · PloS one · 2009 · 8 claims · 7 setups
SNPduo is a command-line (SNPduo++) and web-accessible tool that analyzes and visualizes relatedness between two individuals using identity by state (IBS) from SNP genotypes.
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Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.
PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups
eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs
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InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups
InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.
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The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups
The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.
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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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Has reproduction · 89
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups
TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency
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Has reproduction · 50
The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.
PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 7 claims · 7 setups
Most published adult/other-cohort sepsis gene signatures have limited utility for infant sepsis; only 2 of 7 achieved >80% accuracy in infants
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Sources of variability and effect of experimental approach on expression profiling data interpretation.
PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups
Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling
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The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples.
PMID 18460190 · PMC2391158 · BMC medical genetics · 2008 · 8 claims · 4 setups
A novel candidate-gene selection strategy combining unbiased schizophrenia expression/linkage data with the estrogen hypothesis as a biological filter identifies glycolysis as a candidate pathway network for schizophrenia
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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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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 · 93
A comparative study on recombination activity in cattle.
PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups
Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)
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A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.
PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups
Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.
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Filtering high-throughput protein-protein interaction data using a combination of genomic features.
PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.