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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X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.
PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups
X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.
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Has reproduction · 98
Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era.
PMID 34310590 · PMC8354454 · PLoS computational biology · 2021 · 7 claims · 6 setups
Updated synthetic contact matrices were generated for 177 geographical locations covering 97.2% of the world's population (up from 152 locations/95.9% in 2017).
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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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The flexible pocketome engine for structural chemogenomics.
PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups
A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.
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Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
PMID 17537826 · PMC1933130 · Nucleic acids research · 2007 · 7 claims · 5 setups
StSNP integrates dbSNP, PDB, KEGG, and NCBI Entrez data into a single web server for nsSNP analysis
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A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.
PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups
SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters
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SNP-VISTA: an interactive SNP visualization tool.
PMID 16336665 · PMC1325058 · BMC bioinformatics · 2005 · 7 claims · 3 setups
SNP-VISTA is an interactive Java-based visualization tool with two versions, GeneSNP-VISTA and EcoSNP-VISTA, for exploring large-scale SNP datasets
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Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.
PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups
The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation
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Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.
PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups
Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.
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Sequence determinants of human microsatellite variability.
PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups
Mean and maximum number of repeats across individuals are positively correlated with heterozygosity
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Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups
Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives
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Has reproduction · 63
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.
PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date
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New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.
PMID 18673538 · PMC2553414 · Retrovirology · 2008 · 7 claims · 5 setups
04FR-KZS clusters with two previously described DRC viruses and represents CRF27_cpx, a complex recombinant involving A/E/G/H/J/K/U subtypes.
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Has reproduction · 89
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.
PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups
Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.
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Database resources of the National Center for Biotechnology Information.
PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups
NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis
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Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.
PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups
Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.