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).

Publications 1.3k Datasets 392.5k Experiments 694

System / cell line: snp ✕ Clear

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

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Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl
Reconstructing Indian population history.

PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

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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).

indian pairs gujarati genome-wide principal fst-based
Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

PMID 19772609 · PMC2759955 · BMC genetics · 2009 · 8 claims · 5 setups

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Saudi Arabia differs from other Arabian Peninsula countries by a significantly higher presence of J2-M172 lineages.

saudi same j1-m267 y-chromosome y-str amova
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

simulated same snp type two-locus 2lomb benchmark
FISH and SNP-A karyotyping in myelodysplastic syndromes: improving cytogenetic detection of del(5q), monosomy 7, del(7q), trisomy 8 and del(20q).

PMID 19758696 · PMC2826525 · Leukemia research · 2010 · 7 claims · 4 setups

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MC, FISH, and SNP-A are complementary techniques whose combined use improves diagnostic yield for detecting del(5q), -7/del(7q), trisomy 8, and del(20q) in MDS

bone pellets extracted cd3+ metaphase fluorescence snp
A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

PMID 19756043 · PMC2758715 · Molecular systems biology · 2009 · 8 claims · 4 setups

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A genome-wide AH analysis (GAHA) algorithm can identify disease-associated loci by comparing frequencies of homozygous segments between cases and controls using a z-statistic proportion test

unrelated simulated selected genes genome-wide statistical logistic
A novel mutation in GRK1 causes Oguchi disease in a consanguineous Pakistani family.

PMID 19753316 · PMC2742643 · Molecular vision · 2009 · 8 claims · 6 setups

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A novel nonsense mutation (c.614C>A; p.S205X) in exon 1 of GRK1 causes disease in family RP19

affected family rp19 selected genome-wide microsatellite direct
A novel gammaD-crystallin mutation causes mild changes in protein properties but leads to congenital coralliform cataract.

PMID 19668596 · PMC2722711 · Molecular vision · 2009 · 8 claims · 6 setups

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A novel heterozygous CRYGD mutation c.43C>A (R15S) causes congenital coralliform cataract in Family A

family genomic crygd lens two-point microsatellite direct
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

prehispanic indigenous ancient modern y-chromosome nested real-time
Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.

PMID 36093739 · PMC9828440 · The New phytologist · 2022 · 8 claims · 8 setups

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Natural selection contributed to the establishment and maintenance of the Scandinavian contact zone between the NFE and CSE genetic clusters.

picea swedish subsets exome principal umap
Comparative Genomics Provide Insight Into the Evolution of European Aphanomyces euteiches Strains.

PMID 41832745 · PMC13044513 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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Genome-wide SNP data confirm three genetically distinct A. euteiches populations in Europe, with Italian strains forming a clearly separated group

euteiches aphanomyces ce1 whole-genome busco comparative
Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies.

PMID 41838407 · PMC13197121 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

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Developed a scalable Nextflow workflow that automates phasing, local ancestry inference (LAI), and Tractor GWAS into a reproducible end-to-end pipeline

biobank phased two-way simulated haplotype local gwas
Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

PMID 41918820 · PMC13034039 · NAR molecular medicine · 2026 · 7 claims · 8 setups

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An in vitro cross between L. infantum and L. tarentolae produced a viable inter-subgenus hybrid, demonstrating genomic compatibility between highly divergent Leishmania species.

infantum linf-gfp bone bmdms genetic flow morphological
Complex genetic diseases: controversy over the Croesus code.

PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

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The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

chromosome northern disease large-scale genome-wide database
MuPlex: multi-objective multiplex PCR assay design.

PMID 15980531 · PMC1160138 · Nucleic acids research · 2005 · 8 claims · 3 setups

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MuPlex is a web-enabled system that designs multiplex PCR assays by selecting primer pairs for SNPs and partitioning them into multiplex-compatible tube sets.

user-submitted candidate genomic multiplex primer homogeneous
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

PMID 15774022 · PMC1274256 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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SNPHunter allows ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data (physical position, function class, flanking sequences at user-defined lengths, heterozygosity) from NCBI dbSNP

ncbi candidate tnf batch-mode snp gene
Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates.

PMID 16627870 · PMC1440945 · Nucleic acids research · 2006 · 7 claims · 3 setups

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A GLMM-based test statistic that models the nested structure of array replicate/strand/probe measurements achieves correct type I error, unlike naive or t-test based statistics.

endometriosis individual pooling concentration pcr-based
Haplotype analysis of Lrrk2 R1441H carriers with parkinsonism.

PMID 18952485 · PMC2749264 · Parkinsonism & related disorders · 2009 · 5 claims · 3 setups

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The LRRK2 R1441H substitution has arisen on multiple independent occasions rather than from a single common founder

genomic haplotype direct full
High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach.

PMID 18559660 · PMC2518505 · Diabetes · 2008 · 8 claims · 3 setups

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Primary linkage finding for diabetic nephropathy is on chromosome 19q

sibpairs genotype patients genome-wide statistical urinary

Experiments

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Reconstructing Indian population history.

Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

FISH and SNP-A karyotyping in myelodysplastic syndromes: improving cytogenetic detection of del(5q), monosomy 7, del(7q), trisomy 8 and del(20q).

A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

A novel mutation in GRK1 causes Oguchi disease in a consanguineous Pakistani family.

A novel gammaD-crystallin mutation causes mild changes in protein properties but leads to congenital coralliform cataract.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

Teasing apart the joint effect of demography and natural selection in the birth of a contact zone.

Comparative Genomics Provide Insight Into the Evolution of European Aphanomyces euteiches Strains.

Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies.

Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

Complex genetic diseases: controversy over the Croesus code.

MuPlex: multi-objective multiplex PCR assay design.

SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.

Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates.

Haplotype analysis of Lrrk2 R1441H carriers with parkinsonism.

High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach.