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 39

System / cell line: alleles ✕ Assay: genome ✕ Clear

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
Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

PMID 34576874 · PMC8467633 · Microorganisms · 2021 · 7 claims · 7 setups

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Amitosis causes random assortment of somatic alleles (IESs) in the highly polyploid Paramecium macronucleus, which can be tracked without phenotypic markers using scDNA-seq.

paramecium tetraurelia telomere-capped simulated single-cell bulk bias
Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

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Homozygous truncating mutations in PCNT cause Seckel syndrome

consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence
The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

PMID 20052305 · PMC2801442 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 6 setups

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The Mammalian Phenotype (MP) Ontology enables classification and organization of phenotypic data for mouse and other mammalian species in a computationally useful, standardized manner.

genotypes neural inbred viable phenotype phylogenetic comparative
Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

genome-sequenced trachomatis same concatenated whole-genome multilocus ompa
A SNP-centric database for the investigation of the human genome.

PMID 15046636 · PMC395999 · BMC bioinformatics · 2004 · 8 claims · 3 setups

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SNPper is a web-based, integrated SNP database combining dbSNP, the Human Genome sequence (Goldenpath), LocusLink, GeneOntology, and SWISS-PROT data with querying, visualization, and export tools.

genome genes user-supplied database snp-gene user-submitted
The meso-genomic era.

PMID 11516332 · PMC139414 · Genome biology · 2001 · 8 claims · 8 setups

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Linkage disequilibrium (LD) between SNPs extends much further in Northern European populations (~120 kb) than in a Nigerian population (<10 kb), reflecting differing population histories (bottlenecks vs. constant expansion).

genome chromosome families tomato snp haplotype genetic
Systems biology: where it's at in 2005.

PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

saccharomyces drosophila environmental literature systematic genome-wide
Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

Has reproduction · 68

200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

african lion crater simulated genome principal admixture
Population structure analysis of Salmonella serovar Muenchen to redefine geno-serotyping using genome indexing approaches.

PMID 41743541 · PMC12929376 · Frontiers in microbiology · 2025 · 8 claims · 7 setups

Has reproduction · 54

bettercallsal, leveraging the NCBI Pathogen Detection database, enhances serovar resolution by incorporating genome proximity calls

salmonella same megahit-assembled genome genome-indexing antigen-based cgmlst-based
Discovery and characterization of Alu repeat sequences via precise local read assembly.

PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups

Has reproduction · 69

Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads

hgdp insertion-supporting candidate assembled genome discordant novo
The gentle art of gene arrangement: the meaning of gene clusters.

PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

populations mhc interphase cartilaginous sequence codon comparative
Comparative analysis of cancer genes in the human and chimpanzee genomes.

PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

chimpanzee non-human cancer comparative pcr targeted
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

PMID 17554261 · PMC2628541 · Nature genetics · 2007 · 8 claims · 8 setups

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IRGM SNPs (rs13361189, rs4958847) show strong replicated association with Crohn disease; IRGM induces autophagy and control of intracellular bacteria

wtccc replication population cases genome-wide taqman snp
Malaria research in the post-genomic era.

PMID 18843360 · PMC2705782 · Nature · 2008 · 8 claims · 7 setups

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Genome-dependent methods can partially substitute for forward genetic approaches that are unavailable or limited in malaria parasites.

falciparum plasmodium malaria hela comparative two-hybrid proteomics
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
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
Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq
Integrative functional genomics.

PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

yeast tissue-cultured mammalian genomic comparative targeted chip-chip

Experiments

Complex genetic diseases: controversy over the Croesus code.

Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing.

Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

A SNP-centric database for the investigation of the human genome.

The meso-genomic era.

Systems biology: where it's at in 2005.

Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

Population structure analysis of Salmonella serovar Muenchen to redefine geno-serotyping using genome indexing approaches.

Discovery and characterization of Alu repeat sequences via precise local read assembly.

The gentle art of gene arrangement: the meaning of gene clusters.

Comparative analysis of cancer genes in the human and chimpanzee genomes.

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

Malaria research in the post-genomic era.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

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

Ensembl 2013.

Integrative functional genomics.