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 21

System / cell line: shotgun ✕ Assay: snp ✕ Clear

Rats go genomic.

PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

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A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

recombinant genes serotonin adenomatous genome-wide targeted knockout
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

Has reproduction · 91

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.

gossypium longicalyx nine diploids whole-genome wgs read
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

poodle dogs y-chromosome blast pcr nested
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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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.

bombyx whole-genome snp novo
Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

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The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

rumen blood beef metagenome snp longitudinal
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
The diploid genome sequence of an Asian individual.

PMID 18987735 · PMC2716080 · Nature · 2008 · 8 claims · 8 setups

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First diploid genome sequence of an Asian (Han Chinese) individual generated using massively parallel Illumina sequencing

han donor genome genomic whole-genome g-banded snp
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups

Has reproduction · 79

196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions

rhizobium strains genotype genome whole-genome orthologous snp
Shotgun proteomics and biomarker discovery.

PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

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Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac
The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

chimpanzee chimp population non-human genome snp high-density
The diploid genome sequence of an individual human.

PMID 17803354 · PMC1964779 · PLoS biology · 2007 · 7 claims · 6 setups

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Generated an independently assembled diploid human genome sequence (HuRef) from both chromosome sets of a single individual using whole-genome shotgun Sanger sequencing

donor huref whole-genome assembly-to-assembly snp
Evolutionary toggling of the MAPT 17q21.31 inversion region.

PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

chimpanzee lymphoblastoid donor whole-genome reciprocal bac
Genome sequence, comparative analysis, and population genetics of the domestic horse.

PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups

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Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)

single horse eight twelve genome fish chip-on-chip
Personalized copy number and segmental duplication maps using next-generation sequencing.

PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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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.

genomes genomic interphase na18507 whole-genome array fluorescence
Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular
More biology from the sequence.

PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

schizosaccharomyces chromosome genome cervical whole-genome sequence genome
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
SNPdetector: a software tool for sensitive and accurate SNP detection.

PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

inbred unrelated zebra same pcr manual comparative
Human genomic variation.

PMID 11178257 · PMC138878 · Genome biology · 2000 · 8 claims · 7 setups

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Lewontin's 1972 analysis of 17 blood-group/protein loci found 85% of human genetic variation lies within individuals of a nation/tribe, 8% between populations within races, and only 6% between races

populations individuals composite genome blood-group marker mitochondrial
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

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Rats go genomic.

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

The diploid genome sequence of an Asian individual.

Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.

Shotgun proteomics and biomarker discovery.

The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

The diploid genome sequence of an individual human.

Evolutionary toggling of the MAPT 17q21.31 inversion region.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

Personalized copy number and segmental duplication maps using next-generation sequencing.

Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

More biology from the sequence.

Twin peaks: the draft human genome sequence.

SNPdetector: a software tool for sensitive and accurate SNP detection.

Human genomic variation.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.