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 34

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

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

Has reproduction · 30

MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

simplified genome-scale cerevisiae coli minspan spearman comparative
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

population-based cohorts gwa plasma genome-wide replication candidate
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
A pharmacogene database enhanced by the 1000 Genomes Project.

PMID 19745786 · PMC2935084 · Pharmacogenetics and genomics · 2009 · 7 claims · 4 setups

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The database provides a convenient portal for immediate utilization of newly released 1000 Genomes Project (KGP) data in pharmacogenetic studies

ceu hapmap lymphoblastoid genotype-phenotype whole-genome low-coverage
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

PMID 17166280 · PMC1764022 · BMC genomics · 2006 · 8 claims · 6 setups

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C→T (G→A) changes occur most frequently among nucleotide substitutions in the chimpanzee genome

chimpanzee intergenic genome-wide chi-square nucleotide-content
On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

Has reproduction · 50

Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

gossypium transcripts uq-normalized differentially comparative coding bulk
Epigenetics and phenotypic variation in mammals.

PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

mammalian mhc chromosomes embryonic methylation high-throughput chip
Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

PMID 17900363 · PMC2098775 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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M. ulcerans has evolved into five InDel haplotypes that separate into two distinct phylogenetic lineages: a 'classical' lineage (Africa, Australia, South East Asia) and an 'ancestral' lineage (Asia, South America, Mexico)

ulcerans marinum plasmid-based pcr genome
A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

cases patients postmortem whole-genome cox linear
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Geographical genomics of human leukocyte gene expression variation in southern Morocco.

PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

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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.

peripheral blood genotype randomly genome-wide population admixture
Long-range regulation is a major driving force in maintaining genome integrity.

PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

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Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

opossum genome comparative identification statistical
Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

Has reproduction · 71

Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

cord maternal genes significant genome pm2.5 isolation
The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

PMID 26517373 · PMC4627764 · PLoS genetics · 2015 · 8 claims · 6 setups

Has reproduction · 56

C. metapsilosis is a highly heterozygous hybrid species formed from a single past hybridization event between two parental lineages ~4.5% divergent in sequence.

metapsilosis whole-genome novo pulsed
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
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
Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.

PMID 37133905 · PMC10272873 · Microbial genomics · 2023 · 8 claims · 8 setups

Has reproduction · 92

cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.

jejuni same subset isolate cgmlst hqsnp genome

Experiments

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

Ab initio identification of human microRNAs based on structure motifs.

A pharmacogene database enhanced by the 1000 Genomes Project.

Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome.

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

Population genomics of human gene expression.

Genome-wide survey of allele-specific splicing in humans.

Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Epigenetics and phenotypic variation in mammals.

Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Geographical genomics of human leukocyte gene expression variation in southern Morocco.

Long-range regulation is a major driving force in maintaining genome integrity.

Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

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

Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.