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).

• Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

  PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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  Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

  yeast specified normal coli chip-on-chip chip-sequencing correlation-based

• 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

• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

  PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

  genes candidate simulated alzheimer's genome-wide term null-hypothesis

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental

• Genomics and biology come together to fight HIV.

  PMID 18366259 · PMC2270331 · PLoS biology · 2008 · 8 claims · 6 setups

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  Genome-wide association studies have identified ~100 genetic polymorphisms robustly (genome-wide significant) linked to common human traits/diseases, but the biological mechanisms behind most remain unknown.

  ceph hiv-positive elledge heritability linkage modified

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

  PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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  Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

  human-mouse adjacent est genome splice

• 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

• Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.

  PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups

  Has reproduction · 23

  COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.

  lung sakornsakolpat string bulk microarray gwas

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• Finding disease candidate genes by liquid association.

  PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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  LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

  nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.

  encode liver bulk rna-seq meta-analysis

• G-quadruplexes in promoters throughout the human genome.

  PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

  genome quiescent gene synthetic computational nuclease gene

• Comparative genomics of Drosophila and human core promoters.

  PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

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  Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

  drosophila core genome-wide mono gene

• 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

• Patterns and rates of intron divergence between humans and chimpanzees.

  PMID 17309804 · PMC1852421 · Genome biology · 2007 · 8 claims · 6 setups

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  Intron divergence (Ki) is strongly positively correlated with intron length

  orthologous genome whole-genome cpg recombination

• Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

  PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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  The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

  dbsnp best-hit omicia hgmd genome-wide correlation disease

• Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

  PMID 19653838 · PMC3819565 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 8 claims · 5 setups

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  A subset of probesets (3,414) shows 4-hour test-retest reliability exceeding r=0.70 for detecting individual differences in gene expression.

  blood edta reliably genome-wide twin sub-type

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative