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).
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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups
The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.
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The genome of Brugia malayi - all worms are not created equal.
PMID 18952001 · PMC2668601 · Parasitology international · 2009 · 8 claims · 8 setups
Comparative genome analysis shows conserved long-range synteny but divergent local gene order between B. malayi and C. elegans, reflecting distinct evolutionary trajectories of parasitic and free-living lineages.
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Has reproduction · 30
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups
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.
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A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups
The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.
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Has reproduction · 92
Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.
PMID 28446242 · PMC5406893 · Genome medicine · 2017 · 7 claims · 6 setups
Breast tumors exhibit two discrete GFRN activity phenotypes: a 'survival phenotype' with concordant HER2/IGF1R/AKT activation and a 'growth phenotype' with concordant EGFR/KRAS(G12V)/RAF1/BAD activation, which are typically mutually exclusive.
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A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.
PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups
A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD
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Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups
Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation
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miRGator: an integrated system for functional annotation of microRNAs.
PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups
miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs
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Genomics research and malaria control: great expectations.
PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups
Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.
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Has reproduction · 71
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
Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.
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Has reproduction
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.
PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups
Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.
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Has reproduction · 75
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups
XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations
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Expression profiling of drug response--from genes to pathways.
PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups
Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.
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Genomics against flatulence.
PMID 17635535 · PMC1974822 · Environmental microbiology · 2007 · 8 claims · 8 setups
Methanogenic archaea (not bacteria) in the human gut, chiefly Methanobrevibacter smithii, produce the methane component of intestinal gas, most of which is released via the large intestine (up to 0.5 l day−1) rather than in breath.
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Comparative genomic analysis of three Leishmania species that cause diverse human disease.
PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups
L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species
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Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo.
PMID 18681965 · PMC2519092 · BMC genomics · 2008 · 8 claims · 6 setups
1-h and 6-h intraduodenal exposure of human small intestinal mucosa to L. plantarum WCFS1 induces differential expression of 669 and 424 gene reporters, respectively.
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Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.
PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups
Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age
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A simple and efficient algorithm for genome-wide homozygosity analysis in disease.
PMID 19756043 · PMC2758715 · Molecular systems biology · 2009 · 8 claims · 4 setups
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
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Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?
PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups
A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047
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Protozoan genomics for drug discovery.
PMID 16151400 · PMC7096809 · Nature biotechnology · 2005 · 8 claims · 3 setups
Complete genome sequences of five protozoan parasites (Theileria parva, T. annulata, Leishmania major, Trypanosoma brucei, T. cruzi) were reported, enabling comparative genomics.