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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The post-genomic era for a select few.
PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups
The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.
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Population genomics: diversity and virulence in the Neisseria.
PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups
Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria
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Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.
PMID 19781061 · PMC2768977 · Genome biology · 2009 · 8 claims · 7 setups
The 027 genomes (CD196 and R20291) contain 234 additional genes compared to strain 630, spread across at least 50 regions of genetic difference, including a phage island, transposon genes, two-component response regulators, drug resistance genes and transporters
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Has reproduction · 92
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
cgMLST, wgMLST and hqSNP WGS-based analysis methods clustered C. jejuni and C. coli isolates in concordance with epidemiological data.
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Has reproduction · 66
Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.
PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups
Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient
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Metabolic syndrome: from epidemiology to systems biology.
PMID 18852695 · PMC2829312 · Nature reviews. Genetics · 2008 · 8 claims · 8 setups
MetSyn component traits (obesity, insulin resistance, dyslipidaemia, hypertension) exhibit causal interactions and common etiologies rather than being independent conditions
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Has reproduction · 88
Brown adipose tissue thermogenic adaptation requires Nrf1-mediated proteasomal activity.
PMID 29400713 · PMC5839993 · Nature medicine · 2018 · 8 claims · 10 setups
Cold adaptation increases proteasomal activity in BAT, which is required for non-shivering thermogenesis
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Has reproduction · 68
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.
PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups
The complete genome of L. plantarum ZLP001 comprises a single 3,164,369 bp circular chromosome (GC 44.65%) plus seven plasmids (A–G), encoding 3,264 protein-coding sequences.
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Has reproduction · 90
Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.
PMID 37012284 · PMC10070245 · Scientific reports · 2023 · 7 claims · 8 setups
Batch correction using sequencing platform as the correcting variable (via Combat-Seq) removes technical variability so that samples cluster by injury condition rather than dataset origin.
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Has reproduction · 75
Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.
PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 7 setups
CLAD harbors disease-specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages
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Has reproduction
Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.
PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups
SDSD constitutes a distinct taxonomic entity within S. dysgalactiae, with a mean intra-subspecies average nucleotide identity of 99%.
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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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Metabolomics applied to diabetes research: moving from information to knowledge.
PMID 19875619 · PMC2768174 · Diabetes · 2009 · 8 claims · 7 setups
Metabolomics measures chemical phenotypes that are the net result of genomic, transcriptomic, and proteomic variability, providing the most integrated profile of biological status
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Has reproduction · 64
Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.
PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 7 claims · 8 setups
HLA-DRB5 and ODAPH are causal risk genes for keratoconus, supported by SMR and Bayesian colocalization (HLA-DRB5 PP4=0.844, SMR p=0.001, OR=1.768; ODAPH PP4=1.0, SMR p=0.013, OR=202.851).