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).

• miRGen: a database for the study of animal microRNA genomic organization and function.

  PMID 17108354 · PMC1669779 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  miRGen is an integrated database combining Genomics, Targets, and Clusters interfaces to study miRNA genomic organization and function across 11 animal genomes

  animal genome mouse-human mirna genomic mirna cross-species

• Spontaneous symmetry breaking in genome evolution.

  PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups

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  Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process

  animal homo model genome-wide alternatively computational

• Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

  PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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  145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

  complete mutation sars-cov spike sequence phylogenetic selection

• Large-scale trends in the evolution of gene structures within 11 animal genomes.

  PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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  Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

  annotated animal unannotated comparative all-against-all neighbor-joining

• The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

  PMID 17108355 · PMC1669709 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  ASAP II expands human alternative splicing data ~3-fold over the previous ASAP database, to ~89,078 distinct alternative splicing relationships in 11,717 genes

  genome animal aligned est genome-wide comparative est

• New strategies in drug discovery.

  PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

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  A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

  animal normal low-abundance mice situ microarray taqman

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 7 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirms a positive bidirectional association between DED and DEP (DED patients have increased DEP prevalence and vice versa).

  studies taiwan twb ded meta-analysis genome-wide conditional

• COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

  PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups

  Has reproduction · 84

  COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.

  animal same coexpression gene rnaseq-based microarray-based pathway

• Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

  PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 94

  Both core and accessory genome characteristics show strong association with distinct host animal species, indicating multiple independent adaptive trajectories rather than a single common evolutionary path

  jejuni core whole-genome core k-mer

• Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

  PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene

• Use of genomic data in risk assessment.

  PMID 11983054 · PMC139345 · Genome biology · 2002 · 8 claims · 4 setups

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  New genomic technologies (CGH, SNP analysis, restriction landmark genome scanning, spectral karyotyping, transcript profiling) can be applied to improve risk assessment accuracy

  glioma lung animal genome sensitivity expression snp

• Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

  PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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  A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

  rts rtsβ ccrf-cem comparative mitochondrial subcellular

• Genetic and epigenetic contributions to human nutrition and health: managing genome-diet interactions.

  PMID 18755320 · PMC5421377 · Journal of the American Dietetic Association · 2008 · 8 claims · 7 setups

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  Folate-mediated one-carbon metabolism is a conduit linking the cellular nutrient environment to genome regulation via nucleotide biosynthesis for DNA synthesis and SAM biosynthesis for genome methylation.

  yellow premenopausal men humans dietary mthfr plasma

• Toxicogenomics: an emerging discipline.

  PMID 12460812 · PMC1241126 · Environmental health perspectives · 2002 · 8 claims · 6 setups

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  Toxicogenomics applies genomic tools (microarrays, proteomics, metabolomics) to characterize how cells and organisms respond to chemical/drug exposures.

  drug stated acetaminophen tissues microarray gene genomic

• Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

  PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

  transmembrane simulated age duplicate maximum kernel monte

• The 32nd Annual Congress of the Society of Critical Care Medicine, 28 January - 2 February 2003, San Antonio, USA.

  PMID 12720569 · PMC270663 · Critical care (London, England) · 2003 · 8 claims · 8 setups

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  Proteomics is more useful than genomics for identifying regulatory pathways and druggable targets in disease because transcriptional responses to different stimuli often converge while protein interaction networks reveal distinct regulatory nodes

  macrophages patients animal ards gene histological mechanical

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

  PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

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  Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

  angiosperms animal oryza proteobacteria gene site-heterogeneous codon

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization