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).

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

  PMID 19907644 · PMC2770834 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  Existing pathway databases and tools do not satisfy all requirements for a generic, comprehensive pathway browser (integrated maps, data access, mapping/editing, export, installation-free availability).

  kegg 8192x8192 user-submitted species pathway zoomable sequence

• 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

• Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

  PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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  A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

  lsl-krasg12d soft combined mfh microarray gene oncogenic

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• The Proteomics Identifications database: 2010 update.

  PMID 19906717 · PMC2808904 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  PRIDE has become one of the main repositories for MS-based proteomics data, with substantial growth in data holdings over the last two years.

  species plasma caenorhabditis secretory ms-based quantitative

• Comparative genomic analysis of three Leishmania species that cause diverse human disease.

  PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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  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

  infantum major braziliensis leishmania whole-genome comparative pcr

• Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

  PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups

  Has reproduction · 55

  The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation

  corbicula six sediment filtered 16s radseq picrust2

• Interactome networks: the state of the science.

  PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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  Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

  genes tnfα orf proteins yeast tandem interference

• Metatranscriptomics of the human oral microbiome during health and disease.

  PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

  Has reproduction · 62

  Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

  patient-matched subset health rna-seq rrna comparison metatranscriptomics

• 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

• Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

  PMID 34830313 · PMC8625315 · International journal of molecular sciences · 2021 · 8 claims · 2 setups

  Has reproduction · 79

  TCDD dose-dependently enriches Lactobacillus species, particularly L. reuteri, in the mouse cecum microbiome

  cecum fecal shotgun humann

• Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.

  PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups

  Has reproduction · 77

  Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.

  appswe app gut 16s open picrust2

• Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

  PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

  est gene worm fly blat-based transcription comparative

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

  PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups

  Has reproduction · 58

  A cheetah-specific epigenetic age clock using 52 CpG sites predicts chronological age across blood and liver with r=0.97 and MAE=0.86 years

  cheetah lion genes methylation epigenome-wide differential

• Adaptation, aging, and genomic information.

  PMID 20157529 · PMC2806027 · Aging · 2009 · 8 claims · 6 setups

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  Aging is caused primarily by the absence of adaptive genomic information for later-age survival and function, due to declining forces of natural selection with adult age; this absence secondarily produces misallocation and damage at every level of biological organization.

  drosophila large animal unspecified experimental demographic hormone

• PRIDE: a public repository of protein and peptide identifications for the proteomics community.

  PMID 16381953 · PMC1347500 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  PRIDE is a PSI-compliant public repository for protein and peptide identifications, associated post-translational modifications, and supporting mass spectra from the scientific literature.

  plasma platelet jurkat specified peptide peptide-centric mass

• Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

  PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 59

  Short-term stress and long-term adaptations share common metabolic pathways

  great embryonic gef mapk1 bulk gene transcription