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).

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  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.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

  PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

  Full-text index only

  Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

  saccharomyces correlated chip-chip gene

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• Seeded Bayesian Networks: constructing genetic networks from microarray data.

  PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

  Full-text index only

  Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

  leukemia interactome pubmed-indexed computational microarray yeast literature

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

  PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups

  Full-text index only

  560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space

  genodermatoses phenotype disease gene-phenotype manual correlation principal

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

  Full-text index only

  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• 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

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

  Full-text index only

  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Identification and analysis of co-occurrence networks with NetCutter.

  PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

  publime bipartite randomized co-occurrence null-model signal-to-noise

• PubMatrix: a tool for multiplex literature mining.

  PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups

  Full-text index only

  PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts

  pubmed ovarian genome literature cdna

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

  Full-text index only

  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

  PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

  Full-text index only

  Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

  genome genomic chromosome randomization

• WebGestalt: an integrated system for exploring gene sets in various biological contexts.

  PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

  genes gene est-based enrichment kegg

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.

  PMID 39384533 · PMC11650866 · FEMS microbiology ecology · 2024 · 8 claims · 8 setups

  Has reproduction · 85

  Chloroflexota populations are partitioned according to alternative electron acceptors (Anaerolineae) and electron donors (Dehalococcoidia) among respiratory and fermentative metabolites at and below the sediment-water interface

  lake undisturbed chloroflexota 16s shotgun pore

• Information extraction from full text scientific articles: where are the keywords?

  PMID 12775220 · PMC166134 · BMC bioinformatics · 2003 · 8 claims · 5 setups

  Full-text index only

  The keyword content of the five article sections (A, I, M, R, D) is heterogeneous, i.e., different sections carry different kinds of information.

  corpus same articles keyword validation qualitative

• Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

  PMID 17849004 · PMC1964532 · PloS one · 2007 · 8 claims · 5 setups

  Full-text index only

  mtUPR responsive genes (YME1L1, MPPβ, Tim17A, NDUFB2, Endonuclease G, Thioredoxin 2, plus previously known ClpP, Cpn60/10, MtDnaJ) all contain a CHOP element in their promoters

  genome cos-7 promoters bioinformatic promoter-luciferase site-directed

• Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.

  PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Has reproduction · 67

  Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.

  kyse150 bulk rna-seq-based differential