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).

• Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

  PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  Human disease genes are much closer to aging genes in the PPI network than expected by chance

  protein-protein randomized dan aging network degree-conserved closeness

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• Sys-BodyFluid: a systematical database for human body fluid proteome research.

  PMID 18978022 · PMC2686600 · Nucleic acids research · 2009 · 6 claims · 4 setups

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  Sys-BodyFluid is a web-based database integrating proteomic data from 11 human body fluids (plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, milk, amniotic fluid), containing over 10,000 proteins

  body curated proteins literature sequence cross-body-fluid

• Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.

  PMID 35494238 · PMC9046238 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 60

  A customized bootstrapping/random-forest divide-and-conquer clustering pipeline integrating three scRNA-seq datasets robustly resolves cell states despite high cell-to-cell similarity within compartments

  bone endothelial independent integrated single-cell scrna-seq gene

• Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

  PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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  Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

  genome gene omim known naïve linkage disease-centric

• The identification of a Distinct Astrocyte Subtype that Diminishes in Alzheimer's Disease.

  PMID 38502590 · PMC11567244 · Aging and disease · 2024 · 7 claims · 6 setups

  Has reproduction · 57

  A distinct astrocyte subpopulation marked by low GFAP, plus AQP4 and CD63 expression, exists in normal brain but is diminished in AD samples in both human and mouse.

  prefrontal snrna-seq frontal brain single-nuclei gene cell-cell

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.

  surgically mammary menopaused integrated single-cell scrna-seq mammary

• Integrating herbarium specimen observations into global phenology data systems.

  PMID 30937223 · PMC6426164 · Applications in plant sciences · 2019 · 7 claims · 5 setups

  Has reproduction · 60

  A new PPO release adds terms and properties to relate observations of parts of plants to whole plants, enabling integration of herbarium phenology data with field observation data.

  plant prunus serotina ontology phenological integration

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• Genetical genomics: spotlight on QTL hotspots.

  PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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  Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

  adipose saccharomyces genome-wide permutation gene

• Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

  PMID 18782832 · PMC2686584 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  CTD is a manually curated knowledgebase that integrates chemical-gene interactions, chemical-disease relationships, and gene-disease relationships into a chemical-gene-disease triad

  pubmed ctd manual computational case-study

• ChimerDB--a knowledgebase for fusion sequences.

  PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

  genome candidate pubmed omim blat splice-site ecgene

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour