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).

• Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

  PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

  genes autosomes dog genome comparative blat sliding-window

• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

  PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

  Full-text index only

  Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

  consensus sap query all-against-all blast cross-database

• Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

  PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

  Full-text index only

  Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

  liver atherosclerotic 128-gene independent two-way gene bioinformatic

• Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

  PMID 17982171 · PMC2238866 · Nucleic acids research · 2008 · 6 claims · 5 setups

  Full-text index only

  StellaBase Disease houses homology data for 155,904 invertebrate isoforms of human disease genes across four model systems, including 14,874 predicted Nematostella genes

  nematostella blastp est snp

• Whole genome association mapping by incompatibilities and local perfect phylogenies.

  PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

  Full-text index only

  Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

  coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype

• The RCSB PDB information portal for structural genomics.

  PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

  Full-text index only

  The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

  structural nih genome sequence target production

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.

  lung ipf copd curated hierarchical differential

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

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

  Full-text index only

  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

• The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

  PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

  Has reproduction · 67

  A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

  facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

  Full-text index only

  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray

• Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

  PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

  yeast liver eight-node microarray k-means hybrid

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• The molecular characterization and clinical management of multiple myeloma in the post-genome era.

  PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

  Full-text index only

  GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

  myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted

• Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.

  PMID 39039281 · PMC11319204 · Nature genetics · 2024 · 6 claims · 5 setups

  Has reproduction · 87

  A structured multidisciplinary exome sequencing framework established molecular genetic diagnoses in 32% of patients with suspected ultrarare disorders, comprising 370 distinct molecular causes.

  patients exome deep computer-assisted

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a comprehensive, publicly accessible database integrating bulk RNA-seq, scRNA-seq, and spatial transcriptomics data across 17 skin diseases and 63 independent datasets

  skin scrna-seq scrna-seq transcription cell-cell

• 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

• 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

• CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

  PMID 16995941 · PMC1592126 · BMC bioinformatics · 2006 · 7 claims · 5 setups

  Full-text index only

  CROPPER is a web-based software resource that combines genomic data from heterogeneous sources using identifier and orthologous gene information from the Ensembl database.

  mus substantia transgenic mptp-lesioned western microarray self-organizing

• In silico segmentations of lentivirus envelope sequences.

  PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups

  Full-text index only

  C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.

  eiav hiv hmm-based hmm artificial

• 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