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).

• Ensembl 2006.

  PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

  cow ensembl snps genome gene whole-genome pairwise

• Sequence similarity network reveals common ancestry of multidomain proteins.

  PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

  curated complete well-studied sequence alignment domain

• 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

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

  sequences animal treefam-b lamin phylogenetic homology sequence

• MEROPS: the peptidase database.

  PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

  archaean holotype c-x-c proteins comparative domain substrate

• Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.

  PMID 41767255 · PMC12936829 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 100

  MSI status can be heterogeneous at the single-cell level within a tumor, challenging its use as a binary biomarker

  cancer aggregate single-cell homogeneously single-cell msi cancer

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

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

  Full-text index only

  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

• 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

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

  Full-text index only

  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

  PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups

  Full-text index only

  The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.

  complete genome escherichia environmental comparative pathway local

• Increased DNA microarray hybridization specificity using sscDNA targets.

  PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups

  Full-text index only

  A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA

  cuhr k562 input sscdna microarray quantitative capillary

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• VIRGO: computational prediction of gene functions.

  PMID 16845022 · PMC1538839 · Nucleic acids research · 2006 · 8 claims · 6 setups

  Full-text index only

  VIRGO constructs a functional linkage network (FLN) from gene expression and molecular interaction data, labels genes with GO annotations, and propagates these labels to predict functions of unlabelled genes

  cerevisiae sapiens leave-one-out gene protein-protein

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

  Full-text index only

  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

  PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

  genome protein-protein genes artificial kappa clustering gene

• A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

  PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

  Full-text index only

  Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

  unigene shuffled real genomes genome-wide alignment gene

• 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

• Systematic identification of pseudogenes through whole genome expression evidence profiling.

  PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

  genome ensembl vega celera spliced protein-to-genome pseudogene

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• Ensembl 2007.

  PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.

  low-coverage cow chicken genome genome standard customized