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).

• 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

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• Macrel: antimicrobial peptide screening in genomes and metagenomes.

  PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups

  Has reproduction · 83

  Macrel is an end-to-end pipeline that predicts high-quality AMP candidates from peptides, contigs, or reads of (meta)genomes

  curated hemopi-1 xiao cd-hit random amp homology-aware

• Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

  PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

  liver-derived muscle heart pooled 10x oxford hi-c

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• 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

• 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

• 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

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• EGASP: Introduction.

  PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

  Full-text index only

  Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

  genome computational manual rt-pcr

• 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

• Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

  PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

  Has reproduction

  Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

  types encode chip-seq chromhmm dnase-seq

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse