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).

• Inparanoid: a comprehensive database of eukaryotic orthologs.

  PMID 15608241 · PMC540061 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  The Inparanoid algorithm identifies true ortholog clusters by seeding on reciprocal best-matching pairs, gathering inparalogs (post-speciation duplicates) while excluding outparalogs (pre-speciation duplicates)

  eukaryotic pairwise uniprot sequences whole-genome inparanoid redundancy

• Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

  PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

  Full-text index only

  NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

  cancer proteome pten genome orthology protein-protein

• Prediction of specificity-determining residues for small-molecule kinase inhibitors.

  PMID 19032760 · PMC2655090 · BMC bioinformatics · 2008 · 8 claims · 5 setups

  Full-text index only

  S-Filter is a novel method combining sequence and structural information (within PFAAT) to predict specificity-determining residues and selectivity profiles for small-molecule kinase inhibitors

  panel kinase-inhibitor sequence erk2 caliper radiometric solvent

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

  PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

  Full-text index only

  The human genome encodes at least 71 kelch-repeat proteins

  genome yeast kelch-repeat full-length blast blastp cross-referencing

• More biology from the sequence.

  PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

  schizosaccharomyces chromosome genome cervical whole-genome sequence genome

• epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.

  PMID 35178872 · PMC9311447 · Molecular ecology resources · 2022 · 8 claims · 8 setups

  Has reproduction · 52

  epiGBS2 provides a laboratory protocol and revised bioinformatics pipeline for de novo cytosine methylation and SNP calling in species with or without a reference genome

  arabidopsis great epigbs2 demultiplexed epigbs2 pcr demultiplexing

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

  Full-text index only

  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

  PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

  Full-text index only

  The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

  cloned clinical hominis pcr culture sanger

• polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

  PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

  helicoverpa alternate contigs assemblies long-read short-read duplicate

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based