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).

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray

• 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

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

  PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

  Full-text index only

  fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

  non-coding frnadb-hosted genomic mammalian sequence genome blastn

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.

  PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides

  glycoproteins n-linked serum complex maldi tryptic nonspecific

• Proteomics and genomics: perspectives on drug and target discovery.

  PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma

  proteins blood carbohydrate medicinal x-ray microarrays glycan

• SIRE 2.0: a novel method for estimating polygenic host effects underlying infectious disease transmission, and analytical expressions for prediction accuracies.

  PMID 40169992 · PMC11963337 · Genetics, selection, evolution : GSE · 2025 · 8 claims · 2 setups

  Has reproduction · 83

  SIRE 2.0 is a novel Bayesian methodology and software tool for estimating polygenic contributions (variance components and additive genetic effects) to host susceptibility, infectivity and recoverability from temporal epidemic data using pedigree/genomic relationship matrices.

  simulated bayesian systematic

• 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

• GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

  PMID 15980510 · PMC1160247 · Nucleic acids research · 2005 · 8 claims · 2 setups

  Full-text index only

  The GeneMark website provides web interfaces to the GeneMark family of ab initio gene-finding programs for prokaryotic, eukaryotic and viral genomic sequences

  escherichia arabidopsis initio

• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome.

  PMID 41729082 · PMC12956005 · JCI insight · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  TLR8 A518T is a gain-of-function variant that enhances NF-κB activation and increases secretion of proinflammatory cytokines upon stimulation compared with WT TLR8

  plasma pbmcs expressing tlr8 targeted plasma quantitative

• Conservation and losses of non-coding RNAs in avian genomes.

  PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

  Has reproduction · 100

  Homology-based covariance model (Rfam CM) annotation, combined with tRNAscan-SE and miRBase-derived models, identifies ncRNA loci across 48 avian genomes

  avian bird chicken covariance trna microrna

• Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

  PMID 27832824 · PMC5105290 · Genome biology · 2016 · 8 claims · 7 setups

  Has reproduction · 84

  The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

  single glabripennis amino whole-genome gene busco

• Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.

  PMID 31608047 · PMC6769089 · Frontiers in microbiology · 2019 · 7 claims · 5 setups

  Has reproduction · 93

  Five amplicon sequence variants (unclassified Flavobacteriales, Fusibacter, Planktotalea, Algicola, and Vibrio) were consistently enriched in disease lesions across three coral species (M. cavernosa, D. labyrinthiformis, D. stokesii)

  coral cavernosa 16s differential principal

• GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

  PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups

  Has reproduction · 73

  GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.

  mcf10a nde&dt hypoxia bulk correlation pca

• Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

  PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

  Has reproduction · 94

  Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power

  novel casei genomes selected whole-genome maximum-likelihood pairwise

• Downstream high-speed plasma jet generation as a direct consequence of shock reformation.

  PMID 35105885 · PMC8807623 · Nature communications · 2022 · 7 claims · 6 setups

  Has reproduction · 67

  High-speed downstream jets at Earth's bow shock are generated as a direct consequence of shock reformation.

  earth's mms mms2 upstream in-situ cross-correlation reduced

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction · 94

  ~50–60% of the genomes of S. tuberosum and S. lycopersicum are composed of repetitive elements

  tuberosum orthologous novo synteny orthologous

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

  halite same identified conserved strand-specific genome-resolved srna

• Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

  PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).

  angora domesticated candidate low-coverage multivariate principal