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).

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• Rfam 15: RNA families database in 2025.

  PMID 39526405 · PMC11701678 · Nucleic acids research · 2025 · 8 claims · 6 setups

  Has reproduction · 68

  Rfamseq was expanded to 26 106 genomes, a 76% increase, by incorporating the latest UniProt reference proteomes and additional viral genomes

  rfamseq rfam hepatitis mirbase covariance structure covariation

• 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

• Coverage of whole proteome by structural genomics observed through protein homology modeling database.

  PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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  FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

  orfs predicted modeled representative homology transmembrane intrinsic

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

  PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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  A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

  serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms

• Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.

  PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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  A combined target-selection approach — pursuing both structurally uncharacterised domain families and additional targets from large structurally characterised superfamilies — is essential for comprehensive structural coverage of the genomes.

  sp-trembl hmm-based domain computational

• Calibrating the performance of SNP arrays for whole-genome association studies.

  PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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  Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

  american liver simulated hapmap snp gene simulation-based

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.

  PMID 34614189 · PMC8643649 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 64

  metaGEM enables end-to-end reconstruction of FBA-ready GEMs directly from metagenomes without relying on reference genomes

  metagenomic prokaryotic reconstructed gut mag genome-scale gem

• Kinetoplastid genomics: the thin end of the wedge.

  PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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  Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

  brucei major cruzi kinetoplastid whole-genome gene shotgun

• A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

  PMID 19828875 · PMC2816009 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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  A stacked-ring ion guide (S-lens) increases ion transmission from the source into the instrument roughly 10-fold in MS/MS mode and 3-5-fold in full scan mode

  intact bsa hela model top-down nanoflow ion

• Sequencing of human genomes with nanopore technology.

  PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 75

  A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.

  gm12878 na12878 clinical whole-genome snv read-based

• KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

  PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

  Has reproduction · 42

  KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

  small snps individual hg002 alignment-free kmer-based genotyping

• A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

  PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups

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  Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.

  simulated same repeat whole-genome genome

• The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

  PMID 19654113 · PMC2759552 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 2 setups

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  IGB is an open-source, Java-based desktop genome browser supporting real-time zooming/panning, moveable tiered feature layout, incremental or genome-scale data loading, and dynamic genome graphs

  arabidopsis pyrosequencing expression

• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

  PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

  Has reproduction · 93

  Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

  melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• 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