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).

• Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

  PMID 17335570 · PMC1828162 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  An initial diversification of bHLHs occurred in the pre-Cambrian, prior to metazoan cladogenesis

  metazoan identified amphimedon nematostella genome sequence gene

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Pseudofam: the pseudogene families database.

  PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

  eukaryotic over pseudogenes pseudogene blast family sequence

• TB database: an integrated platform for tuberculosis research.

  PMID 18835847 · PMC2686437 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  TBDB is an integrated database providing access to TB genomic data and resources relevant to discovery/development of TB drugs, vaccines and biomarkers.

  tuberculosis streptomyces tb-infected whole-genome sequence trna

• Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex.

  PMID 18515835 · PMC2475620 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Yeast Med2, Med3/Pgd1 and Med5/Nut1 (Tail module) are homologs of human Med29, Med27 and Med24, respectively

  eukaryotic med genuine psi-blast mafft pssm-based

• Comparing whole genomes using DNA microarrays.

  PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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  DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

  genome saccharomyces mitochondrial sars array comparative resequencing

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• Personalized copy number and segmental duplication maps using next-generation sequencing.

  PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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  mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

  genomes genomic interphase na18507 whole-genome array fluorescence

• MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

  PMID 33849057 · PMC8266615 · Nucleic acids research · 2021 · 8 claims · 7 setups

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  MrHAMER yields >1000s of viral genomes per sample at 99.9% accuracy

  psg3.1 transcribed double-stranded mrhamer transcription reverse mrhamer

• The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

  PMID 37036103 · PMC10084500 · GigaScience · 2022 · 8 claims · 8 setups

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  GEN-ERA is a unified, publicly available toolbox of 13 Nextflow workflows supported by 14 Singularity containers for reproducible microbial genomic/phylogenomic analyses in both bacteria and small eukaryotes.

  gloeobacterales gloeobacteraceae publicly ncbi-deposited phylogenomics ssu genome

• metaTraits: a large-scale integration of microbial phenotypic trait information.

  PMID 41296543 · PMC12807735 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  metaTraits integrates culture-derived trait data from BacDive, BV-BRC, JGI IMG, and GOLD with genome-based predictions for isolate genomes (proGenomes) and MAGs (SPIRE)

  high-quality medium isolate genomes genome-based genome taxonomic

• TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.

  PMID 41494038 · PMC12788660 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  TEPEAK identifies and characterizes polymorphic TEs in populations without any prior TE sequence or loci information, using only a chromosome-level reference assembly.

  horse pooled sequences consensus whole-genome insertion hierarchical

• Epidemiology and phylogenomic characterization of the Clade IIb C.1 Mpox outbreak in Phnom Penh, Cambodia (2023-2024).

  PMID 41575511 · PMC12978180 · Emerging microbes & infections · 2026 · 8 claims · 8 setups

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  All Cambodian Mpox genomes belong to lineage C.1, nested within Clade IIb

  skin mpxv-positive raw cambodian real-time viral bioinformatic

• Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.

  PMID 41641705 · PMC12873609 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  Screening 202 cyanobacterial genomes identified 402 CRSs matching known RNA families (Rfam and Rho-independent terminators) and 409 novel CRSs.

  cyanobacterial peptide aligned local comparative genome sequence

• Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.

  PMID 41656299 · PMC12996302 · Nature communications · 2026 · 8 claims · 6 setups

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  CRISPR-PAMdb is a publicly accessible database compiling Cas9 protein sequences from 3.8 million bacterial/archaeal genomes and PAM profiles from 7.4 million phage/plasmid sequences

  bacterial phage cas9 experimentally hmm-based spacer-protospacer machine

• Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella.

  PMID 41684216 · PMC12902445 · Microbial biotechnology · 2026 · 7 claims · 5 setups

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  Structured, recurrent promoter variation in epigenetically regulated operons is a novel layer of functional adaptation in Salmonella, complementing genetic and epigenetic mechanisms.

  complete annotated 220-nucleotide opvab comparative correlation blastn

• PhyloRef: A Semi-Automated Workflow for eDNA Reference Database Curation via Phylogenetic Anomaly Detection.

  PMID 41766741 · PMC12946455 · Ecology and evolution · 2026 · 8 claims · 5 setups

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  PhyloRef is a Snakemake-based, semi-automated, phylogeny-guided workflow for eDNA reference database curation

  chondrichthyes actinopterygii mitochondrial aligned phylogenetic sequence automated

• The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

  PMID 36262335 · PMC9557141 · F1000Research · 2022 · 7 claims · 3 setups

  Has reproduction · 59

  The third BCM & DNAnexus hackathon produced nine software projects for SV analysis, of which eight are presented in this paper.

  long-read re-sequenced genomic long-read k-mer read-based

• Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues.

  PMID 17029625 · PMC1613252 · BMC genomics · 2006 · 8 claims · 3 setups

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  A database of 82 allergen sequences was compiled and used to search 22 fungal genomes for orthologues.

  fungal fumigatus enolase comparative epitope

• Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

  PMID 18541024 · PMC2446394 · BMC evolutionary biology · 2008 · 8 claims · 3 setups

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  Extant bony vertebrates (osteichthyans) retain only Lbx1- and Lbx2-type genes; no distinct Lbx3/Lbx4 proteins exist.

  osteichthyan aligned genome blast maximum comparative