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).

• Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

  PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 94

  Both core and accessory genome characteristics show strong association with distinct host animal species, indicating multiple independent adaptive trajectories rather than a single common evolutionary path

  jejuni core whole-genome core k-mer

• The application of genomics to emerging zoonotic viral diseases.

  PMID 19855817 · PMC2734983 · PLoS pathogens · 2009 · 8 claims · 8 setups

  Full-text index only

  High-throughput sequencing, mRNA expression profiling, and SNP microarray analysis enable rapid identification and genomic characterization of emerging zoonotic pathogens and host responses to them.

  siv-infected plasmacytoid migratory influenza transcriptional tlr fecal

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

  PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups

  Full-text index only

  Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling

  cd4+ hela influenza-infected liver cdna microarray mass

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

  PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

  Has reproduction · 50

  MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

  bovine simulated cami trimming decontamination assembly

• Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

  PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups

  Has reproduction

  Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.

  horizon six cho-k1 cho genome rna-seq targeted

• Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.

  PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups

  Has reproduction · 90

  Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.

  monocyte-derived raw same trimmed dual fastqc adapter

• Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

  PMID 18637129 · PMC2605190 · Experimental dermatology · 2009 · 8 claims · 5 setups

  Full-text index only

  Strict, rigorous sun protection starting at age 2 resulted in minimal skin disease (only mild lip freckling, no skin cancer) in XP2GO despite an XP diagnosis

  fibroblasts xp2go post-uv host real-time

• Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models.

  PMID 36536288 · PMC9762025 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 4 setups

  Has reproduction · 93

  Structural equation models can decompose the total genetic effect on a production trait into a direct host genetic effect and an indirect effect exerted through the microbiota.

  rabbits cecal host bayesian 16s snp

• The first single-stranded DNA virus targeting Pectobacterium belongs to the family Microviridae and demonstrates a broad host range to Pectobacterium brasiliense soft rot pathogens.

  PMID 41739249 · PMC12935840 · Archives of virology · 2026 · 7 claims · 7 setups

  Has reproduction · 90

  Phage Mimer is the first described single-stranded DNA phage targeting Pectobacterium and belongs to the family Microviridae, subfamily Bullavirinae.

  pectobacterium phage cscl-purified pbr phage whole-genome genome

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups

  Has reproduction · 64

  Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).

  rimicaris foregut deferribacteres shotgun fluorescence yoyo-1

• Glycan arrays for functional glycomics.

  PMID 12537579 · PMC151192 · Genome biology · 2002 · 6 claims · 5 setups

  Full-text index only

  Glycan arrays allow high-throughput characterization of lectin binding specificity in a single experiment, improving on material-intensive hapten inhibition assays

  synthetic biotinylated mono monosaccharides neoglycolipid carbohydrate streptavidin-biotin

• The genomics of probiotic intestinal microorganisms.

  PMID 15998456 · PMC1175979 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Genomic characterization of probiotic and commensal intestinal bacteria will deepen understanding of their beneficial effects on host health

  lactobacillus bacteroides bifidobacterium host whole-genome inflammation microarray

• Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

  PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

  predicted non-masked genome interpro hmm tblastn inter-species

• Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

  PMID 17949499 · PMC2148065 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  ECM-stimulated hMSC and OS-media-stimulated hMSC represent two distinct intermediate/transitional phenotypes en route to becoming osteoblasts

  naive hmsc osteoblasts proteomic lc-ms gene computational

• The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

  PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

  Full-text index only

  Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

  hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

  Full-text index only

  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• A bioinformatic pipeline for simulating viral integration data.

  PMID 35496474 · PMC9046613 · Data in brief · 2022 · 7 claims · 3 setups

  Has reproduction · 96

  A snakemake-based pipeline was developed to simulate integration of a viral or vector genome into a host genome, including sub-genomic fragment integration, structural variation, and host-site deletions.

  aav2 host simulated integration simulated junction-crossing