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).

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• Structural genomics and drug discovery.

  PMID 17488474 · PMC3822824 · Journal of cellular and molecular medicine · 2007 · 8 claims · 8 setups

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  Membrane proteins represent ~70% of current drug targets but only just over 100 high-resolution structures exist for them, versus >30,000 total structures in public databases dominated by soluble proteins.

  coli emre pichia sf9 cell-free bacterial inclusion

• How bacterial communities expand functional repertoires.

  PMID 17238278 · PMC1750926 · PLoS biology · 2006 · 8 claims · 7 setups

  Full-text index only

  The human microbiome contains roughly 100 times as many genes as does the human genome

  bacteroides distal interleukin-10-deficient macrophages transcriptional metagenomic microbiota

• C-terminal mutants of apolipoprotein L-I efficiently kill both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.

  PMID 19997494 · PMC2778949 · PLoS pathogens · 2009 · 8 claims · 8 setups

  Full-text index only

  The C-terminal helix of apoL1 is entirely responsible for its interaction with SRA

  coli brucei computational papio bacterial trypanolytic nickel-bead

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• 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 four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

  PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 94

  A 4-gene whole-blood signature (ITGB4, ITGA7, IFI27, FAM20A) discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90

  hospitalized ari febrile infection bulk rna-seq microarray

• From Pasteur to genomics: progress and challenges in infectious diseases.

  PMID 15516917 · PMC7096024 · Nature medicine · 2004 · 8 claims · 8 setups

  Full-text index only

  Genomic sequencing has revealed the blueprint of most pathogens, enabling new diagnostics, therapeutics and vaccines including for previously uncultivable agents.

  bacterial neisseria sars hiv-infected whole-genome reverse nucleic

• Critical care: applying genomics to inflammation outcomes.

  PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

  Full-text index only

  Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

  leukocytes whole-blood healthy peripheral genomewide whole-genome microarray

• Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods.

  PMID 34307679 · PMC8272456 · BioMed research international · 2021 · 7 claims · 2 setups

  Has reproduction · 32

  A pipeline combining Boruta and mRMR feature selection with incremental feature selection (IFS) was used to identify COVID-19-specific transcriptomic biomarkers from blood gene expression data.

  blood bulk kegg

• Genomics--from Neanderthals to high-throughput sequencing.

  PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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  Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

  bacterial ion-channel drosophila arrays next-generation pooled multiplex

• MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

  PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups

  Has reproduction · 83

  MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences

  simulated mock16 real snailgut novo transcript gene

• Host-pathogen studies in the post-genomic era.

  PMID 11178231 · PMC138846 · Genome biology · 2000 · 7 claims · 7 setups

  Full-text index only

  DNA arrays have been used to study host and/or pathogen gene expression for four viruses (HCMV, HHV8, HIV-1, HPV31) and two bacteria (Listeria monocytogenes, Salmonella)

  foreskin b-cell t-cell normal pathogen host

• RNA interference in functional genomics and medicine.

  PMID 12808314 · PMC3055057 · Journal of Korean medical science · 2003 · 8 claims · 7 setups

  Full-text index only

  RNAi is sequence-specific gene silencing induced by double-stranded RNA and is mediated by ~22-nt siRNAs generated from long dsRNA by the RNase III enzyme Dicer.

  caenorhabditis drosophila mammalian postnatal dsrna biochemical synthetic

• Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.

  PMID 18047719 · PMC2099488 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Deconvoluting gene expression variance into technical (Gaussian, ~6.5% relative SD) and biological components identifies hypervariable (HV) genes that reflect true biological response to infection without requiring replicates

  urothelial clustered genome-wide confocal k-means

• An "omics" approach to uropathogenic Escherichia coli vaccinology.

  PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

  Full-text index only

  An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

  upec vaccination comparative two-dimensional

• Monocarboxylate Transporter-2 Expression Restricts Tumor Growth in a Murine Model of Lung Cancer: A Multi-Omic Analysis.

  PMID 34638954 · PMC8508890 · International journal of molecular sciences · 2021 · 7 claims · 7 setups

  Has reproduction · 53

  Reduced MCT2 expression promotes increased tumor growth and local invasiveness in a murine TC1 lung carcinoma model

  mct2 tumor tumor-associated fecal western tumor transmission

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 78

  INVADE-seq simultaneously captures host and bacterial transcripts to map bacteria-host interactions across diverse testicular cell types at single-cell resolution

  testes testis young testicular invade-seq histology sperm

• Unlocking the microbial studies through computational approaches: how far have we reached?

  PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

  Has reproduction

  Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

  clinical bacteriophage vaginal hbv ngs random whole-genome

• Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens.

  PMID 34438997 · PMC8388888 · Antibiotics (Basel, Switzerland) · 2021 · 8 claims · 5 setups

  Has reproduction · 49

  The S. ambofaciens ATCC 23877 transcriptome was redefined from RNAseq data into 5587 transcriptional units (4433 monocistronic, 1154 polycistronic) covering 90.8% of the linear chromosome

  streptomyces ambofaciens bulk rna-seq target