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).

• An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

  PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

  liver hcv-infected serum bulk chip-seq serum

• Toxoplasma: the next 100years.

  PMID 18672085 · PMC2596634 · Microbes and infection · 2008 · 8 claims · 8 setups

  Full-text index only

  Micronemes, rhoptries, and dense granules are specialized secretory organelles that mediate T. gondii host cell invasion and remodeling

  gondii mammalian cdna affymetrix sage

• 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

• Using DNA microarrays to study host-microbe interactions.

  PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

  Full-text index only

  DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

  streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene

• A genomics-based approach to biodefence preparedness.

  PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

  Full-text index only

  Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

  bacillus brucella neisseria gastric comparative transcriptome two-dimensional

• Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

  PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

  Full-text index only

  MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

  genitalium clinical urine pairwise pcr serial

• Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

  PMID 15785740 · PMC2361973 · British journal of cancer · 2005 · 8 claims · 2 setups

  Full-text index only

  D-loop mutation frequency is significantly higher in both noncancerous and tumour liver tissue of HCC/HBV patients than in normal control liver

  liver pcr

• 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

• Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

  PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

  Full-text index only

  Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

  hiv-1 polyclonally shannon cross-clade ctl

• SARS--beginning to understand a new virus.

  PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups

  Full-text index only

  A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS

  frhk-4 macaques sars-cov coronavirus virus infection whole-genome

• Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

  PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

  hela liver gene peripheral retroviral transposon hydrodynamic

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

  PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

  Full-text index only

  Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

  serum plasmids coli pcr oligonucleotide chip

• Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

  PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

  novel hpv gene h5n1 whole-genome intrinsic statistical

• Global analysis of community-associated methicillin-resistant Staphylococcus aureus exoproteins reveals molecules produced in vitro and during infection.

  PMID 17217429 · PMC2064037 · Cellular microbiology · 2007 · 6 claims · 3 setups

  Full-text index only

  Proteomic analysis (2-DGE coupled with ADI-MS/MS) identified 250 unique exoproteins produced by MW2 and LAC culture supernatants during growth in vitro.

  mw2 mice neutrophils 2-dimensional infection confocal

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 95

  A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data

  clinical hela tumor rutkowski bulk dual negative

• Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

  PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

  n×m common independent viral blood gene random

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page

• Novel dengue virus type 1 from travelers to Yap State, Micronesia.

  PMID 16494770 · PMC3373118 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

  Full-text index only

  DENV-1 responsible for the 2004 Yap State dengue outbreak was isolated from serum of 4 Japanese travelers returning from Yap

  mosquito viral denv-1 full-length virus complete sequence

• Application of ProteinChip array profiling in serum biomarker discovery for patients suffering from severe acute respiratory syndrome.

  PMID 18220240 · PMC7120874 · Methods in molecular biology (Clifton, N.J.) · 2007 · 8 claims · 5 setups

  Full-text index only

  SELDI-TOF-MS ProteinChip array profiling of serum can identify differentially expressed protein biomarkers in SARS-CoV infected patients versus controls.

  serum sars seldi-tof-ms ion serial