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).

• Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

  PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

  gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic

• 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

• The application of genomic technology to combat parasitic disease.

  PMID 16454893 · PMC1914215 · Parasitology · 2004 · 8 claims · 8 setups

  Full-text index only

  Genomic resources from mammalian hosts can be exploited to understand parasitic processes from the host's standpoint, illustrated by host cell penetration by Trypanosoma cruzi.

  trypanosoma toxoplasma parasite eimeria host proteomics comparative

• In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

  PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 6 setups

  Has reproduction · 89

  SARS-CoV-2 infection induces a strong interferon-mediated antiviral response in the nasopharynx, up-regulating antiviral factors (OAS1-3, IFIT1-3, MX2, RSAD2, HERC5) and Th1 chemokines CXCL9/10/11, while down-regulating ribosomal protein transcripts.

  nasopharyngeal airway patient-matched swab shotgun bulk rt-pcr

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 7 setups

  Has reproduction · 80

  After long-term ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin locations, most prominently centromeric satellite/micro-satellite DNA.

  pbmc single cd4 flip-seq mip-seq prip-seq

• 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

• Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

  PMID 37243151 · PMC10224212 · Viruses · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  An exhaustive-search workflow can recover intra-host co-existing SARS-CoV-2 strains from the reference-genome read set (SRR11092062) that de Bruijn-graph assemblers discard.

  sars-cov-2 spike predicted california short-read read sequence

• Cellular proteins in influenza virus particles.

  PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

  Full-text index only

  Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

  influenza deglycosylated sucrose lc-ms mudpit electron

• A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

  PMID 37247570 · PMC10878300 · Ticks and tick-borne diseases · 2023 · 7 claims · 3 setups

  Full-text index only

  The MPAS pipeline is a portable, reproducible Nextflow-based bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay.

  host-seeking mpas same targeted mpas clc

• 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

• Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

  PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 50

  BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

  bovine direct amplified synthetic

• Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

  PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

  Has reproduction · 95

  Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

  solar saltern combined individual metagenomic taxonomic functional

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

  Full-text index only

  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Use of functional genomics to understand influenza-host interactions.

  PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

  Full-text index only

  Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

  hela a549 lung texas cdna microarray infection

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

  PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode

  generic simulated hiv-1 stochastic dynamic regression

• Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.

  PMID 33777521 · PMC7977378 · PeerJ · 2021 · 8 claims · 1 setups

  Has reproduction · 95

  nf-core/eager is a complete redesign and extension of the EAGER pipeline in Nextflow, built within the nf-core framework to ensure high-quality, sustainable software development.

  skeletal whole-genome

• Single-cell transcriptional dynamics of flavivirus infection.

  PMID 29451494 · PMC5826272 · eLife · 2018 · 8 claims · 6 setups

  Has reproduction · 90

  viscRNA-Seq simultaneously quantifies whole single-cell host transcriptome and intracellular viral RNA from the same cell, including non-polyadenylated viruses via a virus-specific oligo

  hepatoma single huh7 denv-infected single-cell qpcr loss-of-function

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD constitutes a distinct taxonomic entity within S. dysgalactiae, with a mean intra-subspecies average nucleotide identity of 99%.

  dysgalactiae sdse sdsd isolates genome multilocus pangenome

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome