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).

Publications 1.3k Datasets 392.5k Experiments 9

System / cell line: pathway ✕ Assay: host ✕ Clear

Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

PMID 41797265 · PMC12968515 · Molecular ecology · 2026 · 7 claims · 6 setups

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Adult female exposure to host plants for egg-laying is associated with differential expression of ecdysteroid and juvenile-hormone pathway genes, consistent with endocrine regulation of reproductive readiness and the oogenesis–flight syndrome

vanessa bulk gene kegg
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

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

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
Systems biology and the host response to viral infection.

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

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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
Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.

PMID 41987828 · PMC13077298 · ISME communications · 2026 · 8 claims · 5 setups

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Transplantation of a microbiome from heat-primed donor clams into non-acclimated recipients is sufficient to enhance host resilience during a subsequent simulated heatwave.

ruditapes philippinarum 16s host enzymatic
TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups

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TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement

gut same uniquely metagenome quality assembly-free
Protozoan genomics for drug discovery.

PMID 16151400 · PMC7096809 · Nature biotechnology · 2005 · 8 claims · 3 setups

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Complete genome sequences of five protozoan parasites (Theileria parva, T. annulata, Leishmania major, Trypanosoma brucei, T. cruzi) were reported, enabling comparative genomics.

theileria leishmania plasmodium whole-genome comparative
Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

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

Has reproduction · 78

INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types

testis young testicular invade-seq histology sperm
Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

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The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis
Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

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Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

trp53-null complete t12 cell-deficient imaging survival tumor

Experiments

Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

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

Systems biology and the host response to viral infection.

Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.

TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

Protozoan genomics for drug discovery.

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

Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.