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 29

System / cell line: infection ✕ Assay: comparative ✕ Clear

Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups

Has reproduction · 95

The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.

catharanthus pacbio smrt pot experimental endpoint smrt
Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

proteins cdc candidate yersinia all-against-all computational cross-species
A genomics-based approach to biodefence preparedness.

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

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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
Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

PMID 17953491 · PMC2039766 · PLoS genetics · 2007 · 8 claims · 5 setups

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CNVs are not easily tagged by SNPs and often fall in genomic regions poorly covered by whole-genome SNP arrays or not genotyped by HapMap, so current GWASs have largely missed their contribution to complex disorders.

genome-wide genome cohorts array-based snp bac
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

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A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

p53 tumor tumors computational retroviral linker-mediated flow
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

PMID 18482458 · PMC2408589 · BMC microbiology · 2008 · 8 claims · 6 setups

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CGS combined with targeted DDT sequencing and whole genome fingerprinting (WGF) can accurately determine a treponemal genome sequence using only three arrays, at accuracy comparable to or better than finished DDT sequencing

treponema pcr-amplified ss14 pcr comparative dideoxy-terminator genome
Toxoplasma: the next 100years.

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

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

gondii mammalian cdna affymetrix sage
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
Managing incidental findings in human subjects research: analysis and recommendations.

PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

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Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.

affected large research consent linkage genomic structural
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
Using DNA microarrays to study host-microbe interactions.

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

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

streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene
Helicobacter pylori: after the genomes, back to biology.

PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups

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STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization

helicobacter diffuse signature-tagged genome yeast
Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

liver genomic hcv-infected agilent two-color semi-quantitative real-time
An "omics" approach to uropathogenic Escherichia coli vaccinology.

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

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

upec vaccination comparative two-dimensional
Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

Has reproduction · 80

AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

b.g parental nicotiana benthamiana qtl comparative rna-sequencing
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

monocytogenes additional food j774 whole-genome comparative pcr
Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups

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Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence

albicans hep-2 rhe blood phenotypic growth adhesion
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

macrophage hela vaccinia bacillus gene protein-protein comparative
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

Has reproduction

The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

gp41 hiv-1 recombination site-specific comparative

Experiments

Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

A genomics-based approach to biodefence preparedness.

Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.

Toxoplasma: the next 100years.

Systems biology and the host response to viral infection.

Managing incidental findings in human subjects research: analysis and recommendations.

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

Using DNA microarrays to study host-microbe interactions.

Helicobacter pylori: after the genomes, back to biology.

Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

An "omics" approach to uropathogenic Escherichia coli vaccinology.

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.