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).

• 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

• VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.

  PMID 37180100 · PMC10172660 · Frontiers in immunology · 2023 · 7 claims · 7 setups

  Has reproduction · 64

  VIGET is a web portal that lets users select vaccines/ImmPort studies, run differential gene expression analysis, and perform Reactome-based pathway enrichment and functional interaction network construction

  blood lists differentially individual differential pathway functional

• TB database: an integrated platform for tuberculosis research.

  PMID 18835847 · PMC2686437 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  TBDB is an integrated database providing access to TB genomic data and resources relevant to discovery/development of TB drugs, vaccines and biomarkers.

  tuberculosis streptomyces tb-infected whole-genome sequence trna

• targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

  PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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  A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

  tuberculosis mtb protein-protein flux transposon

• The past and future of tuberculosis research.

  PMID 19855821 · PMC2745564 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Integrating systems biology with epidemiology ('systems epidemiology') will be required to better predict TB's trajectory and eliminate the disease

  clinical mycobacterium mtbc patients fingerprinting whole-genome microarray

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

  PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups

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  wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables

  serum colon glioblastoma synthetic seldi-tof gene computational

• The future is genome-wide.

  PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups

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  Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level

  schizophrenia myocardial individuals infectious genetic candidate gene

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

  PMID 16614446 · PMC1435984 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  A core termination signal of 4 nt (stop codon plus the following nucleotide) is preferred across most prokaryotic and eukaryotic genomes

  orf coli rabbit cos-7 bioinformatic codon prokaryotic

• A European focus on proteomics.

  PMID 15128441 · PMC416463 · Genome biology · 2004 · 8 claims · 8 setups

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  MALDI-MS and ESI-MS are complementary techniques that identify overlapping but distinct subsets of proteins

  ribosomal breast ovarian prostate maldi-ms laser-capture fticr-ms

• The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

  PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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  Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

  neisseria streptococcus coli vibrio reverse pan-genomic comparative