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).

• Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

  PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

  longissimus muscle snps pig h3k27ac strand-specific starr-seq

• 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

• Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

  PMID 18832376 · PMC2577333 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  A novel enhancer trap method retrofitting BACs with Tn10-based transposons enables nontargeted, functional mapping of noncontiguous cis-regulatory elements as zebrafish transgenes.

  zebrafish bac genomic transgenic field bac

• 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

• Rats go genomic.

  PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

  Full-text index only

  A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

  recombinant genes serotonin adenomatous genome-wide targeted knockout

• 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

  Full-text index only

  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

• 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.

  PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups

  Has reproduction · 78

  A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.

  interrogans canine syrian smrt bulk rt-qpcr

• Helicobacter pylori: after the genomes, back to biology.

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

  Full-text index only

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

  helicobacter diffuse signature-tagged genome yeast

• The malaria secretome: from algorithms to essential function in blood stage infection.

  PMID 18551176 · PMC2408878 · PLoS pathogens · 2008 · 8 claims · 5 setups

  Full-text index only

  An expanded secretome (van Ooij secretome) built from a revised SignalP MaxS cutoff (0.571) plus HMMER-expanded HT-motif search yields 422 proteins (224 excluding RIFIN/STEVOR families).

  falciparum berghei plasmodium signal comparative piggybac

• 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

  Full-text index only

  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

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

  Full-text index only

  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic

• An "omics" approach to uropathogenic Escherichia coli vaccinology.

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

  Full-text index only

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

  upec vaccination comparative two-dimensional

• Mice and more.

  PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

  Full-text index only

  A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

  cftr ciona embryonic chromosome comparative genome bac-based