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).

• Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.

  PMID 17439964 · PMC1888819 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Bisulfite treatment causes DNA strand breakage (via abasic site formation and beta-elimination) in addition to cytosine deamination.

  genomic synthetic bisulfite-treated cloned methylation-sensitive quantitative gel

• High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

  PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups

  Has reproduction · 69

  NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.

  mycobacterium tuberculosis chip-seq input strand-specific

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• A computational study of off-target effects of RNA interference.

  PMID 15800213 · PMC1072799 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The chance of RNAi off-target effects is considerable, ranging from 5% to 80% depending on organism and parameters, when using exact sequence identity between siRNA and transcripts.

  schizosaccharomyces caenorhabditis homo pombe off-target mismatch-tolerant rational

• RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

  PMID 17076887 · PMC1634876 · BMC bioinformatics · 2006 · 7 claims · 4 setups

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  RiboSubstrates is a web-based Perl application that scans a cDNA database for all potential substrates of a given ribozyme, including perfect matches, Wobble base-pair matches, and mismatch-containing matches.

  homo hcv substrate ribozyme

• Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

  PMID 17697348 · PMC2042502 · BMC genetics · 2007 · 8 claims · 5 setups

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  CTCE eliminates the need for laboratory optimization of separation conditions for each exonic target sequence.

  pcr-amplified target exonic cycling ctce

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• A genome annotation-driven approach to cloning the human ORFeome.

  PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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  Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

  chromosome pooled t-tailed naga comparative rt-pcr sanger

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

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  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• Bacteriophage Mu integration in yeast and mammalian genomes.

  PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes

  cerevisiae ab2.2 hela fes29 electroporation southern transposition

• Enrichment of sequencing targets from the human genome by solution hybridization.

  PMID 19835619 · PMC2784331 · Genome biology · 2009 · 8 claims · 5 setups

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  Solution hybridization with 120-mer capture probes efficiently enriches targeted genomic sequences for next-generation sequencing

  genome genomic same technical capture solution-hybridization sequence

• Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

  PMID 15842735 · PMC1087844 · BMC medical genetics · 2005 · 7 claims · 3 setups

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  MLPA was cheaper, more accurate and more precise than Real-Time PCR for detecting LDL receptor gene deletions

  genomic real-time multiplex long-range

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

  PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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  PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

  hpv clinical biotinylated pcr mip molecular microarray

• Genomics research and malaria control: great expectations.

  PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups

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  Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.

  plasmodium anopheles malaria whole-genome computational microarray

• Identification of transformation-related pathways in a breast epithelial cell model using a ribonomics approach.

  PMID 18829526 · PMC2692251 · Cancer research · 2008 · 7 claims · 6 setups

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  Global association of HuR and AUF1 with target mRNAs changes substantially and largely reciprocally between MCT-1-transformed and nontransformed MCF10A cells

  mcf10a xenograft rip-chip real-time western