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).

• 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

• PubMatrix: a tool for multiplex literature mining.

  PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups

  Full-text index only

  PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts

  pubmed ovarian genome literature cdna

• Asthma investigators begin to reap the fruits of genomics.

  PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

  Full-text index only

  Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

  monkey models lung inbred cdna oligonucleotide northern

• MatchMiner: a tool for batch navigation among gene and gene product identifiers.

  PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

  Full-text index only

  MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

  nci-60 fish-mapped random batch fish-mapped cross-validation

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.

  PMID 19806175 · PMC2736377 · PLoS pathogens · 2009 · 8 claims · 6 setups

  Full-text index only

  Genome sequencing of three M. ulcerans strains (NM20/02, NM31/04, Jp8756) identified thousands of SNPs relative to reference strain Agy99

  ulcerans collection snp whole-genome comparative read

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

  PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

  Full-text index only

  Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

  lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl

• BOAT: Basic Oligonucleotide Alignment Tool.

  PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

  Full-text index only

  BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

  same short-read snp

• A chromosome-level genome assembly of Plantago ovata.

  PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 99

  A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.

  plantago ovata pacbio hi-c k-mer

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

• Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

  PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

  Full-text index only

  Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

  genome gene omim known naïve linkage disease-centric

• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

  PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

  Full-text index only

  BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

  reads yoruban cytogenetically predicted simulated paired-end whole-genome

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

  Full-text index only

  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• Mutations in the UBIAD1 gene, encoding a potential prenyltransferase, are causal for Schnyder crystalline corneal dystrophy.

  PMID 17668063 · PMC1925147 · PloS one · 2007 · 8 claims · 7 setups

  Full-text index only

  Mutations in UBIAD1 are causal for Schnyder crystalline corneal dystrophy

  pedigrees pedigree genomic ubiad1 microsatellite fine direct

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

  PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

  Full-text index only

  MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

  genomic lr-pcr uhts v-4 long-range ultra sanger

• Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

  PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

  gossypium transcripts uq-normalized differentially comparative coding bulk

• The vertebrate genome annotation (Vega) database.

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

  Full-text index only

  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