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).

• Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

  PMID 35714765 · PMC9283944 · The Journal of biological chemistry · 2022 · 8 claims · 4 setups

  Has reproduction · 80

  Genome-wide Ψ mapping using HydraPsiSeq and small RNA Ψ-seq identifies Ψ sites on snoRNA, 7SL RNA, vtRNA, SL RNA, and tRNA in T. brucei

  brucei hydrapsiseq small primer

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• Non-linear mapping for exploratory data analysis in functional genomics.

  PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.

  leukaemia small srbct brain relaxation self-organising sammon's

• sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

  PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 3 setups

  Has reproduction

  sRNAtoolbox 2019 adds all major small RNA library preparation protocols (including UMI-based) to sRNAbench with automatic protocol-specific preprocessing.

  biological srp046046 ensembl small consensus genome

• Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data.

  PMID 28045932 · PMC5207757 · PloS one · 2017 · 7 claims · 5 setups

  Has reproduction · 78

  Metavisitor is an open-source suite of modular Galaxy tools and preset workflows enabling non-experts to detect and assemble viral genomes from deep sequence data.

  drosophila deep srp013822 small novo long-read

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

  camellia sinensis small genome mirna

• Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

  PMID 18588689 · PMC2474586 · BMC medical genetics · 2008 · 8 claims · 6 setups

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  A region spanning the gene RAI and the 5' portion of XPD is associated with postmenopausal breast cancer

  peripheral genomic genotype independent linkage targeted genotyping

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

  PMID 17436019 · PMC1914248 · Human genetics · 2007 · 7 claims · 8 setups

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  A homozygous 63.1-kb intragenic deletion in LARGE (exons 9-10) causes Walker-Warburg syndrome in a consanguineous Saudi family

  genomic family skeletal blood microsatellite direct multiplex

• Candidate target genes for loss of heterozygosity on human chromosome 17q21.

  PMID 15187990 · PMC2409524 · British journal of cancer · 2004 · 8 claims · 5 setups

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  JUP (plakoglobin) is the only identified gene physically located between the D17S746 and D17S846 markers that define the smallest common region of LOH on chromosome 17q21

  genomic normal breast p1-phage nucleotide rt-pcr cold

• The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

  PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups

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  fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality

  non-coding frnadb-hosted genomic mammalian sequence genome blastn

• miRGen 2.0: a database of microRNA genomic information and regulation.

  PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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  miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

  lung organ malme embryonic polii small nucleosome

• Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.

  PMID 34795257 · PMC8602323 · Nature communications · 2021 · 8 claims · 12 setups

  Has reproduction · 67

  PYK2 was identified as a putative IRF5 kinase via a kinase inhibitor library screen in macrophages

  raw264.7 hektlr4 hoxb8-derived colon kinase co-immunoprecipitation co-ip

• Mutation survey of known LCA genes and loci in the Saudi Arabian population.

  PMID 18936139 · PMC2695987 · Investigative ophthalmology & visual science · 2009 · 7 claims · 4 setups

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  Mutations in the 13 known LCA genes were identified in only 24% (9/37) of Saudi Arabian LCA families, far lower than the ~65% mutation detection rate reported in European populations

  leukocyte affected kkesh-060 direct str homozygosity

• Telomere-to-telomere assembly of a complete human X chromosome.

  PMID 32663838 · PMC7484160 · Nature · 2020 · 8 claims · 8 setups

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  Produced the first gapless, telomere-to-telomere assembly of a human chromosome (the X chromosome) using the CHM13 cell line

  chm13htert chm13 ultra-long-read pacbio linked-read

• Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

  PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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  A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

  cdna image hbs1l ahi1 rt-pcr est northern

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

  PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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  Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

  yoruba selected subset whole-genome targeted pcr

• 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

• snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

  PMID 16990247 · PMC1636440 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  snoSeeker (comprising CDseeker and ACAseeker) is a computational package that can screen for both guide and orphan snoRNA genes, unlike prior programs limited to guide snoRNAs

  whole-genome genome computational gene northern