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).

• 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

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing

• A unique, consistent identifier for alternatively spliced transcript variants.

  PMID 19865484 · PMC2765725 · PloS one · 2009 · 6 claims · 1 setups

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  Existing transcript identifiers (NM_ accessions, ENST identifiers) are unsuitable for uniquely identifying isoform structure across databases, methods, or organisms

  genes cross-database

• GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

  PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

  transcriptome genome spliced transcripts est genomic splice-orientation

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

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  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• BIPASS: BioInformatics Pipeline Alternative Splicing Services.

  PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

  transcript aligned pre-computed user-submitted sequence alternative database

• Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

  PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

  Has reproduction · 93

  Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

  huvecs huvec long-read bottom-up offline

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Integrating alternative splicing detection into gene prediction.

  PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

  arabidopsis araset thaliana transcript-to-genome initio comparative

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature

• NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

  PMID 15608248 · PMC539979 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  RefSeq provides a curated, non-redundant, explicitly linked collection of genomic, transcript and protein sequences spanning prokaryotes, eukaryotes and viruses.

  refseq honey sequence computational conserved

• Database resources of the National Center for Biotechnology Information.

  PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

  genbank genomic eukaryotic completely sequence rapid est

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

  PMID 29783948 · PMC5963079 · BMC genomics · 2018 · 8 claims · 8 setups

  Has reproduction · 85

  Whole transcriptome sequencing with extensive TSS mapping identified 3078 transcription start sites and 629 ncRNAs in V. cholerae N16961

  cholerae lexa identified directional end rt-pcr

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

  PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

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  A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

  breast carcinogenesis-related nssnp-containing african gene snp functional

• X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

  PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

  ensembl breast mcf7 25-mer probe-to-transcript microarray

• The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

  PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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  Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

  strongylocentrotus sprej purpuratus full-length cdna secondary real-time

• Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

  PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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  GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

  genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic