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 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

• Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

  PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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  A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

  hamster testis predicted cdna northern comparative

• Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

  PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

  full-length deduced alternative panel cdna-to-genome manual motif

• Visualizing the genome: techniques for presenting human genome data and annotations.

  PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

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  Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

  flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation

• Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

  PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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  The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

  ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence

• Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

  PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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  Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

  ptk2 t84 escherichia computational expression immunofluorescence immunoblotting

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

  PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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  Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

  tissues genome full-length genes full-length genome orf

• Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

  PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

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  DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

  nsclc matched lung quantitative pcr genomic

• Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

  PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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  A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

  genomes longin plant phytolongin iterative phylogenetic genomic

• The VIZIER project: preparedness against pathogenic RNA viruses.

  PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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  Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

  viruses virus coli soluble large-scale bioinformatic recombinant

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

  PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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  PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

  pax6 brain yeast sequence yeast semi-quantitative

• ECgene: genome annotation for alternative splicing.

  PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

  brca2 rgs17 organs cdna genomic genome transcript

• IMGT, the international ImMunoGeneTics information system.

  PMID 15608269 · PMC540019 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  IMGT is a high-quality integrated knowledge resource for immunoglobulins (IG), T cell receptors (TR), MHC, and related proteins of the immune system (RPI) across vertebrate species

  igh mhc pairs automated junction structure

• Mining the draft human genome.

  PMID 11236999 · PMC2658632 · Nature · 2001 · 8 claims · 7 setups

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  Protein-coding exons account for only about 3% of the human genome DNA, with repeat sequences making up around 46%.

  genome unfinished drosophila tetraodon psi-blast domain sequence

• Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

  PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

  genome full-length ~3x10^7 isoform whole-genome full-length polysome

• Evolutionarily conserved human targets of adenosine to inosine RNA editing.

  PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

  panel brain chicken flna comparative rt-pcr homology

• Mutations in PIK3CA are infrequent in neuroblastoma.

  PMID 16822308 · PMC1533846 · BMC cancer · 2006 · 8 claims · 6 setups

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  PIK3CA activating mutations are infrequent in human neuroblastoma (2.9%, 2/69 tumors)

  neuroblastoma neuroblastoma-derived patients th-mycn targeted sanger rt-pcr

• Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

  PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

  redundant mammalian genomic vertebrates blast pattern-hit tblastn