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).

• A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation.

  PMID 36149401 · PMC9576273 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  A C-terminal patch of the LRRK2 Armadillo domain (residues ~350–550, 'site #1') binds non-phosphorylated Rab29, Rab8A, and Rab10 with low-micromolar affinity

  recombinant lrrk2 hela hek293t microscale confocal immunoblotting

• 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

• Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

  PMID 16620374 · PMC1464127 · BMC genomics · 2006 · 8 claims · 6 setups

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  Syndecan-encoding sequences are present in Cnidaria and throughout the Bilateria, showing deep conservation of the family.

  invertebrate syndecan full-length chicken wu-blastp clustalw tcoffee

• 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

• 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

• 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

• The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

  PMID 17932789 · PMC2140095 · Journal of structural and functional genomics · 2007 · 8 claims · 6 setups

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  A family-based target selection approach (rather than genome-wide or fold-novelty based selection) maximizes cross-member methodological transfer and biological insight

  recombinant target coli x-ray differential analytical

• 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

• Structural proteomics of the SARS coronavirus: a model response to emerging infectious diseases.

  PMID 17680348 · PMC7088133 · Journal of structural and functional genomics · 2007 · 8 claims · 8 setups

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  Structures of 16 SARS-CoV proteins or functional domains have been determined, and 8 of these have novel folds

  sars-cov x-ray gst emsa

• 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

• Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

  PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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  The human genome encodes at least 71 kelch-repeat proteins

  genome yeast kelch-repeat full-length blast blastp cross-referencing

• Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

  PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

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  Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

  brain cos-7 hek-293 clathrin subcellular western ccv

• Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

  PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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  The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

  chimpanzee retrofitted primate aspm tar restriction genomic

• Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

  PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

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  An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

  anopheles gambiae reanocds05 initio full-length rt-pcr

• The genome of the simian and human malaria parasite Plasmodium knowlesi.

  PMID 18843368 · PMC2656934 · Nature · 2008 · 8 claims · 7 setups

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  The P. knowlesi (H strain) nuclear genome was sequenced and assembled: 23.5 Mb across 14 chromosomes with 5,188 predicted protein-encoding genes.

  knowlesi predicted type whole-genome comparative pfam

• Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin.

  PMID 16122393 · PMC1215486 · BMC neuroscience · 2005 · 8 claims · 8 setups

  Has reproduction

  Plexin B3 strongly and plexin B2 moderately stimulate neurite outgrowth of primary murine cerebellar neurons

  cos-7 cerebellar nih-3t3 yeast northern western situ

• auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

  PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups

  Has reproduction · 50

  auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)

  fish genomic auts2 tissues comparative tblastn phylogenetic

• NovelFam3000--uncharacterized human protein domains conserved across model organisms.

  PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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  NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

  lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining

• SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

  PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

  bombyx whole-genome snp novo

• Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

  PMID 15757514 · PMC1084347 · BMC microbiology · 2005 · 8 claims · 7 setups

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  PSI-BLAST identified several novel homologies between LEE-encoded and Ysc-Yop-associated proteins

  lee-encoded escc sepq escd psi-blast blastp domain