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).

• Protein microarray technology.

  PMID 17126887 · PMC1828913 · Mechanisms of ageing and development · 2007 · 8 claims · 8 setups

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  Protein microarrays enable high-throughput characterization of protein biochemical activities across an entire proteome in a single experiment

  yeast sh2 protein-protein protein-dna chromatin

• Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

  PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

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  Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

  cmt2c affected spinal drg genetic sanger quantitative

• Interaction profile-based protein classification of death domain.

  PMID 15189571 · PMC459208 · BMC bioinformatics · 2004 · 7 claims · 6 setups

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  An SVM-based classifier using Residue Pair Interaction Profiles (RPIPs) can classify death domain superfamily members into subfamilies with 89% average cross-validation accuracy

  homology-modeled death homology putative rigid-body homology model

• 'Genome design' model and multicellular complexity: golden middle.

  PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

  normal genes proteins encoded oligonucleotide gene functional

• Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

  PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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  Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

  cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval

• What makes species unique? The contribution of proteins with obscure features.

  PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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  POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

  eukaryotic animal cerevisiae homo hmmpfam blast tblastn

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular

• 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

• Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

  PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

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  Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

  pdb obligatory same psi-blast solvent residue

• InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

  PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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  InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

  saccharomyces homo bank computational yeast tandem

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Protein co-evolution, co-adaptation and interactions.

  PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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  The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

  nuoe intra-protein coli interacting phylogenetic correlated domain-restricted

• Advances in the study of SR protein family.

  PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

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  SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

  nuclear bovine drosophila caenorhabditis selex rna-binding splicing

• 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

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

  PMID 39256359 · PMC11387733 · Nature communications · 2024 · 8 claims · 7 setups

  Has reproduction · 87

  Heterozygous missense or loss-of-function variants in LRRC7 cause a dominant neurodevelopmental disorder in 33 identified individuals

  genomes genematcher affected 293t genetic exome phenotype