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).

• 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

• A survey of integral alpha-helical membrane proteins.

  PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

  pfam-a organisms 34-genome integral transmembrane comparative sequence

• SysZNF: the C2H2 zinc finger gene database.

  PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links

  user-defined hmm domain all-to-all

• pTARGET: a web server for predicting protein subcellular localization.

  PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups

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  pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)

  eukaryotic complete pfam amino subcellular

• Bioinformatic mapping of AlkB homology domains in viruses.

  PMID 15627404 · PMC544882 · BMC genomics · 2005 · 8 claims · 8 setups

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  AlkB-like domains are found in at least 22 different single-stranded RNA positive-strand plant viruses, mainly within a subgroup of the Flexiviridae family.

  ncbi 146-sequence representative hel psi-blast pfam profile

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

  PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

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  mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

  nonredundant database high-throughput homology

• SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

  PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

  elegans expressed soluble crystallized recombinant solubility purification

• Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.

  PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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  A combined target-selection approach — pursuing both structurally uncharacterised domain families and additional targets from large structurally characterised superfamilies — is essential for comprehensive structural coverage of the genomes.

  sp-trembl hmm-based domain computational

• Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

  PMID 11532213 · PMC55326 · Genome biology · 2001 · 7 claims · 5 setups

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  The human genome contains fewer than 50 functional nuclear receptors, far fewer than C. elegans and about twice as many as Drosophila

  genome elegans genomic panel tblastn hmmer pcr

• Analysis of the glutathione S-transferase (GST) gene family.

  PMID 15607001 · PMC3500200 · Human genomics · 2004 · 8 claims · 4 setups

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  The complete human GST gene family comprises 16 genes in six subfamilies: alpha (GSTA), mu (GSTM), omega (GSTO), pi (GSTP), theta (GSTT) and zeta (GSTZ).

  genome gst gst-related gstk1 gene sequence phylogenetic

• 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

• MEROPS: the peptidase database.

  PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

  archaean holotype c-x-c proteins comparative domain substrate

• The Vertebrate Genome Annotation (Vega) database.

  PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.

  chromosomes genomic manual sequence initio

• The EH1 motif in metazoan transcription factors.

  PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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  There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

  homeobox-containing forkhead-containing complete combined meme hmm logistic

• WebGestalt: an integrated system for exploring gene sets in various biological contexts.

  PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

  genes gene est-based enrichment kegg

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• CanPredict: a computational tool for predicting cancer-associated missense mutations.

  PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

  missense observed sjoblom refseq cross-validation recurrence comparative

• Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

  PMID 16022726 · PMC1187884 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  466 Tetraodon GPCRs (Tnig-GPCRs) were identified genome-wide, of which 457 had not been previously reported

  tetraodon tnig-gpcr non-rhodopsin-like domain sequence transmembrane

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic