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 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

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

  PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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  Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

  organisms cide cideb hmmer tblastn sequence

• 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

• In Silico screening for functional candidates amongst hypothetical proteins.

  PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins

  hypothetical targetp-selected mitochondria-predicted subcellular domain database

• Protein function assignment through mining cross-species protein-protein interactions.

  PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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  CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

  sapiens cross-species majority simple

• Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

  PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

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  Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

  proteomes predicted long prokaryotic coiled-coil all-against-all sequence

• Phylogenetic analysis of RhoGAP domain-containing proteins.

  PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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  RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

  rhogap aligned bayesian domain sequence maximum bayesian

• 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

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• 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

• Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

  PMID 19888473 · PMC2768585 · PLoS computational biology · 2009 · 8 claims · 5 setups

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  Translocation-related human proteins are significantly enriched in intrinsic structural disorder compared to all human proteins

  translocation-related translocation cyclin-dependent intrinsic pfam randomized

• 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

• 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

• 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

• Protein length in eukaryotic and prokaryotic proteomes.

  PMID 15951512 · PMC1150220 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  Eukaryotic proteins are significantly longer than prokaryotic proteins across virtually all functional categories and the majority of protein families

  eukaryotic proteins genomic cog comparative orthology domain

• Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.

  PMID 19709643 · PMC3159575 · Journal of proteomics · 2009 · 7 claims · 5 setups

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  Methanol-based solubilization, alone or combined with PPS, yields significantly higher membrane protein identification/enrichment than PPS alone in monocyte membrane proteomics

  bacteriorhodopsin crude immuno-affinity lc-ms sds-page shotgun facs

• Proteomic-based identification of maternal proteins in mature mouse oocytes.

  PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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  625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

  mature mii identified tissues sds-page acid gene

• The UCSC Proteome Browser.

  PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

  swiss-prot sequence domain isoelectric

• Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

  PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 8 setups

  Has reproduction · 58

  102 GLPs were identified in B. juncea, 51 in B. nigra, and 48 in B. rapa via genome-wide in-silico analysis

  juncea bjuglps bjuglp glp genome-wide phylogenetic motif