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).
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Evolutionary cores of domain co-occurrence networks.
PMID 15788102 · PMC1079808 · BMC evolutionary biology · 2005 · 8 claims · 4 setups
The innermost (globally central) cores of protein domain co-occurrence networks gradually grow in size with increasing evolutionary/developmental complexity of the organism.
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Protein function assignment through mining cross-species protein-protein interactions.
PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups
CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens
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What makes species unique? The contribution of proteins with obscure features.
PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups
POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome
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pTARGET: a web server for predicting protein subcellular localization.
PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups
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)
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Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint.
PMID 17349043 · PMC1829165 · BMC bioinformatics · 2007 · 8 claims · 6 setups
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.
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Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.
PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups
HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.
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The protein-phosphatome of the human malaria parasite Plasmodium falciparum.
PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups
P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.
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Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?
PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups
3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species
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InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups
InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.
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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
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
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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
The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.
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A comparison of programmed cell death between species.
PMID 11178240 · PMC138857 · Genome biology · 2000 · 8 claims · 8 setups
The core apoptotic pathway (CED-3/caspases, CED-4/Apaf-1, CED-9/Bcl-2, EGL-1) is conserved across C. elegans, Drosophila, and mammals.
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SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.
PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups
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.
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Filtering high-throughput protein-protein interaction data using a combination of genomic features.
PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups
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.
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An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups
The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions