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).

Publications 1.3k Datasets 392.5k Experiments 21

System / cell line: peptides ✕ Assay: prediction ✕ Clear

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

peptides peptide sax-spe ip-rp-hplc cross-run
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
Towards alignment independent quantitative assessment of homology detection.

PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

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The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

curated homologene swiss-prot fruit signalp homologene-based fhom
EpiToolKit--a web server for computational immunomics.

PMID 18440979 · PMC2447732 · Nucleic acids research · 2008 · 7 claims · 3 setups

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EpiToolKit is a web server integrating five MHC class I and two MHC class II epitope prediction methods in a unified, user-friendly interface.

randomly novel minor mhc polymorphic
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
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
Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets.

PMID 18925947 · PMC2600787 · BMC structural biology · 2008 · 8 claims · 3 setups

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The extended matrix PP10 (built from a proline-containing peptide library) shows significant improvement in binding prediction over the original nine-residue matrix P9

recombinant peptides awcsdealplgsprcd peptide-mhc quantitative x-ray
Aggregation propensity of the human proteome.

PMID 18927604 · PMC2557143 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Long proteins have, on average, less intense/pronounced aggregation peaks than short proteins

proteome non-membrane proteins membrane sequence-based correlation statistical
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

tuberculosis sanger spectra lc-ms sds-page signal
Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

Has reproduction · 93

Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

huvecs huvec long-read bottom-up offline
In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

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This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

vastus skeletal spectra identified phosphopeptide in-solution strong
Somatic mutations in mitochondria: the chicken or the egg?

PMID 16207343 · PMC1257449 · Arthritis research & therapy · 2005 · 6 claims · 6 setups

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Patients with RA have a higher incidence of somatic mtDNA mutations (in MT-ND1 transcripts) in synoviocytes and synovial tissue compared with OA patients

mutated synovial sequencing mhc expression
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
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

Has reproduction · 76

The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

pyronema confluens fungal whole-genome k-mer rna-seq
Evidence for a novel gene associated with human influenza A viruses.

PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

influenza pre-1950 avian neg8 comparative neighbour-joining fixed
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
Exploring the immunome: A brave new world for human vaccine development.

PMID 20009527 · PMC2919815 · Human vaccines · 2009 · 7 claims · 7 setups

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Screening the Mtb proteome in silico for epitopes ('fishing for antigens using epitopes as bait') revealed a remarkable diversity of human immune responses to Mtb proteins without an ascribed function, suggesting human immune response to Mtb is omnivorous rather than focused on single immunodominant proteins.

mycobacterium subjects francisella autologous epitope-mapping response epitope
Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

hiv-1 polyclonally shannon cross-clade ctl
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

Experiments

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

Towards alignment independent quantitative assessment of homology detection.

EpiToolKit--a web server for computational immunomics.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

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

Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets.

Aggregation propensity of the human proteome.

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

Somatic mutations in mitochondria: the chicken or the egg?

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

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

Evidence for a novel gene associated with human influenza A viruses.

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

Exploring the immunome: A brave new world for human vaccine development.

Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

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