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 102

System / cell line: acid ✕ Assay: identification ✕ Clear

Mass spectrometry group has mass appeal.

PMID 15598607 · PMC1247668 · Environmental health perspectives · 2004 · 7 claims · 4 setups

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Mass spectrometry can identify proteins and their post-translational modifications with high specificity and sensitivity, making it central to toxicoproteomics.

sf9 experimental general mass proteomics combined
Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag
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
A surrogate-based approach for post-genomic partner identification.

PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

biotinylated tnf-β analysis secondary phage sequence secondary
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

acid-extracted hela online offline
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

tuberculosis mtb protein-protein flux transposon
An accurate method for identifying recent recombinants from unaligned sequences.

PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups

Has reproduction · 84

A novel algorithm combining the JHMM (Zilversmit et al. 2013) mosaic representation with a distance-based triple comparison can identify recombinant sequences and their parents from unaligned, gene-length sequences without a reference panel.

simulated dblα coalescent comparative recombinant
Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

mitoproteome orthologous liver mitochondrial sequence-based computational literature
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
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups

Has reproduction · 87

mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.

c57bl strand-specific pol computational
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
Genomic signatures of human versus avian influenza A viruses.

PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

throat clinical 401-genome avian rt-pcr immunofluorescent sequence
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

pooled genome est novel tandem whole-genome est
Proteomics in animal models of Alzheimer's and Parkinson's diseases.

PMID 18703168 · PMC2630427 · Ageing research reviews · 2009 · 8 claims · 6 setups

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Proteomics studies in APPSw transgenic mice reveal differential expression of proteins involved in metabolism, ubiquitin/proteasome system, cellular transport, synaptic/axonal integrity, and inflammation

app swedish p301l gskβ page proteomics redox
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

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TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

pakistani affected retina tissues linkage sanger race

Experiments

Mass spectrometry group has mass appeal.

Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

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

A surrogate-based approach for post-genomic partner identification.

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

Oligomeric protein structure networks: insights into protein-protein interactions.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

Genetic diversity among five T4-like bacteriophages.

targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

An accurate method for identifying recent recombinants from unaligned sequences.

Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

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

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

Genomic signatures of human versus avian influenza A viruses.

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Proteomics in animal models of Alzheimer's and Parkinson's diseases.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.