Department of Molecular Genetics,
Banting and Best Department of Medical Research,
Donnelly Centre,
Department of Medical Genetics and Microbiology,
Banting and Best Department of Medical Research, Donnelly Centre
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Multiple substrates for paraoxonase-1 during oxidation of phosphatidylcholine by peroxynitrite.
Biochemical and biophysical research communications Jan, 2002 | Pubmed ID: 11779181
De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging.
Nature biotechnology Feb, 2002 | Pubmed ID: 11821862
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.
Molecular and cellular biology Oct, 2002 | Pubmed ID: 12242279
Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD.
RNA (New York, N.Y.) Sep, 2002 | Pubmed ID: 12358429
Hsc70 regulates accumulation of cyclin D1 and cyclin D1-dependent protein kinase.
Molecular and cellular biology Mar, 2003 | Pubmed ID: 12588994
JlpA of Campylobacter jejuni interacts with surface-exposed heat shock protein 90alpha and triggers signalling pathways leading to the activation of NF-kappaB and p38 MAP kinase in epithelial cells.
Cellular microbiology Mar, 2003 | Pubmed ID: 12614460
PRISM, a generic large scale proteomic investigation strategy for mammals.
Molecular & cellular proteomics : MCP Feb, 2003 | Pubmed ID: 12644571
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.
Molecular and cellular biology Jun, 2003 | Pubmed ID: 12773564
Mapping of determinants required for the function of the HIV-1 env nuclear retention sequence.
Virology May, 2003 | Pubmed ID: 12788633
A panoramic view of yeast noncoding RNA processing.
Cell Jun, 2003 | Pubmed ID: 12837249
Going global: protein expression profiling using shotgun mass spectrometry.
Current opinion in molecular therapeutics Jun, 2003 | Pubmed ID: 12870439
In silico proteome analysis to facilitate proteomics experiments using mass spectrometry.
Proteome science Aug, 2003 | Pubmed ID: 12946274
A Bayesian networks approach for predicting protein-protein interactions from genomic data.
Science (New York, N.Y.) Oct, 2003 | Pubmed ID: 14564010
Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions.
Blood Mar, 2004 | Pubmed ID: 14630798
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.
Molecular cell Dec, 2003 | Pubmed ID: 14690608
The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion.
Molecular and cellular biology Feb, 2004 | Pubmed ID: 14729968
High-definition macromolecular composition of yeast RNA-processing complexes.
Molecular cell Jan, 2004 | Pubmed ID: 14759368
Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2004 | Pubmed ID: 14982994
Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes.
Journal of proteome research May-Jun, 2004 | Pubmed ID: 15253427
Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.
Molecular & cellular proteomics : MCP Oct, 2004 | Pubmed ID: 15269249
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.
Proceedings of the National Academy of Sciences of the United States of America Sep, 2004 | Pubmed ID: 15353583
Sarcolipin retention in the endoplasmic reticulum depends on its C-terminal RSYQY sequence and its interaction with sarco(endo)plasmic Ca(2+)-ATPases.
Proceedings of the National Academy of Sciences of the United States of America Nov, 2004 | Pubmed ID: 15556994
A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway.
The Journal of biological chemistry Feb, 2005 | Pubmed ID: 15569666
Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae.
The Journal of biological chemistry Feb, 2005 | Pubmed ID: 15590687
Proteasome involvement in the repair of DNA double-strand breaks.
Molecular cell Dec, 2004 | Pubmed ID: 15610744
H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex.
Molecular and cellular biology Feb, 2005 | Pubmed ID: 15657441
Interaction network containing conserved and essential protein complexes in Escherichia coli.
Nature Feb, 2005 | Pubmed ID: 15690043
Integrating gene and protein expression data: pattern analysis and profile mining.
Methods (San Diego, Calif.) Mar, 2005 | Pubmed ID: 15722226
Integrating global proteomic and genomic expression profiles generated from islet alpha cells: opportunities and challenges to deriving reliable biological inferences.
Molecular & cellular proteomics : MCP Apr, 2005 | Pubmed ID: 15741311
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry.
Molecular & cellular proteomics : MCP Apr, 2005 | Pubmed ID: 15741312
Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone.
Cell Mar, 2005 | Pubmed ID: 15766533
Proteome dynamics during C2C12 myoblast differentiation.
Molecular & cellular proteomics : MCP Jul, 2005 | Pubmed ID: 15824125
Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells.
Journal of proteome research May-Jun, 2005 | Pubmed ID: 15952714
Multidimensional protein identification technology: current status and future prospects.
Expert review of proteomics Jan, 2005 | Pubmed ID: 15966850
Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue.
Journal of the American Society for Mass Spectrometry Aug, 2005 | Pubmed ID: 15979338
Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo.
Molecular and cellular biology Aug, 2005 | Pubmed ID: 16024807
Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin.
The Journal of biological chemistry Dec, 2005 | Pubmed ID: 16159877
A skeleton of the human protein interactome.
Cell Sep, 2005 | Pubmed ID: 16179252
Uncovering early markers of cardiac disease by proteomics: avoiding (heart) failure!
Expert review of proteomics Oct, 2005 | Pubmed ID: 16209642
Human tissue profiling with multidimensional protein identification technology.
Journal of proteome research Sep-Oct, 2005 | Pubmed ID: 16212430
Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae.
Molecular and cellular biology Nov, 2005 | Pubmed ID: 16260625
Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4.
Molecular biology of the cell Jan, 2006 | Pubmed ID: 16267268
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.
Cell Nov, 2005 | Pubmed ID: 16286008
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
Nature Jan, 2006 | Pubmed ID: 16299494
Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase.
The Journal of biological chemistry Jan, 2006 | Pubmed ID: 16301313
Practical proteomic biomarker discovery: taking a step back to leap forward.
Drug discovery today Dec, 2005 | Pubmed ID: 16376831
Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation.
FEBS letters Jan, 2006 | Pubmed ID: 16412426
Cardiac-specific overexpression of sarcolipin in phospholamban null mice impairs myocyte function that is restored by phosphorylation.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2006 | Pubmed ID: 16461894
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Nature Mar, 2006 | Pubmed ID: 16554755
A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.
Cell Mar, 2006 | Pubmed ID: 16564010
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.
Cell Apr, 2006 | Pubmed ID: 16615898
Systems-level analyses identify extensive coupling among gene expression machines.
Molecular systems biology , 2006 | Pubmed ID: 16738550
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.
BMC bioinformatics , 2006 | Pubmed ID: 16872538
Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.
Journal of cellular biochemistry Feb, 2007 | Pubmed ID: 16983699
Cardiovascular proteomics: tools to develop novel biomarkers and potential applications.
Journal of the American College of Cardiology Nov, 2006 | Pubmed ID: 17084242
Improved proteomic discovery by sample pre-fractionation using dual-column ion-exchange high performance liquid chromatography.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences Feb, 2007 | Pubmed ID: 17140863
Computational prediction of cancer-gene function.
Nature reviews. Cancer Jan, 2007 | Pubmed ID: 17167517
Analyzing the cardiac muscle proteome by liquid chromatography-mass spectrometry-based expression proteomics.
Methods in molecular biology (Clifton, N.J.) , 2007 | Pubmed ID: 17172675
Difference detection in LC-MS data for protein biomarker discovery.
Bioinformatics (Oxford, England) Jan, 2007 | Pubmed ID: 17237092
Modeling protein tandem mass spectrometry data with an extended linear regression strategy.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference , 2004 | Pubmed ID: 17270923
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.
Nature Apr, 2007 | Pubmed ID: 17314980
Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.
Proteomics Mar, 2007 | Pubmed ID: 17370254
Hardware flexibility of laboratory automation systems: analysis and new flexible automation architectures.
Clinics in laboratory medicine Mar, 2007 | Pubmed ID: 17416299
Retention of protein complex membership by ancient duplicated gene products in budding yeast.
Trends in genetics : TIG Jun, 2007 | Pubmed ID: 17428571
beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint.
The EMBO journal May, 2007 | Pubmed ID: 17431397
hnRNP E1 and E2 have distinct roles in modulating HIV-1 gene expression.
Retrovirology , 2007 | Pubmed ID: 17451601
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.
Molecular systems biology , 2007 | Pubmed ID: 17486137
Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics.
Nature protocols , 2006 | Pubmed ID: 17487171
Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale.
Chemical reviews Aug, 2007 | Pubmed ID: 17630806
Predict, prevent and personalize: Genomic and proteomic approaches to cardiovascular medicine.
The Canadian journal of cardiology Aug, 2007 | Pubmed ID: 17668085
Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p.
BMC biology , 2007 | Pubmed ID: 17880717
Bacteriome.org--an integrated protein interaction database for E. coli.
Nucleic acids research Jan, 2008 | Pubmed ID: 17942431
Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint.
Cell Nov, 2007 | Pubmed ID: 18045534
Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses.
Molecular & cellular proteomics : MCP Mar, 2008 | Pubmed ID: 18056057
Interactions of elongation factor EF-P with the Escherichia coli ribosome.
The FEBS journal Feb, 2008 | Pubmed ID: 18201202
Proteomic methods for drug target discovery.
Current opinion in chemical biology Feb, 2008 | Pubmed ID: 18282485
Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer.
Journal of proteome research Apr, 2008 | Pubmed ID: 18311902
Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.
Molecular and cellular biology Jul, 2008 | Pubmed ID: 18458063
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast.
Genome research Jul, 2008 | Pubmed ID: 18463300
Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery.
Current opinion in molecular therapeutics Jun, 2008 | Pubmed ID: 18535930
eSGA: E. coli synthetic genetic array analysis.
Nature methods Sep, 2008 | Pubmed ID: 18677321
Biosynthesis of the respiratory formate dehydrogenases from Escherichia coli: characterization of the FdhE protein.
Archives of microbiology Dec, 2008 | Pubmed ID: 18716757
Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications.
Analytical chemistry Oct, 2008 | Pubmed ID: 18788753
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome.
FEMS microbiology reviews Jan, 2009 | Pubmed ID: 19054114
Interaction of the deubiquitinating enzyme Ubp2 and the e3 ligase Rsp5 is required for transporter/receptor sorting in the multivesicular body pathway.
PloS one , 2009 | Pubmed ID: 19165343
Conserved network of proteins essential for bacterial viability.
Journal of bacteriology Aug, 2009 | Pubmed ID: 19376873
Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis.
Journal of proteome research Jul, 2009 | Pubmed ID: 19400582
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.
PLoS biology Apr, 2009 | Pubmed ID: 19402753
Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2009 | Pubmed ID: 19521826
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
Molecular systems biology , 2009 | Pubmed ID: 19536198
Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli.
Methods in molecular biology (Clifton, N.J.) , 2009 | Pubmed ID: 19544035
Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes.
Molecular bioSystems Dec, 2009 | Pubmed ID: 19763343
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
RNA (New York, N.Y.) Dec, 2009 | Pubmed ID: 19789211
An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
Nature structural & molecular biology Dec, 2009 | Pubmed ID: 19915592
Recent advances and method development for drug target identification.
Trends in pharmacological sciences Feb, 2010 | Pubmed ID: 20004028
Predicting protein functions by relaxation labelling protein interaction network.
BMC bioinformatics , 2010 | Pubmed ID: 20122240
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.
Proteomics Mar, 2010 | Pubmed ID: 20127684
Single amino acid resolution of proteolytic fragments generated in individual cells.
Cytometry. Part A : the journal of the International Society for Analytical Cytology Apr, 2010 | Pubmed ID: 20187109
A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency.
Molecular & cellular proteomics : MCP May, 2010 | Pubmed ID: 20305087
The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.
Proteins Jul, 2010 | Pubmed ID: 20455264
Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry.
Molecular & cellular proteomics : MCP Nov, 2010 | Pubmed ID: 20467045
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.
Science (New York, N.Y.) Jul, 2010 | Pubmed ID: 20671182
DAnCER: disease-annotated chromatin epigenetics resource.
Nucleic acids research Jan, 2011 | Pubmed ID: 20876685
Constitutively active calcineurin induces cardiac endoplasmic reticulum stress and protects against apoptosis that is mediated by alpha-crystallin-B.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2010 | Pubmed ID: 20937869
Structure of a SLC26 anion transporter STAS domain in complex with acyl carrier protein: implications for E. coli YchM in fatty acid metabolism.
Structure (London, England : 1993) Nov, 2010 | Pubmed ID: 21070944
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.
PloS one , 2010 | Pubmed ID: 21085593
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.
PloS one , 2010 | Pubmed ID: 21124763
Nine steps to proteomic wisdom: A practical guide to using protein-protein interaction networks and molecular pathways as a framework for interpreting disease proteomic profiles.
Proteomics. Clinical applications Sep, 2007 | Pubmed ID: 21136765
High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates.
Proteomics. Clinical applications Oct, 2008 | Pubmed ID: 21136791
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.
Molecular microbiology Jan, 2011 | Pubmed ID: 21219465
Computational refinement of post-translational modifications predicted from tandem mass spectrometry.
Bioinformatics (Oxford, England) Mar, 2011 | Pubmed ID: 21258065
Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation.
PloS one , 2011 | Pubmed ID: 21556145
Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains.
Developmental cell Jun, 2011 | Pubmed ID: 21664583
Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.
Methods in molecular biology (Clifton, N.J.) , 2011 | Pubmed ID: 21815091
Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2011 | Pubmed ID: 21877275
Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.
Methods in molecular biology (Clifton, N.J.) , 2011 | Pubmed ID: 21877280
Filtering and interpreting large-scale experimental protein-protein interaction data.
Methods in molecular biology (Clifton, N.J.) , 2011 | Pubmed ID: 21877287
Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.
PLoS genetics Nov, 2011 | Pubmed ID: 22125496
Nanoparticle size and surface chemistry determine serum protein adsorption and macrophage uptake.
Journal of the American Chemical Society Feb, 2012 | Pubmed ID: 22191645
Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B.
Transcription Sep-Oct, 2011 | Pubmed ID: 22231121
Identification of enzyme-converted peptide products from single cells using capillary electrophoresis and liquid chromatography-mass spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2012 | Pubmed ID: 22323137
Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization.
Molecular & cellular proteomics : MCP Jul, 2012 | Pubmed ID: 22357554
Characterization and evolutionary analysis of protein-protein interaction networks.
Methods in molecular biology (Clifton, N.J.) , 2012 | Pubmed ID: 22399467
Genome-scale genetic manipulation methods for exploring bacterial molecular biology.
Molecular bioSystems Jun, 2012 | Pubmed ID: 22517266
Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program.
Cell host & microbe Jun, 2012 | Pubmed ID: 22704617
Hsp110 is required for spindle length control.
The Journal of cell biology Aug, 2012 | Pubmed ID: 22908312
A census of human soluble protein complexes.
Cell Aug, 2012 | Pubmed ID: 22939629
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.
Nature Sep, 2012 | Pubmed ID: 22940862
ComplexQuant: High-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS.
Journal of proteomics Oct, 2012 | Pubmed ID: 23063720
Application of quantitative proteomics technologies to the biomarker discovery pipeline for multiple sclerosis.
Proteomics. Clinical applications Oct, 2012 | Pubmed ID: 23112123
Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring.
Journal of proteomics Nov, 2012 | Pubmed ID: 23124093
Membrane proteomics by high performance liquid chromatography - tandem mass spectrometry: analytical approaches and challenges.
Proteomics Nov, 2012 | Pubmed ID: 23125154
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