Andrew Emili

Department of Molecular Genetics, University of Toronto

Research Area

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 9	2012
Publication title Cited by 11	2012

Other Publications

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