Andrew Emili

Multiple substrates for paraoxonase-1 during oxidation of phosphatidylcholine by peroxynitrite.

De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging.

RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.

Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD.

Hsc70 regulates accumulation of cyclin D1 and cyclin D1-dependent protein kinase.

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.

PRISM, a generic large scale proteomic investigation strategy for mammals.

Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.

Mapping of determinants required for the function of the HIV-1 env nuclear retention sequence.

A panoramic view of yeast noncoding RNA processing.

Going global: protein expression profiling using shotgun mass spectrometry.

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions.

A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.

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.

High-definition macromolecular composition of yeast RNA-processing complexes.

Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics.

Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes.

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.

Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.

Sarcolipin retention in the endoplasmic reticulum depends on its C-terminal RSYQY sequence and its interaction with sarco(endo)plasmic Ca(2+)-ATPases.

A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway.

Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae.

Proteasome involvement in the repair of DNA double-strand breaks.

H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex.

Interaction network containing conserved and essential protein complexes in Escherichia coli.

Integrating gene and protein expression data: pattern analysis and profile mining.

Integrating global proteomic and genomic expression profiles generated from islet alpha cells: opportunities and challenges to deriving reliable biological inferences.

Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry.

Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone.

Proteome dynamics during C2C12 myoblast differentiation.

Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells.

Multidimensional protein identification technology: current status and future prospects.

Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue.

Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo.

Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin.

A skeleton of the human protein interactome.

Uncovering early markers of cardiac disease by proteomics: avoiding (heart) failure!

Human tissue profiling with multidimensional protein identification technology.

Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae.

Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4.

Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.

A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.

Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase.

Practical proteomic biomarker discovery: taking a step back to leap forward.

Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation.

Cardiac-specific overexpression of sarcolipin in phospholamban null mice impairs myocyte function that is restored by phosphorylation.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.

Systems-level analyses identify extensive coupling among gene expression machines.

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.

Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.

Cardiovascular proteomics: tools to develop novel biomarkers and potential applications.

Improved proteomic discovery by sample pre-fractionation using dual-column ion-exchange high performance liquid chromatography.

Computational prediction of cancer-gene function.

Analyzing the cardiac muscle proteome by liquid chromatography-mass spectrometry-based expression proteomics.

Difference detection in LC-MS data for protein biomarker discovery.

Modeling protein tandem mass spectrometry data with an extended linear regression strategy.

Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.

Hardware flexibility of laboratory automation systems: analysis and new flexible automation architectures.

Retention of protein complex membership by ancient duplicated gene products in budding yeast.

beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint.

hnRNP E1 and E2 have distinct roles in modulating HIV-1 gene expression.

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics.

Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale.

Predict, prevent and personalize: Genomic and proteomic approaches to cardiovascular medicine.

Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p.

Bacteriome.org--an integrated protein interaction database for E. coli.

Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint.

Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses.

Interactions of elongation factor EF-P with the Escherichia coli ribosome.

Proteomic methods for drug target discovery.

Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer.

Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.

The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast.

Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery.

eSGA: E. coli synthetic genetic array analysis.

Biosynthesis of the respiratory formate dehydrogenases from Escherichia coli: characterization of the FdhE protein.

Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications.

Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome.

Interaction of the deubiquitinating enzyme Ubp2 and the e3 ligase Rsp5 is required for transporter/receptor sorting in the multivesicular body pathway.

Conserved network of proteins essential for bacterial viability.

Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis.

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.

Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry.

An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.

Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli.

Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes.

A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.

Recent advances and method development for drug target identification.

Predicting protein functions by relaxation labelling protein interaction network.

Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.

Single amino acid resolution of proteolytic fragments generated in individual cells.

A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency.

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses.

Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry.

Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.

DAnCER: disease-annotated chromatin epigenetics resource.

Constitutively active calcineurin induces cardiac endoplasmic reticulum stress and protects against apoptosis that is mediated by alpha-crystallin-B.

Structure of a SLC26 anion transporter STAS domain in complex with acyl carrier protein: implications for E. coli YchM in fatty acid metabolism.

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.

Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.

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.

High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates.

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.

Computational refinement of post-translational modifications predicted from tandem mass spectrometry.

Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation.

Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains.

Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry.

Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli.

Filtering and interpreting large-scale experimental protein-protein interaction data.

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

Nanoparticle size and surface chemistry determine serum protein adsorption and macrophage uptake.

Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B.

Identification of enzyme-converted peptide products from single cells using capillary electrophoresis and liquid chromatography-mass spectrometry.

Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization.

Characterization and evolutionary analysis of protein-protein interaction networks.

Genome-scale genetic manipulation methods for exploring bacterial molecular biology.

Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program.

Hsp110 is required for spindle length control.

A census of human soluble protein complexes.

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.

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.

Application of quantitative proteomics technologies to the biomarker discovery pipeline for multiple sclerosis.

Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring.

Membrane proteomics by high performance liquid chromatography - tandem mass spectrometry: analytical approaches and challenges.