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List of works by Andrew Emili

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

scientific article

A census of human soluble protein complexes

scientific article

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

scientific article

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

scientific article

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

scientific article

A panoramic view of yeast noncoding RNA processing

scientific article

A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery

scientific article

A skeleton of the human protein interactome

scientific article

Amino Acid Starvation Induced by Invasive Bacterial Pathogens Triggers an Innate Host Defense Program ⬇️

scientific article published on June 14, 2012

An Unbiased Chemical Proteomics Method Identifies FabI as the Primary Target of 6-OH-BDE-47.

scientific article published on 28 September 2016

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

scientific article published on 15 November 2009

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

scientific article

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

scientific article published on January 2007

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

scientific article published on January 2013

Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli ⬇️

scientific article published on January 1, 2011

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

scientific article published on 29 June 2015

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

scientific article

Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data

scientific article published in January 2018

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

scientific article

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

scientific article

BuGZ is required for Bub3 stability, Bub1 kinetochore function, and chromosome alignment

scientific article

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

scholarly article

Cardiovascular proteomics: tools to develop novel biomarkers and potential applications

scientific article published on 17 October 2006

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

scientific article

Characterization and Evolutionary Analysis of Protein–Protein Interaction Networks ⬇️

scientific article published on January 1, 2012

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

scientific article published on 20 November 2003

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

scientific article

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

scientific article

Computational prediction of cancer-gene function

scientific article published on 14 December 2006

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

scientific article published on January 22, 2011

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli

scientific article

Conserved network of proteins essential for bacterial viability

scientific article published on 17 April 2009

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

scientific article published on October 11, 2010

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

scientific article published on September 1, 2011

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

scientific article

DAnCER: disease-annotated chromatin epigenetics resource

scientific article

DLG5 connects cell polarity and Hippo signaling protein networks by linking PAR-1 with MST1/2

scientific article

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

scientific article published in February 2002

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

scientific article published on 6 December 2004

Difference detection in LC-MS data for protein biomarker discovery

scientific article

Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain

scientific article published on 6 January 2013

Discovery of novel disease-specific and membrane-associated candidate markers in a mouse model of multiple sclerosis

scientific article published on 20 December 2013

EPIC: software toolkit for elution profile-based inference of protein complexes

scientific article published on 15 July 2019

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

scientific article

Erratum: Corrigendum: A phosphatase complex that dephosphorylates γH2AX regulates DNA damage checkpoint recovery

scientific article published in Nature

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

scientific article

Exercise-responsive phosphoproteins in the heart

scientific article

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

scientific article

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

scientific article published on 14 July 2007

Extracellular histones identified in crocodile blood inhibit in-vitro HIV-1 infection

scientific article published on 17 May 2016

Extracting high confidence protein interactions from affinity purification data: at the crossroads

scientific article

FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors

scientific article published on 13 December 2017

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

scientific article

G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis

scientific article published on 17 August 2016

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

scientific article

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

scientific article published on April 19, 2012

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins

scientific article

Global landscape of cell envelope protein complexes in Escherichia coli.

scientific article published on 27 November 2017

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

scientific article

Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy

scientific article published on 14 October 2016

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

scientific article published on May 2005

Global proteomic profiling and enrichment maps of dilated cardiomyopathy

scientific article published in January 2013

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

scientific article published in July 2009

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

scientific journal article

Going global: protein expression profiling using shotgun mass spectrometry.

scientific article

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

scientific article published in March 2007

High-definition macromolecular composition of yeast RNA-processing complexes

scientific article

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

scientific journal article

Hsp110 is required for spindle length control ⬇️

scientific article published on August 20, 2012

Human tissue profiling with multidimensional protein identification technology

scientific article published in September 2005

Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation

scientific article

Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice

scientific article published on 22 June 2017

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

scientific article

Identification of Mammalian Protein Complexes by Lentiviral-Based Affinity Purification and Mass Spectrometry ⬇️

scientific article published on January 1, 2011

Identification of Protein Complexes in <em>Escherichia coli</em> using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry ⬇️

scientific article published on November 12, 2012

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

scholarly article

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

scientific article published on January 2012

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae

scientific article published on March 2007

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

scientific article

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

scientific article published on 30 November 2006

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

scientific article

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

scientific article published on 21 July 2004

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

scientific article published on 08 May 2007

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

scientific article

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

scientific article published on March 2005

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

scientific article

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

scientific article

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

scientific article published on 12 January 2008

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

scientific article published on 28 December 2005

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

scientific article published on June 2008

Investigating Bacterial Protein Synthesis Using Systems Biology Approaches

scientific article

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

scientific article published on February 2007

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

scientific article published on March 2003

Large-scale characterization of the murine cardiac proteome

scientific article published on January 2013

Large-scale label-free phosphoproteomics: from technology to data interpretation

scientific article

Large-scale studies to identify biomarkers for heart disease: a role for proteomics?

scientific article published on March 2009

Lost in translation: five grand challenges for proteomic biomarker discovery

scientific article

Mapping bacterial functional networks and pathways in Escherichia Coli using synthetic genetic arrays

scientific article

Mapping signalling perturbations in myocardial fibrosis via the integrative phosphoproteomic profiling of tissue from diverse sources

scientific article published on 13 July 2020

Mass spectrometry methods to study protein-metabolite interactions

scientific article

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

scientific article published on 21 January 2013

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

scientific article

Modulation of lymphocyte-mediated tissue repair by rational design of heterocyclic aryl hydrocarbon receptor agonists

scientific article published on 15 January 2020

Multi-Omics Profiling of Hypertrophic Cardiomyopathy Reveals Altered Mechanisms in Mitochondrial Dynamics and Excitation–Contraction Coupling

scientific article published in March 2023

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

scientific article

Multidimensional protein identification technology: current status and future prospects

scientific article

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

scientific article published in January 2002

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

scientific article published on January 23, 2012

Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition

scientific article published on 13 October 2017

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

scientific article

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry

scientific article

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

scientific article

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

scientific article

PRISM, a generic large scale proteomic investigation strategy for mammals

scientific article published on 10 February 2003

Pancreatic tumor organoids for modeling in vivo drug response and discovering clinically-actionable biomarkers: supplemental

Panomics for Precision Medicine

scientific article published on 4 December 2017

Panorama of ancient metazoan macromolecular complexes

scientific article published on 07 September 2015

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

scientific article

Perinuclear Cohibin Complexes Maintain Replicative Life Span via Roles at Distinct Silent Chromatin Domains ⬇️

scientific article published on June 14, 2011

Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation

scientific article published on 29 July 2015

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

scientific article published on August 2007

Predicting protein functions by relaxation labelling protein interaction network

scientific article

Proteasome Involvement in the Repair of DNA Double-Strand Breaks

Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks.

scientific article published on 18 September 2017

Protein corona fingerprinting predicts the cellular interaction of gold and silver nanoparticles

scientific article

Protein-protein interaction networks: probing disease mechanisms using model systems

scientific article

Proteome dynamics during C2C12 myoblast differentiation

scientific article

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

scientific article

Proteomic methods for drug target discovery

scientific article published on February 2008

Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain

scientific article published on 06 January 2014

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

scientific article

RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation

scientific article

Recent advances and method development for drug target identification

scientific article published on 07 December 2009

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

scientific article

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

scientific article published on 10 April 2007

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

scientific article

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

scientific article

Roles for Pbp1 and caloric restriction in genome and lifespan maintenance via suppression of RNA-DNA hybrids

scientific article

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

scholarly article

Secreted biomolecules alter the biological identity and cellular interactions of nanoparticles

scientific article published on 14 May 2014

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

scientific article

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

scientific article

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

scientific article published on January 2009

Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways

scientific article published on January 2016

Single amino acid resolution of proteolytic fragments generated in individual cells

scientific article

Single-platform 'multi-omic' profiling: unified mass spectrometry and computational workflows for integrative proteomics-metabolomics analysis

scientific article published on 01 October 2018

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Subcellular proteomics

scientific article published on 29 April 2021

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

scientific article

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

scientific article

Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy

scientific article published on 31 October 2014

Systems-level analyses identify extensive coupling among gene expression machines

scientific article published on 17 January 2006

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

scientific article published on 31 July 2009

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

scientific article published on 2 November 2012

The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence

scientific article (publication date: 2013)

The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli

scientific article published on 15 January 2014

The binary protein-protein interaction landscape of Escherichia coli

scientific article

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

scientific article

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

scientific article

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

scientific article published on 7 May 2008

The nitrogen regulatory PII protein (GlnB) and N-acetyl-glucosamine 6-phosphate epimerase (NanE) allosterically activate glucosamine 6-phosphate deaminase (NagB) in Escherichia coli

scientific article published on 11 December 2017

The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli

scientific article published on 20 June 2017

The profile of adsorbed plasma and serum proteins on methacrylic acid copolymer beads: Effect on complement activation

scientific article published on 25 November 2016

Two-Dimensional Biochemical Purification for Global Proteomic Analysis of Macromolecular Protein Complexes

scientific article published on 01 January 2019

Ubp2 regulates Rsp5 ubiquitination activity in vivo and in vitro

scientific article

Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages

scientific article

Using phosphoproteomics to monitor disregulated signaling networks in cardiac disease preceding heart failure.

scientific article

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

scientific article

eSGA: E. coli synthetic genetic array analysis

scientific article

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

scientific article published on 23 April 2007

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