Andrew Emili

发表

Difference detection in LC-MS data for protein biomarker discovery

Radford M. Neal, Jennifer Listgarten, Sam T. Roweis, 2007, Bioinform..

Incorporating Correlations among Gene Ontology Terms into Predicting Protein Functions

Hui Jiang, Pingzhao Hu, Andrew Emili, 2011 .

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

Jian Liu, Brendan J. Frey, Clement Chung, 2011, Bioinform..

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

Chong Su, John Parkinson, Andrew Emili, 2007, Nucleic Acids Res..

A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements

Brendan J. Frey, Anitha Kannan, Andrew Emili, 2007, RECOMB.

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

Albert Chan, Ashkan Golshani, Frank Dehne, 2006, BMC Bioinformatics.

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

Andrew Emili, Ruth Isserlin, A. Emili, 2008, Current opinion in molecular therapeutics.

Constructing Treatment Portfolios Using Affinity Propagation

Brendan J. Frey, Nebojsa Jojic, Delbert Dueck, 2008, RECOMB.

Mapping global protein contacts

Sandor Vajda, Andrew Emili, 2019, Science.

A scalable robotic-based laboratory automation system for medium-sized biotechnology laboratories

Andrew A. Goldenberg, Andrew Emili, Peyman Najmabadi, 2005, IEEE International Conference on Automation Science and Engineering, 2005..

Characterization and evolutionary analysis of protein-protein interaction networks.

Zhaolei Zhang, Andrew Emili, Gabriel Musso, 2012, Methods in molecular biology.

Conceptual Design for an Automated High-Throughput Magnetic Protein Complex Purification Workcell

Andrew A. Goldenberg, Andrew Emili, Peyman Najmabadi, 2003 .

Hardware Flexibility of Laboratory Automation Systems: Analysis and New Flexible Automation Architectures

Andrew Emili, Peyman Najmabadi, Andrew A Goldenberg, 2007, Clinics in laboratory medicine.

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

Andrew A. Goldenberg, Andrew Emili, Peyman Najmabadi, 2007 .

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

Brendan J. Frey, Clement Chung, Andrew Emili, 2013, Bioinform..

Predicting protein functions by relaxation labelling protein interaction network

Hui Jiang, Pingzhao Hu, Andrew Emili, 2010, BMC Bioinformatics.

Faculty Opinions recommendation of Assigning function to yeast proteins by integration of technologies.

Andrew Emili, 2004 .

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

Gary D Bader, Andrew Emili, Florian Goebels, 2018, Methods in molecular biology.

DAnCER: Disease-Annotated Chromatin Epigenetics Resource

Andrei L. Turinsky, Zhaolei Zhang, Shoshana J. Wodak, 2010, Nucleic Acids Res..

Multiple Alignment of Continuous Time Series

Radford M. Neal, Jennifer Listgarten, Sam T. Roweis, 2004, NIPS.

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

Gary D Bader, Andrew Emili, Sadhna Phanse, 2019, Nature Methods.

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

Zhaolei Zhang, Andrew Emili, Gabriel Musso, 2011, Methods in molecular biology.

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

Gary D. Bader, Gary D Bader, Ashkan Golshani, 2015, Bioinform..

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

Andrew Emili, Benjamin C Blum, Fatemeh Mousavi, 2018, Molecular omics.

Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry*S

Yongyi Mao, Soyoung Ryu, Andrew Emili, 2004, Molecular & Cellular Proteomics.

Panomics for Precision Medicine.

Andrew Emili, Charanjit Sandhu, Alia Qureshi, 2018, Trends in molecular medicine.

Systems-level analyses identify extensive coupling among gene expression machines

Nevan J Krogan, Tom Maniatis, Andrew Emili, 2006, Molecular systems biology.

eSGA: E. coli Synthetic Genetic Array analysis

Andrew Emili, Mohan Babu, Gareth Butland, 2008 .

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

Olga Kagan, John Parkinson, Edward M. Marcotte, 2015, Data in brief.

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

Nevan J Krogan, Andrew Emili, Timothy R Hughes, 2009, RNA.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

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

Andrew Emili, Thomas Kislinger, A. Emili, 2004, Proceedings of the National Academy of Sciences of the United States of America.

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

Andrew Emili, Yoram Cohen, Warren C W Chan, 2014, ACS nano.

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery.

Ashkan Golshani, Andrew Emili, Mohan Babu, 2016, Cell reports.

Cotranscriptional Set2 Methylation of Histone H3 Lysine 36 Recruits a Repressive Rpd3 Complex

Nevan J. Krogan, Brian D. Strahl, Timothy R. Hughes, 2005, Cell.

A Genome-Wide Screen Identifies the Evolutionarily Conserved KEOPS Complex as a Telomere Regulator

David Lydall, Nevan J. Krogan, Andrew Emili, 2006, Cell.

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

Andrew Emili, Ruth Isserlin, Uros Kuzmanov, 2016, Proceedings of the National Academy of Sciences.

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

Andrew Emili, Mohan Babu, Alla Gagarinova, 2011, Methods in molecular biology.

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

Huiming Ding, Nevan J Krogan, Andrew Emili, 2003, Molecular cell.

Multiparameter functional diversity of human C2H2 zinc finger proteins

Andrew Emili, Jussi Taipale, Timothy R Hughes, 2016, Genome research.

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

Jennifer Listgarten, Andrew Emili, J. Listgarten, 2005, Drug discovery today.

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

Andrew Emili, Gerard Cagney, G. Cagney, 2002, Nature Biotechnology.

Human tissue profiling with multidimensional protein identification technology.

Clement Chung, Andrew Emili, Gerard Cagney, 2005, Journal of proteome research.

Navigating the Chaperone Network: An Integrative Map of Physical and Genetic Interactions Mediated by the Hsp90 Chaperone

Andrew Emili, Charles Boone, Jack Greenblatt, 2005, Cell.

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

Andrew Emili, Dajana Vuckovic, A. Emili, 2012, Cell host & microbe.

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

Andrei L. Turinsky, Shoshana J. Wodak, James Vlasblom, 2015, Journal of proteomics.

Proteomic methods for drug target discovery.

Andrew Emili, A. Emili, L. Sleno, 2008, Current opinion in chemical biology.

A Lentiviral Functional Proteomics Approach Identifies Chromatin Remodeling Complexes Important for the Induction of Pluripotency*

Anne-Claude Gingras, Andrew Emili, Ruth Isserlin, 2010, Molecular & Cellular Proteomics.

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

Masahiro Fukuoka, Andrew Emili, Douglas S Lee, 2007, The Canadian journal of cardiology.

Expanding the Landscape of Chromatin Modification (CM)-Related Functional Domains and Genes in Human

Andrei L. Turinsky, Zhaolei Zhang, Shoshana J. Wodak, 2010, PloS one.

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

Clement Chung, Marlena Maziarz, Andrew Emili, 2005, Molecular & cellular proteomics : MCP.

Recent advances and method development for drug target identification.

Corey Nislow, Andrew Emili, A. Emili, 2010, Trends in pharmacological sciences.

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.

Edward M Marcotte, Andrew Emili, Vincent Fong, 2013, Journal of proteomics.

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

Zhaolei Zhang, Andrew Emili, Jack Greenblatt, 2009, Molecular systems biology.

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

Andrew Emili, Thomas Kislinger, A. Emili, 2005, Methods.

Nonparametric Bayesian Approach to Post-translational Modification Refinement of Predictions from Tandem Mass Spectrometry

Clement Chung, Andrew Emili, B. Frey, 2012 .

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

Andrew Emili, Mohan Babu, Eugene V Koonin, 2011, Molecular microbiology.

Defining the SUMO-modified Proteome by Multiple Approaches in Saccharomyces cerevisiae*

Andrew Emili, Heinrich Heide, Mary B. Kroetz, 2005, Journal of Biological Chemistry.

Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses*S

Andrew Emili, Anitha Kannan, Thomas Kislinger, 2008, Molecular & Cellular Proteomics.

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

Ashkan Golshani, Andrew Emili, Gareth Butland, 2007, Journal of cellular biochemistry.

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

Peipei Ping, Andrew Emili, Thomas Kislinger, 2006, Journal of the American College of Cardiology.

Multidimensional protein identification technology: current status and future prospects

Andrew Emili, Thomas Kislinger, A. Emili, 2005, Expert review of proteomics.

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

Zhaolei Zhang, Michael Costanzo, Corey Nislow, 2008, Genome research.

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

Andrew Emili, Sadhna Phanse, A. Emili, 2013, Journal of proteomics.

Cotranscriptional Set 2 Methylation of Histone H 3 Lysine 36 Recruits a Repressive Rpd 3 Complex

Nevan J. Krogan, Brian D. Strahl, Timothy R. Hughes, 2005 .

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

Andrew Emili, Timothy R Hughes, Gwenael Badis, 2008, Journal of proteome research.

A Snf 2 Family ATPase Complex Required for Recruitment of the Histone H 2 A Variant Htz

Nevan J. Krogan, Huiming Ding, Timothy R. Hughes, 2003 .

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

Andrei L. Turinsky, Zhaolei Zhang, John Parkinson, 2010, Proteins.

Secreted biomolecules alter the biological identity and cellular interactions of nanoparticles.

Andrew Emili, Alexandre Albanese, Warren C. W. Chan, 2014, ACS nano.

Going global: protein expression profiling using shotgun mass spectrometry.

Andrew Emili, Thomas Kislinger, A. Emili, 2003, Current opinion in molecular therapeutics.

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

Andrew Emili, Gerard Cagney, G. Cagney, 2003, Proteome Science.

Conceptual Design for an Automated High-Throughput Magnetic Protein Complex Purification Workcell

Andrew A. Goldenberg, Andrew Emili, Peyman Najmabadi, 2003 .

Proteome Dynamics during C2C12 Myoblast Differentiation*S

Andrew Emili, Thomas Kislinger, David H. MacLennan, 2005, Molecular & Cellular Proteomics.

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

Ashkan Golshani, Omar Wagih, John Parkinson, 2016, Cell reports.

A Panoramic View of Yeast Noncoding RNA Processing

Brendan J. Frey, Mark D. Robinson, Nevan J. Krogan, 2003, Cell.

Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-( 3-5 )-cyclic-GMP in virulence

Timothy R. Hughes, Andrew Emili, Natalie J. Thompson, 2006 .

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae

Andrew Emili, Shoshana J Wodak, Jack Greenblatt, 2007, Proteomics.

Computational prediction of cancer-gene function

Pingzhao Hu, Andrew Emili, Dennis A. Wigle, 2007, Nature Reviews Cancer.

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

Andrew Emili, Warren C W Chan, A. Emili, 2012, Journal of the American Chemical Society.

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

Andrew Emili, Mohan Babu, A. Emili, 2008, FEMS microbiology reviews.

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

Andrew Emili, Dajana Vuckovic, Laura F. Dagley, 2013, Proteomics.

PRISM, a Generic Large Scale Proteomic Investigation Strategy for Mammals*S

Andrew Emili, Dragan Radulovic, Janet Rossant, 2003, Molecular & Cellular Proteomics.

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

Igor Jurisica, Andrew Emili, Anitha Kannan, 2022 .

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

Andrew Emili, Thomas Kislinger, A. Emili, 2005, Journal of the American Society for Mass Spectrometry.

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

Andrew Emili, Gareth Butland, A. Emili, 2006, FEBS letters.

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

Zhaolei Zhang, Andrew Emili, A. Emili, 2007, Chemical reviews.

eSGA: E. coli synthetic genetic array analysis

Huiming Ding, Andrew Emili, Gabriel Moreno-Hagelsieb, 2008, Nature Methods.

SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors

Andrew Emili, Chao Gao, Richard D. Cummings, 2020, bioRxiv.

A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities

Roland Arnold, Laurence Pelletier, Andrew Emili, 2013, Molecular systems biology.