Andrew Emili | Profiles RNS

Andrew Emili, PhD

Professor

Boston University College of Arts and Sciences

Dept of Biology

PhD, University of Toronto
MS, University of Toronto

Websites

	Biology Faculty
	Biochemistry Faculty
	BU Center for Network Systems Biology
	College of Engineering Faculty
	Emili Lab
	Google Scholar
	ResearchGate

Systems Biology
Molecular / Protein Interaction Networks
Mass Spectrometry
Molecular Genetics/Genomics, Proteomics, Biochemistry, Bioinformatics

Professor
Boston University School of Medicine
Biochemistry

Founding Professor
Boston University School of Medicine, Graduate Medical Sciences
Computing & Data Sciences Administration

Graduate Faculty (Primary Mentor of Grad Students)
Boston University School of Medicine, Graduate Medical Sciences

Member
Boston University
Genome Science Institute

2007 Heart & Stroke/Lewar Centre Excellence, University of Toronto: Subash Verma Research Award

1997-2000 Damon Runyon Cancer Research Foundation, USA: Cancer Research Fellow

1991-1997 Medical Research Council, Canada: Graduate Fellowships

1990 McGill University, QC Canada: Summa Cum Laude

BU Research

Mapping Protein Interaction Networks Essential for Gonococcal Pathogenesis
05/06/2021 - 04/30/2026 (PI)
NIH/National Institute of Allergy & Infectious Diseases
1R01AI146941-01A1

Multiscale analysis of metabolic inflammation as a driver of breast cancer
09/09/2020 - 08/31/2025 (Multi-PI)
PI: Andrew Emili, PhD
NIH/National Cancer Institute
1U01CA243004-01A1

Genetic Modifiers of Protein Interaction Networks in Tauopathy
08/01/2019 - 03/31/2024 (Multi-PI)
PI: Andrew Emili, PhD
NIH/National Institute on Aging
5R01AG064932-03

Systems-level functional proteomics analysis assemblies in Alzheimer's disease and mouse models of tauopathy
02/15/2019 - 01/31/2024 (Multi-PI)
PI: Andrew Emili, PhD
NIH/National Institute on Aging
1RF1AG061706-01

RAPID: Transcription Factor Profiling for SARS-CoV2 Tolerance/Symbiosis Regulation
06/01/2020 - 05/31/2022 (Multi-PI)
PI: Andrew Emili, PhD
National Science Foundation
IOS-2031624

A new human iPSC in vitro system to model the inception of lung adenocarcinoma (2nd Year Renewal - WWDA)
12/01/2020 - 12/31/2021 (Multi-PI)
PI: Andrew Emili, PhD
Janssen Research & Development, LLC

Engineering a smart CAR platform for human regulatory T cells
09/30/2019 - 09/29/2021 (Co-Investigator)
NIH/National Institute of Biomedical Imaging & Bioengineering
1R56EB027729-01A1

Mapping Pathogenic Coronavirus Viral-Host Protein Interaction Environments for Target Discovery
08/03/2020 - 08/02/2021 (Multi-PI)
PI: Andrew Emili, PhD
Merck, Sharp & Dohme Corp

Ultra-High Precision Mass Spectrometer
07/01/2020 - 06/30/2021 (PI)
NIH/Office of the Director
1S10OD026807-01A1

A new human iPSC in vitro system to model the inception of lung adenocarcinoma
06/01/2020 - 11/30/2020 (Multi-PI)
PI: Andrew Emili, PhD
Johnson & Johnson Enterprise Innovation, Inc.

Showing 10 of 13 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Xu C, Wang B, Yang L, Zhongming Hu L, Yi L, Wang Y, Chen S, Emili A, Wan C. Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. Genomics Proteomics Bioinformatics. 2021 Feb 23. PMID: 33636367

Deehan M, Lin W, Blum B, Emili A, Frydman H. Intracellular Density of Wolbachia Is Mediated by Host Autophagy and the Bacterial Cytoplasmic Incompatibility Gene cifB in a Cell Type-Dependent Manner in Drosophila melanogaster. mBio. 2021 01 12; 12(1).View Related Profiles.

Emili, Andrew
Blum, Benjamin
Frydman, Horacio

PMID: 33436431; PMCID: PMC7844536; DOI: 10.1128/mBio.02205-20;

Chan S, Smith E, Gao Y, Kwan J, Blum BC, Tilston-Lunel AM, Turcinovic I, Varelas X, Cardamone MD, Monti S, Emili A, Perissi V. Loss of G-Protein Pathway Suppressor 2 Promotes Tumor Growth Through Activation of AKT Signaling. Front Cell Dev Biol. 2020; 8:608044.View Related Profiles.

Emili, Andrew
Tilston-Lunel, Andrew
Blum, Benjamin
Cardamone, Maria
Chan, Stefanie
Monti, Stefano
Perissi, Valentina
Varelas, Xaralabos

PMID: 33490071; PMCID: PMC7817781; DOI: 10.3389/fcell.2020.608044;

Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell. 2021 Jan 07; 81(1):212.View Related Profiles. PMID: 33417854; PMCID: PMC7831449; DOI: 10.1016/j.molcel.2020.12.028;

Basu A, Ash PE, Wolozin B, Emili A. Protein Interaction Network Biology in Neuroscience. Proteomics. 2021 Feb; 21(3-4):e1900311.View Related Profiles.

Emili, Andrew
Basu, Avik
Wolozin, Benjamin
Ash, Peter

PMID: 33314619; PMCID: PMC7900949; DOI: 10.1002/pmic.201900311;

Paul I, White C, Turcinovic I, Emili A. Imaging the future: the emerging era of single-cell spatial proteomics. FEBS J. 2020 Dec 22. PMID: 33351222

Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell. 2020 12 17; 80(6):1104-1122.e9.View Related Profiles. PMID: 33259812; PMCID: PMC7674017; DOI: 10.1016/j.molcel.2020.11.028;

Lee ES, Wolf EJ, Ihn SSJ, Smith HW, Emili A, Palazzo AF. TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes. Nucleic Acids Res. 2020 11 18; 48(20):11645-11663. PMID: 33091126; PMCID: PMC7672458; DOI: 10.1093/nar/gkaa919;

Huang L, Bockorny B, Paul I, Akshinthala D, Frappart PO, Gandarilla O, Bose A, Sanchez-Gonzalez V, Rouse EE, Lehoux SD, Pandell N, Lim CM, Clohessy JG, Grossman J, Gonzalez R, Del Pino SP, Daaboul G, Sawhney MS, Freedman SD, Kleger A, Cummings RD, Emili A, Muthuswamy LB, Hidalgo M, Muthuswamy SK. PDX-derived organoids model in vivo drug response and secrete biomarkers. JCI Insight. 2020 11 05; 5(21). PMID: 32990680; PMCID: PMC7710298; DOI: 10.1172/jci.insight.135544;

Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Kapell S, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway. bioRxiv. 2020 Oct 28.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Kotton, Darrell
Douam, Florian
Connor, John
Saeed, Mohsan
Crossland, Nicholas
Goel, Raghuveera
Kapell, Sebastian
Chitalia, Vipul

PMID: 33140044; PMCID: PMC7605551; DOI: 10.1101/2020.10.27.358259;

Showing 10 of 223 results. Show More

Schäkermann S, Wüllner D, Yayci A, Emili A, Bandow JE. Applicability of Chromatographic Co-Elution for Antibiotic Target Identification. Proteomics. 2021 01; 21(1):e2000038. PMID: 32951352

Gold AS, Feitosa-Suntheimer F, Araujo RV, Hekman RM, Asad S, Londono-Renteria B, Emili A, Colpitts TM. Dengue Virus Infection of Aedes aegypti Alters Extracellular Vesicle Protein Cargo to Enhance Virus Transmission. Int J Mol Sci. 2020 Sep 10; 21(18).View Related Profiles.

Emili, Andrew
Colpitts, Tonya

PMID: 32927629; PMCID: PMC7555558; DOI: 10.3390/ijms21186609;

Dost AFM, Moye AL, Vedaie M, Tran LM, Fung E, Heinze D, Villacorta-Martin C, Huang J, Hekman R, Kwan JH, Blum BC, Louie SM, Rowbotham SP, Sainz de Aja J, Piper ME, Bhetariya PJ, Bronson RT, Emili A, Mostoslavsky G, Fishbein GA, Wallace WD, Krysan K, Dubinett SM, Yanagawa J, Kotton DN, Kim CF. Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells. Cell Stem Cell. 2020 10 01; 27(4):663-678.e8.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Kotton, Darrell
Mostoslavsky, Gustavo

PMID: 32891189; PMCID: PMC7541765; DOI: 10.1016/j.stem.2020.07.022;

Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Al Abdullatif A, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst. 2020 Aug 26; 11(2):208.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Wolozin, Benjamin
Bryant, Camron
Apicco, Daniel
Ash, Peter

PMID: 32853540

Gao C, Zeng J, Jia N, Stavenhagen K, Matsumoto Y, Zhang H, Li J, Hume AJ, Mühlberger E, van Die I, Kwan J, Tantisira K, Emili A, Cummings RD. SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors. bioRxiv. 2020 Jul 30.View Related Profiles.

Hume, Adam
Emili, Andrew
Muhlberger, Elke

PMID: 32766577; PMCID: PMC7402034; DOI: 10.1101/2020.07.29.227462;

Kim S, Rabhi N, Blum BC, Hekman R, Wynne K, Emili A, Farmer S, Schlezinger JJ. Triphenyl phosphate is a selective PPAR? modulator that does not induce brite adipogenesis in vitro and in vivo. Arch Toxicol. 2020 09; 94(9):3087-3103.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Schlezinger, Jennifer
Rabhi, Nabil
Farmer, Stephen

PMID: 32683515; PMCID: PMC7443879; DOI: 10.1007/s00204-020-02815-1;

Kuzmanov U, Wang EY, Vanderlaan R, Kim DH, Lee SH, Hadipour-Lakmehsari S, Guo H, Zhao Y, McFadden M, Sharma P, Billia F, Radisic M, Gramolini A, Emili A. Mapping signalling perturbations in myocardial fibrosis via the integrative phosphoproteomic profiling of tissue from diverse sources. Nat Biomed Eng. 2020 09; 4(9):889-900. PMID: 32661320

Wolf EJ, Miles A, Lee ES, Nabeel-Shah S, Greenblatt JF, Palazzo AF, Tropepe V, Emili A. MKRN2 Physically Interacts with GLE1 to Regulate mRNA Export and Zebrafish Retinal Development. Cell Rep. 2020 05 26; 31(8):107693. PMID: 32460013

Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst. 2020 04 22; 10(4):333-350.e14.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Wolozin, Benjamin
Bryant, Camron
Apicco, Daniel
Ash, Peter

PMID: 32325033; PMCID: PMC7938770; DOI: 10.1016/j.cels.2020.03.003;

Muraoka S, Lin W, Chen M, Hersh SW, Emili A, Xia W, Ikezu T. Assessment of separation methods for extracellular vesicles from human and mouse brain tissues and human cerebrospinal fluids. Methods. 2020 05 01; 177:35-49.View Related Profiles.

Emili, Andrew
Ikezu, Tsuneya
Xia, Weiming
Lin, Weiwei

PMID: 32035230; PMCID: PMC7667497; DOI: 10.1016/j.ymeth.2020.02.002;

Chen J, Haller CA, Jernigan FE, Koerner SK, Wong DJ, Wang Y, Cheong JE, Kosaraju R, Kwan J, Park DD, Thomas B, Bhasin S, De La Rosa RC, Premji AM, Liu L, Park E, Moss AC, Emili A, Bhasin M, Sun L, Chaikof EL. Modulation of lymphocyte-mediated tissue repair by rational design of heterocyclic aryl hydrocarbon receptor agonists. Sci Adv. 2020 01; 6(3):eaay8230.View Related Profiles.

Moss, Alan
Emili, Andrew

PMID: 31998845; PMCID: PMC6962035; DOI: 10.1126/sciadv.aay8230;

Ruan QT, Yazdani N, Blum BC, Beierle JA, Lin W, Coelho MA, Fultz EK, Healy AF, Shahin JR, Kandola AK, Luttik KP, Zheng K, Smith NJ, Cheung J, Mortazavi F, Apicco DJ, Ragu Varman D, Ramamoorthy S, Ash PEA, Rosene DL, Emili A, Wolozin B, Szumlinski KK, Bryant CD. A Mutation in Hnrnph1 That Decreases Methamphetamine-Induced Reinforcement, Reward, and Dopamine Release and Increases Synaptosomal hnRNP H and Mitochondrial Proteins. J Neurosci. 2020 01 02; 40(1):107-130.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Wolozin, Benjamin
Bryant, Camron
Apicco, Daniel
Rosene, Douglas
Mortazavi, Farzad
Beierle, Jacob
Yazdani, Neema
Ash, Peter
Lin, Weiwei

PMID: 31704785; PMCID: PMC6939476; DOI: 10.1523/JNEUROSCI.1808-19.2019;

Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A. EPIC: software toolkit for elution profile-based inference of protein complexes. Nat Methods. 2019 08; 16(8):737-742. PMID: 31308550; PMCID: PMC7995176; DOI: 10.1038/s41592-019-0461-4;

Vajda S, Emili A. Mapping global protein contacts. Science. 2019 07 12; 365(6449):120-121. PMID: 31296755; PMCID: PMC7299175; DOI: 10.1126/science.aay1440;

O'Meara TR, O'Meara MJ, Polvi EJ, Pourhaghighi MR, Liston SD, Lin ZY, Veri AO, Emili A, Gingras AC, Cowen LE. Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen. PLoS Biol. 2019 07; 17(7):e3000358. PMID: 31283755; PMCID: PMC6638986; DOI: 10.1371/journal.pbio.3000358;

Mohtar O, Ozdemir C, Roy D, Shantaram D, Emili A, Kandror KV. Egr1 mediates the effect of insulin on leptin transcription in adipocytes. J Biol Chem. 2019 04 12; 294(15):5784-5789.View Related Profiles.

Emili, Andrew
Roy, Debasish
Kandror, Konstantin
Mohtar, Omar

PMID: 30846562; PMCID: PMC6463691; DOI: 10.1074/jbc.AC119.007855;

Pourhaghighi R, O'Meara TR, Cowen LE, Emili A. Protein-Protein Interaction Profiling in Candida albicans Revealed by Biochemical Purification-Mass Spectrometry (BP/MS). Methods Mol Biol. 2019; 2049:203-211. PMID: 31602613

Pourhaghighi R, Emili A. Two-Dimensional Biochemical Purification for Global Proteomic Analysis of Macromolecular Protein Complexes. Methods Mol Biol. 2019; 1871:445-454. PMID: 30276754

Blum BC, Mousavi F, Emili A. Single-platform 'multi-omic' profiling: unified mass spectrometry and computational workflows for integrative proteomics-metabolomics analysis. Mol Omics. 2018 10 08; 14(5):307-319.View Related Profiles.

Emili, Andrew
Blum, Benjamin

PMID: 30211418

Rodionova IA, Goodacre N, Babu M, Emili A, Uetz P, Saier MH. The Nitrogen Regulatory PII Protein (GlnB) and N-Acetylglucosamine 6-Phosphate Epimerase (NanE) Allosterically Activate Glucosamine 6-Phosphate Deaminase (NagB) in Escherichia coli. J Bacteriol. 2018 03 01; 200(5). PMID: 29229699; PMCID: PMC5809692; DOI: 10.1128/JB.00691-17;

Pourhaghighi R, Emili A. Global Characterization of Protein Complexes by Biochemical Purification-Mass Spectrometry (BP/MS). Methods Mol Biol. 2018; 1764:185-191. PMID: 29605916

Goebels F, Hu L, Bader G, Emili A. Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data. Methods Mol Biol. 2018; 1764:391-399. PMID: 29605929

Yoon C, Song H, Yin T, Bausch-Fluck D, Frei AP, Kattman S, Dubois N, Witty AD, Hewel JA, Guo H, Emili A, Wollscheid B, Keller G, Zandstra PW. FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. Stem Cell Reports. 2018 01 09; 10(1):87-100. PMID: 29249665; PMCID: PMC5768897; DOI: 10.1016/j.stemcr.2017.11.008;

Sandhu C, Qureshi A, Emili A. Panomics for Precision Medicine. Trends Mol Med. 2018 01; 24(1):85-101. PMID: 29217119; PMCID: PMC5839674; DOI: 10.1016/j.molmed.2017.11.001;

Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A. Global landscape of cell envelope protein complexes in Escherichia coli. Nat Biotechnol. 2018 01; 36(1):103-112. PMID: 29176613; PMCID: PMC5922438; DOI: 10.1038/nbt.4024;

Mahadevan V, Khademullah CS, Dargaei Z, Chevrier J, Uvarov P, Kwan J, Bagshaw RD, Pawson T, Emili A, De Koninck Y, Anggono V, Airaksinen M, Woodin MA. Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition. Elife. 2017 Oct 13; 6. PMID: 29028184; PMCID: PMC5640428; DOI: 10.7554/eLife.28270;

Guo H, Peng H, Emili A. Mass spectrometry methods to study protein-metabolite interactions. Expert Opin Drug Discov. 2017 Dec; 12(12):1271-1280. PMID: 28933205

Havugimana PC, Hu P, Emili A. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks. Expert Rev Proteomics. 2017 Oct; 14(10):845-855. PMID: 28918672

Guo H, Isserlin R, Emili A, Burniston JG. Exercise-responsive phosphoproteins in the heart. J Mol Cell Cardiol. 2017 Oct; 111:61-68. PMID: 28826663

Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO. Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice. J Proteome Res. 2017 Aug 04; 16(8):2836-2847. PMID: 28641008

Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH. The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli. J Biol Chem. 2017 Aug 25; 292(34):14250-14257. PMID: 28634232; PMCID: PMC5572926; DOI: 10.1074/jbc.M117.795294;

Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Neel BG, Babu M, Gingras AC, Stagljar I. A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. Mol Cell. 2017 Jan 19; 65(2):347-360. PMID: 28065597; PMCID: PMC5663465; DOI: 10.1016/j.molcel.2016.12.004;

Kwan J, Sczaniecka A, Heidary Arash E, Nguyen L, Chen CC, Ratkovic S, Klezovitch O, Attisano L, McNeill H, Emili A, Vasioukhin V. DLG5 connects cell polarity and Hippo signaling protein networks by linking PAR-1 with MST1/2. Genes Dev. 2016 12 15; 30(24):2696-2709. PMID: 28087714; PMCID: PMC5238729; DOI: 10.1101/gad.284539.116;

Wells LA, Guo H, Emili A, Sefton MV. The profile of adsorbed plasma and serum proteins on methacrylic acid copolymer beads: Effect on complement activation. Biomaterials. 2017 Feb; 118:74-83. PMID: 27940384

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR. Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Res. 2016 Dec; 26(12):1742-1752. PMID: 27852650; PMCID: PMC5131825; DOI: 10.1101/gr.209643.116;

Kuzmanov U, Guo H, Buchsbaum D, Cosme J, Abbasi C, Isserlin R, Sharma P, Gramolini AO, Emili A. Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy. Proc Natl Acad Sci U S A. 2016 11 01; 113(44):12592-12597. PMID: 27742792; PMCID: PMC5098613; DOI: 10.1073/pnas.1606444113;

Gagarinova A, Stewart G, Samanfar B, Phanse S, White CA, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown ED, Babu M, Emili A. Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery. Cell Rep. 2016 Oct 11; 17(3):904-916. PMID: 27732863

Peng H, Guo H, Pogoutse O, Wan C, Hu LZ, Ni Z, Emili A. An Unbiased Chemical Proteomics Method Identifies FabI as the Primary Target of 6-OH-BDE-47. Environ Sci Technol. 2016 Oct 18; 50(20):11329-11336. PMID: 27682841

Kozlowski HN, Lai ET, Havugimana PC, White C, Emili A, Sakac D, Binnington B, Neschadim A, McCarthy SD, Branch DR. Extracellular histones identified in crocodile blood inhibit in-vitro HIV-1 infection. AIDS. 2016 Aug 24; 30(13):2043-52. PMID: 27191975

Olsen JB, Wong L, Deimling S, Miles A, Guo H, Li Y, Zhang Z, Greenblatt JF, Emili A, Tropepe V. G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. Stem Cell Reports. 2016 Sep 13; 7(3):454-470. PMID: 27546533; PMCID: PMC5031922; DOI: 10.1016/j.stemcr.2016.06.012;

Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep. 2016 Jan 26; 14(3):648-61. PMID: 26774489; DOI: 10.1016/j.celrep.2015.12.060;

Kwan JHM, Emili A. Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways. Methods Mol Biol. 2016; 1394:181-187. PMID: 26700049

Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data Brief. 2016 Mar; 6:715-21. PMID: 26870755; PMCID: PMC4738005; DOI: 10.1016/j.dib.2015.11.062;

Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A. Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics. Elife. 2015 Sep 29; 4. PMID: 26418743; PMCID: PMC4630677; DOI: 10.7554/eLife.09579;

Guo H, Garcia-Vedrenne AE, Isserlin R, Lugowski A, Morada A, Sun A, Miao Y, Kuzmanov U, Wan C, Ma H, Foltz K, Emili A. Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation. Proteomics. 2015 Dec; 15(23-24):4080-95. PMID: 26227301; DOI: 10.1002/pmic.201500159;

Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Panorama of ancient metazoan macromolecular complexes. Nature. 2015 Sep 17; 525(7569):339-44. PMID: 26344197; PMCID: PMC5036527; DOI: 10.1038/nature14877;

Cassar PA, Carpenedo RL, Samavarchi-Tehrani P, Olsen JB, Park CJ, Chang WY, Chen Z, Choey C, Delaney S, Guo H, Guo H, Tanner RM, Perkins TJ, Tenenbaum SA, Emili A, Wrana JL, Gibbings D, Stanford WL. Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. EMBO Rep. 2015 Oct; 16(10):1334-57. PMID: 26265008; PMCID: PMC4670460; DOI: 10.15252/embr.201540974;

Chamberlain MD, Wells LA, Lisovsky A, Guo H, Isserlin R, Talior-Volodarsky I, Mahou R, Emili A, Sefton MV. Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages. Proc Natl Acad Sci U S A. 2015 Aug 25; 112(34):10673-8. PMID: 26261332; PMCID: PMC4553830; DOI: 10.1073/pnas.1508826112;

Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods. 2015 Aug; 12(8):725-31. PMID: 26121405; DOI: 10.1038/nmeth.3472;

Pu S, Vlasblom J, Turinsky A, Marcon E, Phanse S, Trimble SS, Olsen J, Greenblatt J, Emili A, Wodak SJ. Extracting high confidence protein interactions from affinity purification data: at the crossroads. J Proteomics. 2015 Apr 06; 118:63-80. PMID: 25782749; DOI: 10.1016/j.jprot.2015.03.009;

Gagarinova A, Emili A. Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. Adv Exp Med Biol. 2015; 883:21-40. PMID: 26621460; DOI: 10.1007/978-3-319-23603-2_2;

Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. Mol Biosyst. 2015 Jan; 11(1):239-51. PMID: 25361207; PMCID: PMC4856157; DOI: 10.1039/c4mb00265b;

Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics. 2015 Feb 01; 31(3):306-10. PMID: 25316676; PMCID: PMC4308668; DOI: 10.1093/bioinformatics/btu671;

Guo H, Isserlin R, Lugowski A, Kuzmanov U, Emili A. Large-scale label-free phosphoproteomics: from technology to data interpretation. Bioanalysis. 2014 Sep; 6(18):2403-20. PMID: 25384593; DOI: 10.4155/bio.14.188;

Salvi JS, Chan JN, Szafranski K, Liu TT, Wu JD, Olsen JB, Khanam N, Poon BP, Emili A, Mekhail K. Roles for Pbp1 and caloric restriction in genome and lifespan maintenance via suppression of RNA-DNA hybrids. Dev Cell. 2014 Jul 28; 30(2):177-91. PMID: 25073155

Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, Marcon E, Zhong G, Guo H, Kuo WW, Li J, Young P, Olsen JB, Wan C, Loppnau P, El Bakkouri M, Senisterra GA, He H, Huang H, Sidhu SS, Emili A, Murphy S, Mosley AL, Arrowsmith CH, Min J, Greenblatt JF. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat Struct Mol Biol. 2014 Aug; 21(8):686-695. PMID: 24997600; PMCID: PMC4124035; DOI: 10.1038/nsmb.2853;

Marcon E, Ni Z, Pu S, Turinsky AL, Trimble SS, Olsen JB, Silverman-Gavrila R, Silverman-Gavrila L, Phanse S, Guo H, Zhong G, Guo X, Young P, Bailey S, Roudeva D, Zhao D, Hewel J, Li J, Gräslund S, Paduch M, Kossiakoff AA, Lupien M, Emili A, Wodak SJ, Greenblatt J. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Rep. 2014 Jul 10; 8(1):297-310. PMID: 24981860; DOI: 10.1016/j.celrep.2014.05.050;

Albanese A, Walkey CD, Olsen JB, Guo H, Emili A, Chan WC. Secreted biomolecules alter the biological identity and cellular interactions of nanoparticles. ACS Nano. 2014 Jun 24; 8(6):5515-26. PMID: 24797313; DOI: 10.1021/nn4061012;

Walkey CD, Olsen JB, Song F, Liu R, Guo H, Olsen DW, Cohen Y, Emili A, Chan WC. Protein corona fingerprinting predicts the cellular interaction of gold and silver nanoparticles. ACS Nano. 2014 Mar 25; 8(3):2439-55. PMID: 24517450; DOI: 10.1021/nn406018q;

Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P. The binary protein-protein interaction landscape of Escherichia coli. Nat Biotechnol. 2014 Mar; 32(3):285-290. PMID: 24561554; PMCID: PMC4123855; DOI: 10.1038/nbt.2831;

Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet. 2014 Feb; 10(2):e1004120. PMID: 24586182; PMCID: PMC3930520; DOI: 10.1371/journal.pgen.1004120;

Toledo CM, Herman JA, Olsen JB, Ding Y, Corrin P, Girard EJ, Olson JM, Emili A, DeLuca JG, Paddison PJ. BuGZ is required for Bub3 stability, Bub1 kinetochore function, and chromosome alignment. Dev Cell. 2014 Feb 10; 28(3):282-94. PMID: 24462187; PMCID: PMC3995079; DOI: 10.1016/j.devcel.2013.12.014;

Wong KS, Snider JD, Graham C, Greenblatt JF, Emili A, Babu M, Houry WA. The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli. PLoS One. 2014; 9(1):e85529. PMID: 24454883; PMCID: PMC3893208; DOI: 10.1371/journal.pone.0085529;

Dagley LF, White CA, Liao Y, Shi W, Smyth GK, Orian JM, Emili A, Purcell AW. Quantitative proteomic profiling reveals novel region-specific markers in the adult mouse brain. Proteomics. 2014 Feb; 14(2-3):241-61. PMID: 24259518

Dagley LF, Croft NP, Isserlin R, Olsen JB, Fong V, Emili A, Purcell AW. Discovery of novel disease-specific and membrane-associated candidate markers in a mouse model of multiple sclerosis. Mol Cell Proteomics. 2014 Mar; 13(3):679-700. PMID: 24361864; PMCID: PMC3945902; DOI: 10.1074/mcp.M113.033340;

Kuzmanov U, Emili A. Using phosphoproteomics to monitor disregulated signaling networks in cardiac disease preceding heart failure. Bioanalysis. 2013 Dec; 5(23):2863-6. PMID: 24295112; DOI: 10.4155/bio.13.271;

Vizeacoumar FJ, Arnold R, Vizeacoumar FS, Chandrashekhar M, Buzina A, Young JT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J. A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Mol Syst Biol. 2013 Oct 08; 9:696. PMID: 24104479; PMCID: PMC3817404; DOI: 10.1038/msb.2013.54;

Lam MH, Emili A. Ubp2 regulates Rsp5 ubiquitination activity in vivo and in vitro. PLoS One. 2013; 8(9):e75372. PMID: 24069405; PMCID: PMC3777918; DOI: 10.1371/journal.pone.0075372;

Hansen AM, Chaerkady R, Sharma J, Díaz-Mejía JJ, Tyagi N, Renuse S, Jacob HK, Pinto SM, Sahasrabuddhe NA, Kim MS, Delanghe B, Srinivasan N, Emili A, Kaper JB, Pandey A. The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathog. 2013; 9(6):e1003403. PMID: 23785281; PMCID: PMC3681748; DOI: 10.1371/journal.ppat.1003403;

Kuzmanov U, Emili A. Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med. 2013; 5(4):37. PMID: 23635424; PMCID: PMC3706760; DOI: 10.1186/gm441;

Guo H, Isserlin R, Chen X, Wang W, Phanse S, Zandstra PW, Paddison PJ, Emili A. Integrative network analysis of signaling in human CD34(+) hematopoietic progenitor cells by global phosphoproteomic profiling using TiO2 enrichment combined with 2D LC-MS/MS and pathway mapping. Proteomics. 2013 Apr; 13(8):1325-33. PMID: 23401153; PMCID: PMC3883140; DOI: 10.1002/pmic.201200369;

Chung C, Emili A, Frey BJ. Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. Bioinformatics. 2013 Apr 01; 29(7):821-9. PMID: 23419374

Vuckovic D, Dagley LF, Purcell AW, Emili A. Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges. Proteomics. 2013 Feb; 13(3-4):404-23. PMID: 23125154; DOI: 10.1002/pmic.201200340;

James LI, Barsyte-Lovejoy D, Zhong N, Krichevsky L, Korboukh VK, Herold JM, MacNevin CJ, Norris JL, Sagum CA, Tempel W, Marcon E, Guo H, Gao C, Huang XP, Duan S, Emili A, Greenblatt JF, Kireev DB, Jin J, Janzen WP, Brown PJ, Bedford MT, Arrowsmith CH, Frye SV. Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol. 2013 Mar; 9(3):184-91. PMID: 23292653; PMCID: PMC3577944; DOI: 10.1038/nchembio.1157;

Dagley LF, Emili A, Purcell AW. Application of quantitative proteomics technologies to the biomarker discovery pipeline for multiple sclerosis. Proteomics Clin Appl. 2013 Jan; 7(1-2):91-108. PMID: 23112123

Cosme J, Emili A, Gramolini AO. Large-scale characterization of the murine cardiac proteome. Methods Mol Biol. 2013; 1005:1-10. PMID: 23606244

Isserlin R, Merico D, Emili A. Global proteomic profiling and enrichment maps of dilated cardiomyopathy. Methods Mol Biol. 2013; 1005:53-66. PMID: 23606248

Babu M, Kagan O, Guo H, Greenblatt J, Emili A. Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry. J Vis Exp. 2012 Nov 12; (69). PMID: 23168686; PMCID: PMC3520577; DOI: 10.3791/4057;

Gagarinova A, Babu M, Greenblatt J, Emili A. Mapping bacterial functional networks and pathways in Escherichia Coli using synthetic genetic arrays. J Vis Exp. 2012 Nov 12; (69). PMID: 23168417; PMCID: PMC3520574; DOI: 10.3791/4056;

Hewel JA, Phanse S, Liu J, Bousette N, Gramolini A, Emili A. Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring. J Proteomics. 2013 Apr 09; 81:159-72. PMID: 23124093; DOI: 10.1016/j.jprot.2012.10.020;

Wan C, Liu J, Fong V, Lugowski A, Stoilova S, Bethune-Waddell D, Borgeson B, Havugimana PC, Marcotte EM, Emili A. 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. J Proteomics. 2013 Apr 09; 81:102-11. PMID: 23063720; DOI: 10.1016/j.jprot.2012.10.001;

Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, Burston HE, Vizeacoumar FJ, Snider J, Phanse S, Fong V, Tam YY, Davey M, Hnatshak O, Bajaj N, Chandran S, Punna T, Christopolous C, Wong V, Yu A, Zhong G, Li J, Stagljar I, Conibear E, Wodak SJ, Emili A, Greenblatt JF. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature. 2012 Sep 27; 489(7417):585-9. PMID: 22940862; DOI: 10.1038/nature11354;

Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A. A census of human soluble protein complexes. Cell. 2012 Aug 31; 150(5):1068-81. PMID: 22939629; PMCID: PMC3477804; DOI: 10.1016/j.cell.2012.08.011;

Makhnevych T, Wong P, Pogoutse O, Vizeacoumar FJ, Greenblatt JF, Emili A, Houry WA. Hsp110 is required for spindle length control. J Cell Biol. 2012 Aug 20; 198(4):623-36. PMID: 22908312; PMCID: PMC3514029; DOI: 10.1083/jcb.201111105;

Tattoli I, Sorbara MT, Vuckovic D, Ling A, Soares F, Carneiro LA, Yang C, Emili A, Philpott DJ, Girardin SE. Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program. Cell Host Microbe. 2012 Jun 14; 11(6):563-75. PMID: 22704617; DOI: 10.1016/j.chom.2012.04.012;

Gagarinova A, Emili A. Genome-scale genetic manipulation methods for exploring bacterial molecular biology. Mol Biosyst. 2012 Jun; 8(6):1626-38. PMID: 22517266; DOI: 10.1039/c2mb25040c;

Chan JN, Vuckovic D, Sleno L, Olsen JB, Pogoutse O, Havugimana P, Hewel JA, Bajaj N, Wang Y, Musteata MF, Nislow C, Emili A. Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization. Mol Cell Proteomics. 2012 Jul; 11(7):M111.016642. PMID: 22357554; PMCID: PMC3394955; DOI: 10.1074/mcp.M111.016642;

Walkey CD, Olsen JB, Guo H, Emili A, Chan WC. Nanoparticle size and surface chemistry determine serum protein adsorption and macrophage uptake. J Am Chem Soc. 2012 Feb 01; 134(4):2139-47. PMID: 22191645; DOI: 10.1021/ja2084338;

Brown RB, Hewel JA, Emili A, Audet J. Identification of enzyme-converted peptide products from single cells using capillary electrophoresis and liquid chromatography-mass spectrometry. Methods Mol Biol. 2012; 853:17-28. PMID: 22323137; DOI: 10.1007/978-1-61779-567-1_3;

Musso G, Emili A, Zhang Z. Characterization and evolutionary analysis of protein-protein interaction networks. Methods Mol Biol. 2012; 856:363-80. PMID: 22399467

Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 2011 Nov; 7(11):e1002377. PMID: 22125496; PMCID: PMC3219608; DOI: 10.1371/journal.pgen.1002377;

Ni Z, Olsen JB, Guo X, Zhong G, Ruan ED, Marcon E, Young P, Guo H, Li J, Moffat J, Emili A, Greenblatt JF. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Transcription. 2011 Sep-Oct; 2(5):237-42. PMID: 22231121; PMCID: PMC3265782; DOI: 10.4161/trns.2.5.17803;

Chan JN, Poon BP, Salvi J, Olsen JB, Emili A, Mekhail K. Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains. Dev Cell. 2011 Jun 14; 20(6):867-79. PMID: 21664583

Babu M, Aoki H, Chowdhury WQ, Gagarinova A, Graham C, Phanse S, Laliberte B, Sunba N, Jessulat M, Golshani A, Emili A, Greenblatt JF, Ganoza MC. Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation. PLoS One. 2011 Apr 27; 6(4):e18510. PMID: 21556145; PMCID: PMC3083400; DOI: 10.1371/journal.pone.0018510;

Chung C, Liu J, Emili A, Frey BJ. Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinformatics. 2011 Mar 15; 27(6):797-806. PMID: 21258065; PMCID: PMC3051323; DOI: 10.1093/bioinformatics/btr017;

Ni Z, Olsen JB, Emili A, Greenblatt JF. Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry. Methods Mol Biol. 2011; 781:31-45. PMID: 21877275

Musso G, Emili A, Zhang Z. Filtering and interpreting large-scale experimental protein-protein interaction data. Methods Mol Biol. 2011; 781:295-309. PMID: 21877287

Babu M, Gagarinova A, Emili A. Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol. 2011; 781:99-126. PMID: 21877280; DOI: 10.1007/978-1-61779-276-2_7;

Babu M, Gagarinova A, Greenblatt J, Emili A. Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol Biol. 2011; 765:125-53. PMID: 21815091; DOI: 10.1007/978-1-61779-197-0_9;

Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol. 2011 Jan; 79(2):484-502. PMID: 21219465; PMCID: PMC3071548; DOI: 10.1111/j.1365-2958.2010.07465.x;

Pu S, Turinsky AL, Vlasblom J, On T, Xiong X, Emili A, Zhang Z, Greenblatt J, Parkinson J, Wodak SJ. Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PLoS One. 2010 Nov 29; 5(11):e14122. PMID: 21124763; PMCID: PMC2993927; DOI: 10.1371/journal.pone.0014122;

Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One. 2010 Nov 15; 5(11):e13984. PMID: 21085593; PMCID: PMC2981572; DOI: 10.1371/journal.pone.0013984;

Babu M, Greenblatt JF, Emili A, Strynadka NC, Reithmeier RA, Moraes TF. Structure of a SLC26 anion transporter STAS domain in complex with acyl carrier protein: implications for E. coli YchM in fatty acid metabolism. Structure. 2010 Nov 10; 18(11):1450-62. PMID: 21070944; DOI: 10.1016/j.str.2010.08.015;

Bousette N, Chugh S, Fong V, Isserlin R, Kim KH, Volchuk A, Backx PH, Liu P, Kislinger T, MacLennan DH, Emili A, Gramolini AO. Constitutively active calcineurin induces cardiac endoplasmic reticulum stress and protects against apoptosis that is mediated by alpha-crystallin-B. Proc Natl Acad Sci U S A. 2010 Oct 26; 107(43):18481-6. PMID: 20937869; PMCID: PMC2972971; DOI: 10.1073/pnas.1013555107;

Turinsky AL, Turner B, Borja RC, Gleeson JA, Heath M, Pu S, Switzer T, Dong D, Gong Y, On T, Xiong X, Emili A, Greenblatt J, Parkinson J, Zhang Z, Wodak SJ. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Res. 2011 Jan; 39(Database issue):D889-94. PMID: 20876685; PMCID: PMC3013761; DOI: 10.1093/nar/gkq857;

Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010 Jul 30; 329(5991):533-8. PMID: 20671182; PMCID: PMC2922915; DOI: 10.1126/science.1188308;

On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 2010 Jul; 78(9):2075-89. PMID: 20455264

Hewel JA, Liu J, Onishi K, Fong V, Chandran S, Olsen JB, Pogoutse O, Schutkowski M, Wenschuh H, Winkler DF, Eckler L, Zandstra PW, Emili A. Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics. 2010 Nov; 9(11):2460-73. PMID: 20467045; PMCID: PMC2984235; DOI: 10.1074/mcp.M900456-MCP200;

Brown RB, Hewel JA, Emili A, Audet J. Single amino acid resolution of proteolytic fragments generated in individual cells. Cytometry A. 2010 Apr; 77(4):347-55. PMID: 20187109; DOI: 10.1002/cyto.a.20880;

Mak AB, Ni Z, Hewel JA, Chen GI, Zhong G, Karamboulas K, Blakely K, Smiley S, Marcon E, Roudeva D, Li J, Olsen JB, Wan C, Punna T, Isserlin R, Chetyrkin S, Gingras AC, Emili A, Greenblatt J, Moffat J. A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics. 2010 May; 9(5):811-23. PMID: 20305087; PMCID: PMC2871416; DOI: 10.1074/mcp.M000002-MCP201;

Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics. 2010 Mar; 10(6):1316-27. PMID: 20127684; PMCID: PMC2879143; DOI: 10.1002/pmic.200900412;

Hu P, Jiang H, Emili A. Predicting protein functions by relaxation labelling protein interaction network. BMC Bioinformatics. 2010 Jan 18; 11 Suppl 1:S64. PMID: 20122240; PMCID: PMC3009538; DOI: 10.1186/1471-2105-11-S1-S64;

Chan JN, Nislow C, Emili A. Recent advances and method development for drug target identification. Trends Pharmacol Sci. 2010 Feb; 31(2):82-8. PMID: 20004028

Kim HS, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bähler J, Keogh MC. An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Nat Struct Mol Biol. 2009 Dec; 16(12):1286-93. PMID: 19915592; PMCID: PMC2788674; DOI: 10.1038/nsmb.1688;

Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA. 2009 Dec; 15(12):2174-85. PMID: 19789211; PMCID: PMC2779666; DOI: 10.1261/rna.1790509;

Babu M, Musso G, Díaz-Mejía JJ, Butland G, Greenblatt JF, Emili A. Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes. Mol Biosyst. 2009 Dec; 5(12):1439-55. PMID: 19763343; DOI: 10.1039/B907407d;

White CA, Oey N, Emili A. Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis. J Proteome Res. 2009 Jul; 8(7):3653-65. PMID: 19400582

Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA. An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol. 2009; 5:275. PMID: 19536198; PMCID: PMC2710862; DOI: 10.1038/msb.2009.26;

Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 2009 Apr 28; 7(4):e96. PMID: 19402753; PMCID: PMC2672614; DOI: 10.1371/journal.pbio.1000096;

Handford JI, Ize B, Buchanan G, Butland GP, Greenblatt J, Emili A, Palmer T. Conserved network of proteins essential for bacterial viability. J Bacteriol. 2009 Aug; 191(15):4732-49. PMID: 19376873; PMCID: PMC2715707; DOI: 10.1128/JB.00136-09;

Chugh S, Liu P, Emili A, Gramolini A. Large-scale studies to identify biomarkers for heart disease: a role for proteomics? Expert Opin Med Diagn. 2009 Mar; 3(2):133-41. PMID: 23485160

Lam MH, Urban-Grimal D, Bugnicourt A, Greenblatt JF, Haguenauer-Tsapis R, Emili A. 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; 4(1):e4259. PMID: 19165343; PMCID: PMC2626285; DOI: 10.1371/journal.pone.0004259;

Babu M, Butland G, Pogoutse O, Li J, Greenblatt JF, Emili A. Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli. Methods Mol Biol. 2009; 564:373-400. PMID: 19544035; DOI: 10.1007/978-1-60761-157-8_22;

Babu M, Krogan NJ, Awrey DE, Emili A, Greenblatt JF. Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. Methods Mol Biol. 2009; 548:187-207. PMID: 19521826; DOI: 10.1007/978-1-59745-540-4_11;

Díaz-Mejía JJ, Babu M, Emili A. Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. FEMS Microbiol Rev. 2009 Jan; 33(1):66-97. PMID: 19054114; PMCID: PMC2704936; DOI: 10.1111/j.1574-6976.2008.00141.x;

Liu J, Erassov A, Halina P, Canete M, Nguyen DV, Chung C, Cagney G, Ignatchenko A, Fong V, Emili A. Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications. Anal Chem. 2008 Oct 15; 80(20):7846-54. PMID: 18788753

Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, Emili A. eSGA: E. coli synthetic genetic array analysis. Nat Methods. 2008 Sep; 5(9):789-95. PMID: 18677321; DOI: 10.1038/nmeth.1239;

Hewel JA, Emili A. High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates. Proteomics Clin Appl. 2008 Oct; 2(10-11):1422-34. PMID: 21136791; DOI: 10.1002/prca.200800030;

Lüke I, Butland G, Moore K, Buchanan G, Lyall V, Fairhurst SA, Greenblatt JF, Emili A, Palmer T, Sargent F. Biosynthesis of the respiratory formate dehydrogenases from Escherichia coli: characterization of the FdhE protein. Arch Microbiol. 2008 Dec; 190(6):685-96. PMID: 18716757

Isserlin R, Emili A. Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery. Curr Opin Mol Ther. 2008 Jun; 10(3):231-42. PMID: 18535930

Musso G, Costanzo M, Huangfu M, Smith AM, Paw J, San Luis BJ, Boone C, Giaever G, Nislow C, Emili A, Zhang Z. The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res. 2008 Jul; 18(7):1092-9. PMID: 18463300; PMCID: PMC2493398; DOI: 10.1101/gr.076174.108;

Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, Allis CD, Keogh MC, Greenblatt JF. Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol. 2008 Jul; 28(13):4342-53. PMID: 18458063; PMCID: PMC2447148; DOI: 10.1128/MCB.00182-08;

Sleno L, Emili A. Proteomic methods for drug target discovery. Curr Opin Chem Biol. 2008 Feb; 12(1):46-54. PMID: 18282485

Sandhu C, Hewel JA, Badis G, Talukder S, Liu J, Hughes TR, Emili A. Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer. J Proteome Res. 2008 Apr; 7(4):1529-41. PMID: 18311902; DOI: 10.1021/pr700836q;

Aoki H, Xu J, Emili A, Chosay JG, Golshani A, Ganoza MC. Interactions of elongation factor EF-P with the Escherichia coli ribosome. FEBS J. 2008 Feb; 275(4):671-81. PMID: 18201202

Ghavidel A, Kislinger T, Pogoutse O, Sopko R, Jurisica I, Emili A. Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint. Cell. 2007 Nov 30; 131(5):915-26. PMID: 18045534

Gramolini AO, Kislinger T, Alikhani-Koopaei R, Fong V, Thompson NJ, Isserlin R, Sharma P, Oudit GY, Trivieri MG, Fagan A, Kannan A, Higgins DG, Huedig H, Hess G, Arab S, Seidman JG, Seidman CE, Frey B, Perry M, Backx PH, Liu PP, MacLennan DH, Emili A. Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Mol Cell Proteomics. 2008 Mar; 7(3):519-33. PMID: 18056057

Arab S, Liu PP, Emili A. Lost in translation: five grand challenges for proteomic biomarker discovery. Expert Opin Med Diagn. 2007 Nov; 1(3):325-36. PMID: 23489353

Su C, Peregrin-Alvarez JM, Butland G, Phanse S, Fong V, Emili A, Parkinson J. Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res. 2008 Jan; 36(Database issue):D632-6. PMID: 17942431; PMCID: PMC2238847; DOI: 10.1093/nar/gkm807;

Suter B, Pogoutse O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A. Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p. BMC Biol. 2007 Sep 19; 5:38. PMID: 17880717; PMCID: PMC2140264; DOI: 10.1186/1741-7007-5-38;

Isserlin R, Emili A. 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 Clin Appl. 2007 Sep; 1(9):1156-68. PMID: 21136765

Ouzounian M, Lee DS, Gramolini AO, Emili A, Fukuoka M, Liu PP. Predict, prevent and personalize: Genomic and proteomic approaches to cardiovascular medicine. Can J Cardiol. 2007 Aug; 23 Suppl A:28A-33A. PMID: 17668085; PMCID: PMC2787001; DOI: 10.1016/s0828-282x(07)71003-6;

Musso GA, Zhang Z, Emili A. Experimental and computational procedures for the assessment of protein complexes on a genome-wide scale. Chem Rev. 2007 Aug; 107(8):3585-600. PMID: 17630806

Cox B, Kislinger T, Wigle DA, Kannan A, Brown K, Okubo T, Hogan B, Jurisica I, Frey B, Rossant J, Emili A. Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Mol Syst Biol. 2007; 3:109. PMID: 17486137; PMCID: PMC2673710; DOI: 10.1038/msb4100151;

Woolaway K, Asai K, Emili A, Cochrane A. hnRNP E1 and E2 have distinct roles in modulating HIV-1 gene expression. Retrovirology. 2007 Apr 23; 4:28. PMID: 17451601; PMCID: PMC1863430; DOI: 10.1186/1742-4690-4-28;

Li X, Kusmierczyk AR, Wong P, Emili A, Hochstrasser M. beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. EMBO J. 2007 May 02; 26(9):2339-49. PMID: 17431397; PMCID: PMC1864979; DOI: 10.1038/sj.emboj.7601681;

Musso G, Zhang Z, Emili A. Retention of protein complex membership by ancient duplicated gene products in budding yeast. Trends Genet. 2007 Jun; 23(6):266-9. PMID: 17428571

Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics. 2007 Mar; 7(6):944-60. PMID: 17370254

Najmabadi P, Goldenberg AA, Emili A. Hardware flexibility of laboratory automation systems: analysis and new flexible automation architectures. Clin Lab Med. 2007 Mar; 27(1):1-28. PMID: 17416299

Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007 Apr 12; 446(7137):806-10. PMID: 17314980

Butland G, Krogan NJ, Xu J, Yang WH, Aoki H, Li JS, Krogan N, Menendez J, Cagney G, Kiani GC, Jessulat MG, Datta N, Ivanov I, Abouhaidar MG, Emili A, Greenblatt J, Ganoza MC, Golshani A. Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs. J Cell Biochem. 2007 Feb 15; 100(3):642-52. PMID: 16983699

Listgarten J, Neal RM, Roweis ST, Wong P, Emili A. Difference detection in LC-MS data for protein biomarker discovery. Bioinformatics. 2007 Jan 15; 23(2):e198-204. PMID: 17237092

Gramolini AO, Kislinger T, Liu P, MacLennan DH, Emili A. Analyzing the cardiac muscle proteome by liquid chromatography-mass spectrometry-based expression proteomics. Methods Mol Biol. 2007; 357:15-31. PMID: 17172675; PMCID: PMC3706331; DOI: 10.1385/1-59745-214-9:15;

Hu P, Bader G, Wigle DA, Emili A. Computational prediction of cancer-gene function. Nat Rev Cancer. 2007 Jan; 7(1):23-34. PMID: 17167517

Havugimana PC, Wong P, Emili A. Improved proteomic discovery by sample pre-fractionation using dual-column ion-exchange high performance liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Feb 15; 847(1):54-61. PMID: 17140863

Arab S, Gramolini AO, Ping P, Kislinger T, Stanley B, van Eyk J, Ouzounian M, MacLennan DH, Emili A, Liu PP. Cardiovascular proteomics: tools to develop novel biomarkers and potential applications. J Am Coll Cardiol. 2006 Nov 07; 48(9):1733-41. PMID: 17084242

Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics. 2006 Jul 27; 7:365. PMID: 16872538; PMCID: PMC1557541; DOI: 10.1186/1471-2105-7-365;

Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell. 2006 Apr 07; 125(1):173-86. PMID: 16615898

Downey M, Houlsworth R, Maringele L, Rollie A, Brehme M, Galicia S, Guillard S, Partington M, Zubko MK, Krogan NJ, Emili A, Greenblatt JF, Harrington L, Lydall D, Durocher D. A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell. 2006 Mar 24; 124(6):1155-68. PMID: 16564010

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30; 440(7084):637-43. PMID: 16554755

Gramolini AO, Trivieri MG, Oudit GY, Kislinger T, Li W, Patel MM, Emili A, Kranias EG, Backx PH, Maclennan DH. Cardiac-specific overexpression of sarcolipin in phospholamban null mice impairs myocyte function that is restored by phosphorylation. Proc Natl Acad Sci U S A. 2006 Feb 14; 103(7):2446-51. PMID: 16461894; PMCID: PMC1413737; DOI: 10.1073/pnas.0510883103;

Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol. 2006; 2:2006.0003. PMID: 16738550; PMCID: PMC1681477; DOI: 10.1038/msb4100045;

Cox B, Emili A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Nat Protoc. 2006; 1(4):1872-8. PMID: 17487171

Butland G, Zhang JW, Yang W, Sheung A, Wong P, Greenblatt JF, Emili A, Zamble DB. Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation. FEBS Lett. 2006 Jan 23; 580(2):677-81. PMID: 16412426

Listgarten J, Emili A. Practical proteomic biomarker discovery: taking a step back to leap forward. Drug Discov Today. 2005 Dec; 10(23-24):1697-702. PMID: 16376831

Snider J, Gutsche I, Lin M, Baby S, Cox B, Butland G, Greenblatt J, Emili A, Houry WA. Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase. J Biol Chem. 2006 Jan 20; 281(3):1532-46. PMID: 16301313

Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Datta N, Galicia S, Emili A, Lieberman J, Shen X, Buratowski S, Haber JE, Durocher D, Greenblatt JF, Krogan NJ. A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature. 2006 Jan 26; 439(7075):497-501. PMID: 16299494

Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005 Nov 18; 123(4):593-605. PMID: 16286008

Roberts TM, Kobor MS, Bastin-Shanower SA, Ii M, Horte SA, Gin JW, Emili A, Rine J, Brill SJ, Brown GW. Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell. 2006 Jan; 17(1):539-48. PMID: 16267268; PMCID: PMC1345688; DOI: 10.1091/mbc.E05-08-0785;

Prather D, Krogan NJ, Emili A, Greenblatt JF, Winston F. Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Nov; 25(22):10122-35. PMID: 16260625; PMCID: PMC1280281; DOI: 10.1128/MCB.25.22.10122-10135.2005;

Gramolini AO, Emili A. Uncovering early markers of cardiac disease by proteomics: avoiding (heart) failure! Expert Rev Proteomics. 2005 Oct; 2(5):631-4. PMID: 16209642

Ghavidel A, Cagney G, Emili A. A skeleton of the human protein interactome. Cell. 2005 Sep 23; 122(6):830-2. PMID: 16179252

McCracken S, Longman D, Marcon E, Moens P, Downey M, Nickerson JA, Jessberger R, Wilde A, Caceres JF, Emili A, Blencowe BJ. Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin. J Biol Chem. 2005 Dec 23; 280(51):42227-36. PMID: 16159877; DOI: 10.1074/jbc.M507410200;

Cagney G, Park S, Chung C, Tong B, O'Dushlaine C, Shields DC, Emili A. Human tissue profiling with multidimensional protein identification technology. J Proteome Res. 2005 Sep-Oct; 4(5):1757-67. PMID: 16212430

Rosonina E, Ip JY, Calarco JA, Bakowski MA, Emili A, McCracken S, Tucker P, Ingles CJ, Blencowe BJ. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol. 2005 Aug; 25(15):6734-46. PMID: 16024807; PMCID: PMC1190332; DOI: 10.1128/MCB.25.15.6734-6746.2005;

Kislinger T, Gramolini AO, MacLennan DH, Emili A. Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue. J Am Soc Mass Spectrom. 2005 Aug; 16(8):1207-20. PMID: 15979338

Sandhu C, Connor M, Kislinger T, Slingerland J, Emili A. Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells. J Proteome Res. 2005 May-Jun; 4(3):674-89. PMID: 15952714

Kislinger T, Gramolini AO, Pan Y, Rahman K, MacLennan DH, Emili A. Proteome dynamics during C2C12 myoblast differentiation. Mol Cell Proteomics. 2005 Jul; 4(7):887-901. PMID: 15824125

Zhao R, Davey M, Hsu YC, Kaplanek P, Tong A, Parsons AB, Krogan N, Cagney G, Mai D, Greenblatt J, Boone C, Emili A, Houry WA. Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell. 2005 Mar 11; 120(5):715-27. PMID: 15766533

Maziarz M, Chung C, Drucker DJ, Emili A. Integrating global proteomic and genomic expression profiles generated from islet alpha cells: opportunities and challenges to deriving reliable biological inferences. Mol Cell Proteomics. 2005 Apr; 4(4):458-74. PMID: 15741311

Listgarten J, Emili A. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics. 2005 Apr; 4(4):419-34. PMID: 15741312

Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005 Feb 03; 433(7025):531-7. PMID: 15690043

Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL. H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol. 2005 Feb; 25(3):1162-72. PMID: 15657441; PMCID: PMC544016; DOI: 10.1128/MCB.25.3.1162-1172.2005;

Cox B, Kislinger T, Emili A. Integrating gene and protein expression data: pattern analysis and profile mining. Methods. 2005 Mar; 35(3):303-14. PMID: 15722226

Kislinger T, Emili A. Multidimensional protein identification technology: current status and future prospects. Expert Rev Proteomics. 2005 Jan; 2(1):27-39. PMID: 15966850

Krogan NJ, Lam MH, Fillingham J, Keogh MC, Gebbia M, Li J, Datta N, Cagney G, Buratowski S, Emili A, Greenblatt JF. Proteasome involvement in the repair of DNA double-strand breaks. Mol Cell. 2004 Dec 22; 16(6):1027-34. PMID: 15610744

Hannich JT, Lewis A, Kroetz MB, Li SJ, Heide H, Emili A, Hochstrasser M. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem. 2005 Feb 11; 280(6):4102-10. PMID: 15590687

Zhang JW, Butland G, Greenblatt JF, Emili A, Zamble DB. A role for SlyD in the Escherichia coli hydrogenase biosynthetic pathway. J Biol Chem. 2005 Feb 11; 280(6):4360-6. PMID: 15569666

Gramolini AO, Kislinger T, Asahi M, Li W, Emili A, MacLennan DH. Sarcolipin retention in the endoplasmic reticulum depends on its C-terminal RSYQY sequence and its interaction with sarco(endo)plasmic Ca(2+)-ATPases. Proc Natl Acad Sci U S A. 2004 Nov 30; 101(48):16807-12. PMID: 15556994; PMCID: PMC534750

Krogan NJ, Baetz K, Keogh MC, Datta N, Sawa C, Kwok TC, Thompson NJ, Davey MG, Pootoolal J, Hughes TR, Emili A, Buratowski S, Hieter P, Greenblatt JF. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci U S A. 2004 Sep 14; 101(37):13513-8. PMID: 15353583; PMCID: PMC518788

Radulovic D, Jelveh S, Ryu S, Hamilton TG, Foss E, Mao Y, Emili A. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics. 2004 Oct; 3(10):984-97. PMID: 15269249

Zeghouf M, Li J, Butland G, Borkowska A, Canadien V, Richards D, Beattie B, Emili A, Greenblatt JF. Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res. 2004 May-Jun; 3(3):463-8. PMID: 15253427

Pan Y, Kislinger T, Gramolini AO, Zvaritch E, Kranias EG, MacLennan DH, Emili A. Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics. Proc Natl Acad Sci U S A. 2004 Feb 24; 101(8):2241-6. PMID: 14982994; PMCID: PMC356935

Baetz KK, Krogan NJ, Emili A, Greenblatt J, Hieter P. 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. Mol Cell Biol. 2004 Feb; 24(3):1232-44. PMID: 14729968; PMCID: PMC321452

Krogan NJ, Peng WT, Cagney G, Robinson MD, Haw R, Zhong G, Guo X, Zhang X, Canadien V, Richards DP, Beattie BK, Lalev A, Zhang W, Davierwala AP, Mnaimneh S, Starostine A, Tikuisis AP, Grigull J, Datta N, Bray JE, Hughes TR, Emili A, Greenblatt JF. High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell. 2004 Jan 30; 13(2):225-39. PMID: 14759368

Liu H, Bonner AJ, Emili A. Modeling protein tandem mass spectrometry data with an extended linear regression strategy. Conf Proc IEEE Eng Med Biol Soc. 2004; 4:3055-9. PMID: 17270923

Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec; 12(6):1565-76. PMID: 14690608

Coppinger JA, Cagney G, Toomey S, Kislinger T, Belton O, McRedmond JP, Cahill DJ, Emili A, Fitzgerald DJ, Maguire PB. Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions. Blood. 2004 Mar 15; 103(6):2096-104. PMID: 14630798

Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003 Oct 17; 302(5644):449-53. PMID: 14564010

Cagney G, Amiri S, Premawaradena T, Lindo M, Emili A. In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci. 2003 Aug 13; 1(1):5. PMID: 12946274

Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR. A panoramic view of yeast noncoding RNA processing. Cell. 2003 Jun 27; 113(7):919-33. PMID: 12837249

Kislinger T, Emili A. Going global: protein expression profiling using shotgun mass spectrometry. Curr Opin Mol Ther. 2003 Jun; 5(3):285-93. PMID: 12870439

Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun; 23(12):4207-18. PMID: 12773564; PMCID: PMC427527

Suh D, Seguin B, Atkinson S, Ozdamar B, Staffa A, Emili A, Mouland A, Cochrane A. Mapping of determinants required for the function of the HIV-1 env nuclear retention sequence. Virology. 2003 May 25; 310(1):85-99. PMID: 12788633

Diehl JA, Yang W, Rimerman RA, Xiao H, Emili A. Hsc70 regulates accumulation of cyclin D1 and cyclin D1-dependent protein kinase. Mol Cell Biol. 2003 Mar; 23(5):1764-74. PMID: 12588994; PMCID: PMC151693

Jin S, Song YC, Emili A, Sherman PM, Chan VL. 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. Cell Microbiol. 2003 Mar; 5(3):165-74. PMID: 12614460

Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A. PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics. 2003 Feb; 2(2):96-106. PMID: 12644571

Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002 Oct; 22(20):6979-92. PMID: 12242279; PMCID: PMC139818

Emili A, Shales M, McCracken S, Xie W, Tucker PW, Kobayashi R, Blencowe BJ, Ingles CJ. Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA. 2002 Sep; 8(9):1102-11. PMID: 12358429; PMCID: PMC1370324

Cagney G, Emili A. De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging. Nat Biotechnol. 2002 Feb; 20(2):163-70. PMID: 11821862

Ahmed Z, Ravandi A, Maguire GF, Emili A, Draganov D, La Du BN, Kuksis A, Connelly PW. Multiple substrates for paraoxonase-1 during oxidation of phosphatidylcholine by peroxynitrite. Biochem Biophys Res Commun. 2002 Jan 11; 290(1):391-6. PMID: 11779181

Emili AQ, Cagney G. Large-scale functional analysis using peptide or protein arrays. Nat Biotechnol. 2000 Apr; 18(4):393-7. PMID: 10748518

Peng S, Liu LP, Emili AQ, Deber CM. Cystic fibrosis transmembrane conductance regulator: expression and helicity of a double membrane-spanning segment. FEBS Lett. 1998 Jul 10; 431(1):29-33. PMID: 9684859

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 223 publications over 22 distinct years, with a maximum of 22 publications in 2005