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

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

Professor
Boston University School of Medicine
Biochemistry

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 Sponsored Research

Mapping the blood cell protein complexosome
07/01/2017 - 05/31/2019 (PI)
University of Texas at Austin NIH NIDDK
1R01DK110520-01

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.

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 Mar 01; 200(5). PMID: 29229699.

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 Jan 09; 10(1):87-100. PMID: 29249665.

Sandhu C, Qureshi A, Emili A. Panomics for Precision Medicine. Trends Mol Med. 2018 Jan; 24(1):85-101. PMID: 29217119.

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 Jan; 36(1):103-112. PMID: 29176613.

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.

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.

Showing 10 of 194 results. Show More

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; 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.

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.

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.

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.

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 07. 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.

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.

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.

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.

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;.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 194 publications over 19 distinct years, with a maximum of 22 publications in 2005