Donnelly Centre for Cellular and Biomolecular Research

Andrew Emili PhD
Contact Info
T: (416) 946-7281
Room 914
Research Interests
Proteomics, Functional Genomics, Molecular Biology, Bioinformatics

Please note that Dr. Emili has been appointed Director of the Center for Network Systems Biology at Boston University and can be reached at

View Dr. Emili's web page at Boston University



  • Fred Hutchinson Cancer Research Center, Seattle, WA, U.S., Research Fellow in its Division of Human Biology, 2000.
  • University of Toronto, PhD in Molecular and Medical Genetics, 1997.
  • University of Toronto, MSc in Molecular and Medical Genetics, 1993.


  • Department of Molecular Genetics, University of Toronto.


Charting the molecular networks of cells and tissues


In the same way a mechanic needs to know how each part of an engine works, scientists around the world are striving to understand how even the smallest part of a living organism functions. The better we understand how each part of the human engine works, the better we’ll be at diagnosing and treating disease. I use advanced technologies to investigate the biological roles and proprieties of the many different proteins and genes found in a typical organism or cell. My research team has outstanding skills in sophisticated, state-of-the-art techniques to investigate protein and gene function in a global, genome-wide manner. The team performs comprehensive studies of the complete set of gene products (the proteome) expressed by the genomes of a variety of model organisms, including budding yeast, the bacterium E. coli and mouse, using advanced proteomic, genomic and bioinformatics methods. We expect to contribute breakthrough understanding as to how cells and tissues function, and to translate this basic knowledge to enhance the clinical discovery of novel diagnostics and therapeutics. We are particularly working to identify protein biomarkers of early-stage disease, with an emphasis on cardiovascular disorders. 


schematic depicting interconnections between proteins

The Donnelly Centre offers an outstanding environment for collaborative, multi-disciplinary genomics research. Together we harness the power of new technologies with different areas of expertise to create pioneering studies into the molecular architecture of cells and tissues. Computer scientists guide the experientialists while technologists facilitate the studies of a cadre of biologists in a positive feedback loop. Collectively, our collaborations have afforded us the ability to explore previously inaccessible biological problems. Exciting new avenues for joint discovery are opening up. My lab’s collaborations range from computational data mining, multi-team efforts, to multi-lab data generation exercises.


Genes usually encode for proteins. Physical interactions between these proteins are essential to virtually all biological processes, and their disruption underlies most, if not all, of human pathology. Yet despite rapid advances in genomics, we still do not know which proteins work together to support human health and development, or which interactions are altered in important diseases such as cardiovascular disease, a major focus of my group, as well as cancer and neurodegeneration.   By systematically mapping protein interaction networks and identifying macromolecular complexes of exceptional biological, clinical and pharmaceutical value, my research program addresses fundamental questions:  What are the components and functions of protein complexes in different cells and organelles? What are the features and principles governing protein interaction networks in different tissues? How are macromolecular interaction networks organized during development under normal physiological conditions, and how are they perturbed in disease states?

Current projects include:

1. Identifying the complement of soluble protein complexes present in biomedically important cell types and tissues (e.g heart, blood, brain).

2. Mapping the physical interaction networks of membrane complexes that are key drug targets.

3. Defining the dynamic networks of protein interactions underlying development and disease using tractable model systems.

Using unique multidisciplinary approaches and our proven platform, we have already made excellent preliminary progress towards each of these three complementary objectives. The rich mechanistic insights arising from the many thousands of unexpected functional associations we are discovering will spearhead new high-impact publications and serve as lasting resources for biomedical researchers in many disciplines. Because improper connectivity leading to aberrant protein function is the root cause of pathology, our interaction maps also improve understanding of the molecular basis of common diseases, particularly heart disease, neurodegeneration, and cancer.

My research program aims to extend my laboratory’s international leadership in interaction network biology, recent investments in our world-class infrastructure, and our strong track record in mentorship and training.  We are world leaders in proteomics, molecular interaction mapping and biomarker discovery, and we publish global ‘connectivity’ diagrams of unprecedented quality, scope and resolution that are useful to hundreds of biomedical research teams.  My group continuously develops and uses innovative technologies to characterize macromolecules of broad clinical significance. We operate highly productive facilities for protein biochemistry, precision mass spectrometry, molecular biology and computational analysis. Our multidisciplinary research environment fosters entrepreneurial post-doctoral fellows and graduate students, who learn how to apply cutting-edge proteomic, genomic and bioinformatic techniques to solve important biomedical problems and who are exceptionally well prepared for independent biomedical research careers in network and ‘systems’ biology.       


  • Panorama of ancient metazoan macromolecular complexes. 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, R Tillier E, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Nature. 2015 Sep 17, 525: 339–344.
  • A census of human soluble protein complexes. 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. Cell. 2012 Aug 31;150(5):1068-81.

  • Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. 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. Nature. 2012 Sep 27;489(7417):585-9.  

View Pubmed search of Dr. Emili's full list of publications.