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About the Emili Lab

Human health and development depend on dynamic networks of physical, and functional, interactions between proteins. However, the identity, composition and structure of the myriad of multiprotein ‘machines’ required by all essential cellular processes still largely unknown. Indeed, despite rapid progress in genomics and interaction mapping in simple models like microbes by us and others, it remains unclear which proteins associate together to form the different cell types and tissues of the body or how these networks go awry in important disorders like cancer, neurodegeneration, or cardiovascular disease. These questions form the basic focus of the Emili research laboratory.


Our group is recognized internationally for our groundbreaking work in Functional Proteomics, Protein Mass Spectrometry and Network Biology, and our goal is leadership in these competitive, evolving domains.


As a pioneer of 'interactome' science, our team is expert in the generation, analysis and translation of molecular interaction networks to explore fundamental biological processes and disease mechanisms. Our lab’s research output is prolific. Since 2000, we have performed >25,000 mass spectrometry experiments and have reported tens of thousands of protein interactions in diverse models, ranging from microbes to human cells.  


Because protein interactions are essential to proper development and health, and because defective protein assemblies underlie most pathologies, work by the Emili group is relevant to multiple biomedical disciplines, including mechanistic studies, structural modeling, protein annotation, experimental design, and healthcare. Our research findings are widely accessed via public databases, and our own dedicated web portals and publications.  As of fall 2016, we have produced 190+ high-impact peer-reviewed papers, including 75 in the past 5 years alone, which have garnered over 20,000 citations (h-index 67+). These include the first proteome-scale studies of soluble and membrane protein interaction networks for yeast [eg. Molecular Cell (2004); Cell (2005); Nature (2006); Nature (2012)], E. coli [eg. Nature (2005); PLoS Biology (2009)], humans [eg. Cell (2012); Cell Reports (2014)] and metazoa [eg Nature (2015)].  

Meet Our Team

Meet Our Team

Currently, our group consists of 16 highly skilled and productive members active in protein mass spectrometry, biochemistry, molecular biology, analytical chemistry, and bioinformatics. The Emili group strives for leadership, service and research excellence. To date, our laboratory has mentored over 150 research trainees/highly qualified personnel, many of whom now occupy senior academic leadership positions.  

In addition to teaching cutting-edge methods and concepts, we strive for a dynamic learning environment, fostering entrepreneurial post-doctoral fellows and graduate students who tackle important biomedical problems using integrative ‘systems’ approaches.  Our training plan, honed over 20 years, cultivates scientific excellence, multidisciplinary skills, and collaboration, to produce high confident and capable individuals who are well prepared for independent research careers. Many alumnae now occupy leadership positions in academia, industry and healthcare, including Professors Gerard Cagney (University College Dublin), Lekha Sleno (University of Quebec in Montreal), Thomas Kislinger (University of Toronto), Dajana Vuckovic (Concordia University), Mohan Babu (University of Regina), and Senior Scientist Gareth Buland (Lawrence Berkeley National Laboratories).


PI / Group Leader

Andrew Emili University Of Toronot

Professor Andrew Emili


Andrew Emili is the Principal Investigator at the OHSU Knight Cancer Institute in Portland, Oregon; operating within the Department of Oncological Services. Dr. Emili recently made the move to OHSU in late 2022, hailing from Boston University. Dr. Emili was a Full Professor in the Department of Biology and Department of Biochemistry, Cell Biology and Genomics at Boston University. Prior to joining BU in July 2017, Prof. Emili was a Principal Investigator (since 2000) and founding member of the Donnelly Centre for Cellular and Biomolecular Research, and a Professor in Molecular Genetics, at the University of Toronto, and the Ontario Research Chair in Biomarker Discovery (2007-2017).

Dr. Emili is an internationally recognized leader in protein interaction networks and the development of innovative technologies to systematically characterize protein complexes on a proteome-scale. He directs a multidisciplinary research laboratory with a track record in cutting-edge proteomics and systems biology. His group develops and applies innovative methods to characterize macromolecules of broad biomedical significance, publishing ‘global’ interaction maps of unprecedented quality, scope and resolution (eg. Babu, Nature 2012; Havugimana, Cell, 2012, Wan, Nature 2015).

Dr. Emili received his PhD in Molecular and Medical Genetics from the University of Toronto in 1997. From 1997 to 2000, he pursued post-doctoral studies as a Damon Runyon/Walter Winchell Cancer Research Fellow with the Nobel laureate Leland Hartwell at the Fred Hutchison Cancer Research Center in Seattle, while learning protein mass spectrometry with John Yates III at the University of Washington.

Since establishing his independent research laboratory in 2000, Dr. Emili has developed and applied innovative proteomics, functional genomics and bioinformatics methods to investigate biological systems and molecular association networks in human cells and model organisms. In particular, his lab uses quantitative, high precision mass spectrometry to characterize protein complexes in a comprehensive, high-throughput manner. His group aims for breakthrough insights into the composition and mechanistic role of protein complexes in diverse cells and tissues, with the long-term goal of translating this basic knowledge into new diagnostics, prognostics and therapeutics.

Dr. Emili has published 200 papers with >24,000 citations (h-index 68), including genome-wide studies of soluble and membrane protein complexes in yeast (Cell 2005; Nature 2006; Mol Cell 2004; Nature 2012), E. coli (Nature 2005; PLoS Biol 2009; 2017 in review), and human (Cell 2012; Cell Rep 2014; Nature 2015), documenting hundreds of complexes linked to disease. His influence is widely recognized; he reviews regularly for prominent journals, serves on grant review panels, and his groups data is often accessed via public databases. Dr. Emili was editor of "Network Biology" and "Systems Analysis" books with >24,000 e-downloads, and he has given >140 talks at research conferences, international symposia and workshops.


1990-1996       MSc+PhD - Molecular and Medical Genetics, University of Toronto

1997-2000       Postdoctoral Fellow, Fred Hutchinson Cancer Research Center, Seattle WA


Science, family, white wine (not all at once)

Want to read more about Dr. Emili and his research? Click here.

Postdoctoral Fellows

Avik Basu
Head of Spatial Proteomics

Avik is interested  in dynamic protein interaction networks. The main goal of his research project is how the protein-protein interactions in synapse change during Alzheimer’s Disease (AD) progression. Using genetically engineered mouse models, Avik has developed a novel in vivo proximity labelling technique (iPL) to identify protein networks in pre and postsynaptic density regions of synapse (in collaboration with Benjamin Wolozin lab, BU).

Weiwei Lin

Weiwei has been developing and optimizing a mass spectrometry platform for proteomic and nanoflow metabolomic analysis (PANAMA), which generates reproducible, high-sensitivity, high-resolution protein and metabolite data in parallel for a broad array of biospecimens with minimal sample consumption. She is also examining synaptic protein complex of Alzheimer’s disease.

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Staff Scientists

Raghuveera Goel
Head of Signaling Proteomics

Raghuveera is engaged in multi-level proteomics profiling of cancer and normal cells of the lung and breast, with the goal of characterizing molecular deficits underlying malignant transformation and disease progression. A unique dimension of his work also relates to uncovering molecular trajectories adopted by stem cells that give rise to adipocytes and separately, bronchial epithelial cells.

Eashita Das
Head of Cancer Models

​​Eashita is primarily interested in understanding the impact of extracellular vesicles and secreted proteins on the communication of different types of tumors with the surrounding cells of microenvironment. Her research is focused on the molecular mechanisms of oncogenic miRNAs and miRNA addiction in cancer.

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Jacob Porter
Head of LC/MS Facility

Jacob’s primary area of expertise is in mass spectrometry. He has experience working with several forms of ultrahigh resolution mass spectrometry and ion mobility spectrometry. He has applied this expertise to environmental, forensic and clinical samples. After several years of using imaging mass spectrometry on microbiological and clinical specimens, his current focus is on development of novel spatial techniques and LC-MS/MS proteomic analysis of cancer samples.

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Carl White

Carl assists lab members with analyses and helps manage the lab’s data storage and computational infrastructure. He also implements and troubleshoots software to facilitate running standardized analysis workflows. Additionally, he integrates new methodologies for data analysis.

Sadhna Phanse

Sadhna assists lab members in the analysis of multi-level proteomic interaction networks, from scoring and analysis to generation of publication level figures. She additionally develops and manages project-based websites for publication.

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Other Support Staff

Devri Hartle 
Administrative Assistant

Devri is the assistant to Dr. Emili and assists the lab as well. She is responsible for lab supply ordering, event coordination and assistance, lab media efforts, calendar management, travel management and planning, reimbursements, and other administrative tasks. 

Join our Team
Join Our Team

Join Our Team

Available Positions

We are always looking for talented, passionate and dedicated people to join our team. Discover today where you and your bright future fit in with the Emili Group.

We have many interesting genome-scale projects for enthusiastic and enterprising graduate students and postdoctoral fellows (with experience in Biochemistry, Bioanalytical Chemistry, Proteomics/Genomics, and Molecular and Cell Biology), to complement the methods and concepts that you have worked on in your undergraduate and Ph.D. studies, respectively, and to get you on the way with your own productive and successful scientific career.

Email us if you are interested in hearing more about our open positions.


Post-doctoral Applicants 


We have a number of challenging collaborative and independent research projects for Post-doctoral Applicants. 


  • Proficiency in spoken and written English, and a demonstrated command of a relevant scientific discipline. If we cannot discuss science on a high-level, you will not gain from or contribute to our ongoing research activities. Most of our current studies are concept-driven and you will learn best if you can critically discuss research problems and fundamental scientific concepts. 

  • Your resume should demonstrate a proven track record in terms of productivity and long-term independent research potential, as evidenced by first-author peer-reviewed publications and public presentations. 

  • Familiarity with our laboratory's research, and the literature in our main areas of interest. Please take time to fully understand what our group's research interests are, what we do and how we do it, and how this relates to your own academic goals. You should express clearly why you want to become a member of our group. 

  • Strong academic training (experimental and/or computational skills) with relevant laboratory and/or computer programming experience and demonstrated strengths in problem solving. 

  • You should also be comfortable with social interactions, and have strong personal qualities related to self-initiative, organization, determination, and persistence. 

  • Above all, we require a rigorous and curiosity-driven mind, well suited to critical reasoning and scientific inquiry. Successful members in my laboratory have diverse backgrounds, with demonstrated academic achievements (e.g. publications), and generally secure funding independently through competitive scholarships. 

Graduate Students


We have a number of stimulating projects for Graduate Students.


  • Prospective undergraduate or MSc students need a strong academic standing to be competitive.

  • You should also be familiar with the requirements and demands of academic research and graduate school, and have confidence in your scholarly potential, your laboratory and/or computer skills, and be comfortable with spoken and written English, social interactions, and have a sense of inquisitiveness and determination for performing independent research in a challenging area.

  • You must complete your own applications. Dr. Emili does not participate in the application process and will not write support letters for people who have not yet worked in the lab. 

Undergraduate Students


A few competitive internship positions are available for highly motivated Undergraduate students with strong academic track records and strong letters of recommendation.



  • To be considered for a summer project, you should familiarize yourself with our work (e.g. browse our Website) and understand the nature of our research publications before you apply. You should become familiar as to what we do and how this relates to your own academic training and interests.

  • You should understand the requirements and demands of academic research, and be confident in your own strengths, your potential for academic research, your laboratory and/or computer skills, and your ability to communicate in spoken and written English.

  • You should be confident in daily social interactions with members of a team, and feel confident in assuming independent responsibility and for performing and reporting assigned tasks.

Current posted positions

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