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


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 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)

Graduate Students

Ahmed Youssef

BSc (Computer Science, Biology - Fordham University)


Ahmed is a Bioinformatics PhD student at Boston University. His fascination with the applications of computational techniques to biomedical problems that drew him to the field of bioinformatics. His research interests mainly fall in the area of network biology, where he aims to develop novel methods to make sense of the multitude of connections that underpin biological systems. This goal has led him to projects that leverage technologies such as single-cell sequencing to investigate the complex sets of interactions that govern different biological processes. Outside of bioinformatics, his hobbies include reading, tennis, and a passion for soccer.



Benjamin Blum


Benjamin is interested in the study of cells as complex, dynamic, networked systems, the molecular interactions that define those systems, and understanding how those systems are perturbed in disease as a first step to developing novel, targeted therapeutics. Benjamin joined BU after several years in biotech research and development.



Jarrod Moore

BA (Behavioral Biology - Boston University)


Jarrod is a MD/PhD student in the Biochemistry department at Boston University. He is interested in consolidating the fields of analytical chemistry, computational biology, and medicine to characterize disease at the molecular level. Currently, his research goals range from studying the systemic effects of chronic kidney disease to ascertaining the mechanisms of progression from Barrett’s esophagus to esophageal adenocarcinoma.



Basketball, video games, good food, lazy days.



Matthew Lawton

BA (Cellular, Molecular, and Genetic Biology - Boston University)


Matt is interested in uncovering signaling pathways and protein networks in an immune-cell setting. He is currently using proteomics/phosphoproteomics to look at signaling within an innovative Chimeric Antigen Receptor (CAR) T cell system, as well as unravelling pathways that are involved in immune exhaustion in untapped patient populations.


Interests: Hiking, trail running, obstacle course racing, sailing, skiing, food



Alejandro N. Rondón Ortiz


Matt is interested in uncovering signaling pathways and protein networks in an immune-cell setting. He is currently using proteomics/phosphoproteomics to look at signaling within an innovative Chimeric Antigen Receptor (CAR) T cell system, as well as unravelling pathways that are involved in immune exhaustion in untapped patient populations.




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Postdoctoral Fellows

Avik Basu

PhD (Biotechnology - University of Calcutta, India)


Avik is a biochemist with keen interest in mass spectrometry-based proteomics. His principal focus is protein interaction networks and their implications in health and disease.


Music, cricket, and hiking.



Raghuveera Goel

PhD (Biochemistry - University of Saskatchewan)


At the Center for Network Systems Biology (CNSB) I utilize state-of-the-art Mass spectrometry (Q-Exactive HF/-X) and RNAseq platforms together with robust data analyses/integration tools to gain systems level insights into the complex signaling landscape of tumor cells. I also apply proximity ligation-based labeling approaches to profile contextual and physiologically relevant signaling proteins.

An integrated and unbiased approach to understanding the cancer-associated signaling modalities is central to my overarching goal of identifying candidate targets for novel therapies.



Suprama Datta

PhD (Biotechnology - Institute of Chemical Technology, India)


My focus is to study the physical interface linking metabolism and the proteome using chemical proteomic approaches, and understand how these supra-networks are regulated mechanistically and coordinated under different physiological conditions. The goal is to address some of the fundamental questions in biology such as protein moonlighting and/or enzyme promiscuity which are key factors in bacterial antibiotic resistance, inherited metabolic disorders, etc.


Travel and painting



Weiwei Lin

PhD (Pharmaceutical Analysis - Peking University)


Weiwei is developing a mass spectrometry platform for integrative metabolomics and proteomics. She is also examining protein complex of neurodegenerative disease.


Science and badminton



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Carl White

BMath (Computer Science - University of Waterloo)

BSc (Molecular Biology - University of Waterloo)

MSc (Molecular Genetics - University of Toronto)


Adaptation of single molecule super-resolution imaging techniques, particularly the optics, toward next-generation protein sequencing. Computational analysis and processing of proteomics data.


Genealogy. Hobbyist combination of 3D printing and electronics.



Christian Heckendorf

BS (Computer Network and Information Systems - Wentworth Institute of Technology)
MS (Computer Science - Boston University)


Christian is developing software for metabolomics.



Sadhna Phanse

BSc, MSc Microbiology (University of Bombay)

Ontario College Graduate Certificate - Bioinformatics, Seneca College


Drug target identification through thermal shift assay/ligand stabilization; develop web based platform for analysis of chemical proteomics samples; study of membrane protein complexes in E.coli; develop and manage project databases, websites and web-based sample trackers.


Reading, Music, Family


srphanse@gmail.com | Google Scholar

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Research Staff

Mark McComb - Res. Assoc. Prof.

PhD (Mass Spectrometry - Manitoba)


Mark's research aims are directed towards the development and application of state-of-the art mass spectrometry approaches to study mechanisms of human disease and to the training and dissemination of these approaches to the scientific community.


hiking, beach, skiing.



Ryan Hekman - Spectrometer Specialist

BS (Biochemistry, University of the Pacific)
MS (Biological Sciences, University of the Pacific)


​Ryan had a background in qualitative molecular biology techniques when mass spectrometry captured his interest for its quantitative nature. He is excited to be working in the field of biology when more quantitative techniques are revolutionizing its landscape, and hopes to help develop more powerful applications for modern instrumentation.


Hiking, household construction, nerding out about ramjets, black holes, etc.



Indranil Paul - Research Scientist

Ph.D (Biotechnology, University of Calcutta)


Indranil learned, and developed a passion for, mass spectrometry-based proteomic technologies at the Novo Nordisk Foundation Center for Protein Research (University of Copenhagen, Denmark) while working as a postdoc in the laboratory of Prof. Jesper V Olsen (Department head, Prof. Matthias Mann).

In the Emili lab, Indranil is developing high-throughput multiplexed mass spectrometry methods to generate maps of multi-omic networks, with an emphasis on pancreatic cancer.



Julian Kwan - Research Scientist

PhD (Molecular Genetics - University of Toronto)


Julian is an expert in mapping protein-protein interactions. He supports large and small collaborations and diverse proteomic activities. He also acts as lab manager for the Emili Lab.


Julian enjoys rock climbing and cycling.



Pierre Havugimana - Sr. Research Scientist

PhD (Molecular and Medical Genetics - University of Toronto)


Pierre's research interest is the use of functional and structural proteomic approaches to elucidate the identity and contribution of protein complexes to human health and disease.



Jaymie Zapata - Administrative Coordinator

MSW (Boston University)


Jaymie assists faculty, staff and graduate students with the day-to-day operations of the office. She provides support with laboratory and office requests such as ordering lab supplies and equipment. She is also a dual-degree candidate at Boston University's School of Public Health and School of Social Work, with a focus on health care access and equity.



Bird-watching, tabletop RPGs



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Undergraduate Students

Isabella Turcinovic

Isabella is involved in ongoing molecular imaging and thermal proteome profiling projects.


biochemistry, cycling, medicine, coffee, tacos, 20th century history



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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.


Join Our Team

Available 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.