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.

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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).

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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.

Education

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

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

Interests

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

Undergraduate Students

Christian Arthur

Christian is an undergraduate studying Biomedical Engineering who joined the Emili Lab this summer (2021). He is interested in the application of microscopy and other related techniques in various forms of research in biological studies. He is currently working closely with Dr. Anderson (Ichun) Chen from the BOAS Lab and BU’s MNI Core Facility and also the Beeler Chemistry Research Group in analyzing and optimizing features of novel dyes in development.

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Yashasvi Tharani

Yashasvi is studying immunology and stem cells. She will be working with Matthew Lawton on the identification of downstream signaling pathway of TIM-3, a T-cell inhibitory receptor.

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Adam Lazowski

Adam joined the Emili Lab in March 2022 during his sophomore year of college at Boston University. He has interests in learning more about how protein interactions and specific biomarkers can be identified before end-stage diseases become clinically incurable in select patients. In the Emili Lab, he will be assisting Noah Lampl and Ben Fitzsimmons in the aliquoting process of select metabolites for the creation of a Metabolite Library. 

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Graduate Students

During his time in the lab, his research involved developing computational approaches to studying protein interaction networks. These projects included investigating the dynamics of bacterial protein interactions in response to different growth conditions, as well as using single-cell sequencing data to infer cell-level protein interactomes. 

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Jarrod is an MD/PhD candidate who joined the Emili laboratory fall 2019. Since then, he has fulfilled his coursework requirements, was a featured student for the Biochemistry department, and passed the oral portion of his qualifying exam. His projects are focused on mapping the aberrant signaling pathways in two pathologies: Barrett’s Esophagus and Hypertrophic Cardiomyopathy. 

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Ahmed Youssef
Jarrod Moore

Matt’s research has focused on the investigation of signaling and proteomic changes in T lymphocytes. He has driven a number of projects, such as comparing phosphorylation dynamics in chimeric antigen receptor (CAR) T cells and T cell exhaustion. He has also worked in collaboration with many labs, performing proteomics and phosphoproteomics on projects ranging from immune cells in diabetes, to special “organoid primed T cells”, to immune-inhibitory mechanisms of cancer cells.

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Alejandro N. Rondón Ortiz

Alejandro is currently developing genetic tools to identify protein interactions and how these can be affected in neurodegenerative disorders. He is performing this project in collaboration with Dr. Benjamin Wolozin and Dr. Peter Ash. Additionally, he is interested in developing brain organoids and how these can be affected by COVID-19. 

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Matthew Lawton
Stanley Goldstein

Stan is working on a chemoproteomic platform to identify the protein targets of bioactive small molecules, with the goals of improving phenotypic screening strategies, repurposing drugs, and discovering molecular probes. Stan also has a pet interest in psychopharmacology and will collaborate with the Laboratory of Addiction Genetics to identify proteins involved in opioid addiction.

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Ethan is a graduate student in the Molecular Biology, Cell biology and Biochemistry (MCBB) Program and joined the Emili Lab in May 2021. Ethan’s interests are in the fields of precision medicine and drug targeting.  During his time with CNSB Ethan will focus on Cellular Thermal Shift Assay (CETSA), examining the interactions of candidate drug compounds in cells.

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Ari (Ben) Fitzsimmons

Ben is a PhD student in the biomedical engineering program and just joined the lab in May 2021. He is co-advised by Dr. Ahmad ‘Mo’ Khalil. His project currently involves developing a mass spectrometry pull-down workflow for identifying native and exogenous ligands of human nuclear receptors in the Emili Lab. This will transition into developing synthetic nuclear receptors using the Khalil Lab’s eVOLVER system.

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Postdoctoral Fellows

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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Raghuveera Goel

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.

Suprama Datta

Suprama is studying the interaction of endogenous cellular metabolites and other bioactive small molecules with human proteins, including nuclear receptors which are master regulators of human cell gene expression that are linked to diverse human diseases and are important drug targets of broad interest to the biomedical research community.

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Analysts

Carl White
Analyst

Carl performs feasibility analyses and develops data analysis software for PRISM, a novel approach to protein
identification. He also assesses protein cross-linking methodologies and provides computational support for other projects.

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Sadhna Phanse
 Analyst

Sadhna performs drug target identification analysis of thermal shift assay/ligand stabilization CETSA assay
samples; develops a web-based platform for analysis of chemical proteomics samples; performs protein-protein interaction scoring and
analysis; and develops and manages project-based websites for publication.

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Christian assists lab members with analyses and develops software to facilitate running standardized analysis workflows. He also helps manage the lab’s data storage and compute infrastructure. In addition, he is building a data warehouse to link experimental CETSA-MS data with known protein–drug interactions and associated information to streamline the discovery process.

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Christian Heckendorf
Bioinformatics Analyst

Research Staff

 Professor McComb contributes to the management of LCMS and related
proteomics platforms and bioinformatics infrastructure within the CNSB Medical Campus and Charles River Campus laboratories. He takes
part in methods development and collaborative research in all aspects of CNSB MS related research and conducts training and mentoring
within the laboratory and the classroom.

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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. Ryan's current projects include standard phosphoproteomic profiling of tissues and cells, as well as identifying novel drug-protein interactions.

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Ryan Hekman
Spectrometer Specialist
Mark McComb
Res. Assoc. Prof.

Indranil is currently leading several multi-scale proteomics projects within the center. Of note was the development of a workflow for concurrently acquiring data for up to 12 omic modalities from the same samples for a comprehensive systems characterization of biological processes with potential translational impact. Indranil is involved in developing streamlined pipelines for incorporating latest developments and best practices in mass-spectrometry and proteomics. He also provides his expert consultations and experimental support on mass spectrometry and other proteomic tools to academic- and industry-collaborators, within and beyond Boston University. Contact him at indranil@bu.edu.

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Jaymie is the administrative coordinator for the Center, managing the purchase of supplies and equipment, as well as heading the Center’s social media efforts. Jaymie is a dual degree master’s candidate at BU’s School of Public Health and School of Social Work. Her focus is on advancing health equity for marginalized populations.

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Jaymie Zapata
Admin. Coordinator
Indranil Paul
Research Scientist
Avik Basu
Research Scientist

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).

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Noah joined the Emili Lab in June 2021, directly after graduating from Washington & Jefferson College. During his sophomore year of college, he was awarded the Maxwell Summer Internship, which supported his research in a Molecular and Cellular Biology Lab at American University. Since then, he has been interested in learning the processes of discovering how cellular and protein interactions may untimely contribute to a patient’s clinical outcome. In the Emili lab, he will be assisting Dr. Lin in her research.

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Noah Lampl
Research Assistant

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.

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Post-doctoral Applicants

 

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

Requirements:

  • 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.

Requirements:

  • 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.

Requirements:

 

  • 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.