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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

Currently, our group consists of 15 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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Group Leader and PI - 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.

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)

Emili Lab Team

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Dr. Raghuveera Kumar 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.

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Dr. 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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Dr. 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).

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Dr. 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

Senior Analyst

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.

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Sadhna Phanse

Senior Analyst

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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Dr. Nazmin Bithi

Senior Research Associate 

Nazmin is a highly skilled professional specializing in mass spectrometry-based proteomics and metabolomics. With several years of experience, she has mastered various forms of ultrahigh resolution mass spectrometry, employing advanced bioanalytical techniques in her research. Nazmin possesses a profound understanding of pathophysiology and has expertise across multiple therapeutic areas in clinical research. Currently, her focus revolves around the development and analysis of mass spectrometry-based methods for cancer and infectious disease specimens.

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Brad Leupold

Research Assistant

Brad is interested in the intersection of pathology and systems biology to better understand mechanism of disease. His current focus is the characterization of disease progression in breast pathology.

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Dr. Nima Sistani

Post Doctoral Scholar

Nima's expertise is in identification, quantification, modeling, and functional mapping by performing precise metabolomics and proteomics. He is interested in the application of integrated analytical pipelines associated with systems biology, especially proteomics and metabolomics by using ultra-high resolution and cutting-edge mass spectrometry analysis in cancer biology. He hopes to overcome the challenges by using the innovative proteomics emerging from the Prof. Emili lab.

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Dr. Saman Rahmati

Post Doctoral Scholar

Saman's expertise is in the fields of structural bioinformatics (homology modeling, molecular docking, and molecular dynamics) and protein engineering to design protein and peptide with high binding affinity to their targets. He is interested in determining novel cancer cell surface proteins, protein macromolecular assemblies, and soluble cellular proteome interaction networks to aid early cancer diagnosis and drug development.

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Devri Hartle

Administrative Coordinator

Devri is the assistant to Dr. Emili and his lab. She is responsible for grant submission tracking and organization, event coordination and assistance, lab media efforts, calendar management, travel management and planning, reimbursements, and other administrative tasks. 

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Baelee Whitinger

Research Assistant

Baelee is a recent grad from Gonzaga University and is interested in the research behind medicine. She has experience in researching BcHMGR and is refining her research focus and skills under the guidance of Eashita and Avik.

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Sammantha Avaylon

Computational Biologist

Sammantha is a current graduate student in the Bioinformatics and Computational Biomedicine program at Oregon Health and Science University. With her background in cancer translational research, Sammantha is focused on honing her computational skills and utilizing her research experience to understand the underlying mechanisms of cancer.

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Grace Potter

Computational Biologist

Grace is a graduate student in OHSU's Bioinformatics and Computational Biomedicine program. With a background in Biology from the University of Portland, she enjoys exploring the ways computation can provide insights regarding biological systems and processes.

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Elias (Eli) Wisdom

MD-PhD Student

Eli is a Neuroscience Graduate Program student co-mentored by Andrew Emili and Vivek Unni. He is interested in the proteomics of neurodegenerative diseases. His current project is utilizing the latest proximity labeling technologies across in vitro and in vivo systems to probe the molecular protein-protein interactions that instigate Alzheimer's Disease and Parkinson's Disease.

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Neha Somalwar

PhD Student

Neha is a graduate student in the Biomedical Engineering Program, co-mentored by Dr. Andrew Emili and Dr. Xiaolin Nan. She holds a master's degree in Biotechnology and is experienced in Applied Nanotechnology. Within the Emili lab, Neha's research focuses on the investigation of the tumor micro-environment through the mapping and visualization of protein-protein interactions.

Join our Team

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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