Andrew Emili, Ph.D.

  • Professor of Division of Oncological Sciences, School of Medicine
  • Professor of Biomedical Engineering Graduate Program, School of Medicine
  • Professor of Chemical Physiology and Biochemistry, School of Medicine
  • OHSU Knight Cancer Institute, School of Medicine


Professor Emili is an internationally recognized leader in functional proteomics, systems biology and protein mass spectrometry. Since 2000, his group has been at the forefront of innovative experimental and computational approaches to systematically map protein interaction networks, biochemical pathways, and macromolecular complexes on a proteome-scale in diverse model systems, ranging from microbes to human. For twenty years, Professor Emili has led a multidisciplinary laboratory with a distinguished track record in both basic (mechanistic) and translationally-oriented studies, publishing global ‘interactome’ maps of unprecedented quality, scope and resolution. He has supervised over 50 graduate students and postdocs, and 100 staff and undergraduates, and is very experienced at leading, mentoring, and teaching trainees in systems-level analyses using multi-‘omic’ strategies.

Professor Emili’s scientific career has been focused on illuminating biological processes relevant to health and disease. Human development depends on dynamic networks of physical (functional) interactions between proteins, but the identity and composition of the multiprotein ‘machines’ that mediate the cellular processes critical to health and disease are still largely unknown. Indeed, despite immense progress in genomics, it remains unclear which proteins associate together to support the formation and function of the different cell types and tissues in the human body, or how these networks go awry in common disorders like cancer, neurodegeneration or cardiovascular disease. Hence, a major overarching goal of the Emili group research program is to define the macromolecules associated with essential biological systems in different pathophysiological contexts. The Emili team’s efforts have led to substantive findings and a unique expertise in molecular biology, network biology, bioinformatics and quantitative systems biology.

In the summer of 2022, Professor Emili was recruited from Boston University, where he was the Founding Director of the Center for Network Systems Biology, as a Senior Faculty Member in the Division of Oncological Sciences at the Knight Cancer Institute at OHSU, ostensibly to synergize with, support and expand on its current main research pillars. Professor Emili’s ambitious vision for his research program at the KCI/OHSU is to continue his long-standing interest and leadership in engaging in large-scale, collaborative, multi-group team science and to devise and apply high-throughput methods to characterize the molecular association networks that are altered in cancer and other diseases with broad biomedical significance.

Prior to joining BU, Professor Emili was a Professor in Molecular Genetics at the University of Toronto and a Founding Principal Investigator at the Donnelly Centre for Cellular and Molecular Biology, a leading integrative biology research institute in Canada. For 7 years, he was also the Ontario Research Chair in Biomarkers of Disease Management. During this formative period, his group contributed to the discovery, validation and clinical translation of novel markers of disease.  

Since establishing his own laboratory in 2000, Professor Emili has secured ~$20M in operating funds as a PI, and >$50M as a co-applicant. His groups’ scholarly output has been prolific, with >40,000 mass spectrometry experiments performed and tens of thousands of novel protein interactions reported for diverse species across eubacteria and metazoa. Professor Emili’s work has addressed fundamental questions in cell biology, molecular biology, pathophysiology, and chemical biology and has impacted multiple disciplines, including systems biology, gene annotation and biomedicine. As a senior PI, he have co-authored 280 peer-reviewed publications, including 88 in the past 5 years alone, which have garnered over 30,000 citations (h-index 82). These include high profile studies of soluble and membrane protein complexes in microbes (Cell 2005; Molecular Cell 2004; Nature 2005; Nature 2006; Nature 2012; PLoS Biology 2009) and mammals (Cell 2012; Nature 2015; Cell Systems, 2020). His lab’s data, documenting hundreds of assemblies with links to disease, is widely accessed via public databases and our own web portals. Professor Emili was Editor of popular "Network Biology" & "Systems Analysis" e-books with >30,000 downloads, and has given >200 talks at scientific symposia, and has a dozen patent submissions.

Professor Emili's main goal at KCI/OHSU is to establish institutional leadership in network biology, through implementation of world-class infrastructure, ambitious collaborative projects, and community engagement.  His group will develop and apply powerful new methods to probe macromolecules of high biomedical significance. He plans to establish a dynamic learning environment that fosters entrepreneurial post-doctoral fellows and graduate students to tackle fundamental biomedical problems using integrative approaches, producing highly skilled and motivated trainees who are well prepared for independent research careers.

Through his commitment to analytical excellence, innovative technology, and productive partnerships bridging disciplines, Professor Emili aims to forge a robust research enterprise that thrives in an increasingly competitive funding environment.

Please check out the Emili Lab Website:

Areas of interest

  • As a pioneer of 'interactome' science, the Emili lab uses precision mass spectrometry and other high-throughput technologies to map cellular networks on a global scale.