Headshot photo of Andrew Emili, Ph.D.

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 Andrew Emili is an internationally recognized leader in functional proteomics, systems biology, and protein mass spectrometry.

Since 2000, Professor Emili and his team have mapped protein interaction networks, biochemical pathways, and macromolecular complexes.

Professor Emili joined the OHSU Knight Cancer Institute in 2022, having previously served as the founding director of the Center for Network Systems Biology at Boston University. He has now established the Collaboratory for Network Systems Biology here in Portland. He is synergizing with and supporting multiple current pillars at the Knight.

Throughout his scientific career, Professor Emili has illuminated biological processes relevant to health and disease. The human body is characterized by various types of cells and tissues that are formed and functioned by proteins that associate with each other, and there is still a lot to learn about how these networks malfunction in common disorders such as cancer, neurodegeneration, and heart disease. The Emili team’s efforts have led to substantive findings and a unique expertise in molecular biology, network biology, bioinformatics and quantitative systems biology. Emili and his team will continue to further their research and contribute to existing research at the Knight.

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 metazoan. Emili’s work has impacted several disciplines, such as systems biology, gene annotation, and biomedicine, by challenging fundamental questions in cell biology, molecular biology, pathophysiology, and chemical biology.

Professor Emili's main goal at the Knight 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.


Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.  (Nature Communications, 2023)

Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Nat Commun. 2023 Feb 8;14(1):688. PMID: 36755019 

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. (Molecular Cell, 2020).

Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Mol Cell. 2020 Dec 17;80(6):1104-1122.e9.  PMID: 33259812 

BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. (Cell Systems, 2020).

Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. Cell Syst. 2020 Apr 22;10(4):333-350.e14.  PMID: 32325033 

Global landscape of cell envelope protein complexes in Escherichia coli. (National Center for Biotechnology Information, 2018).

Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A. Nat Biotechnol. 2018 Jan;36(1):103-112. MID: 29176613 

Panorama of ancient metazoan macromolecular complexes. (National Center for Biotechnology Information, 2015).

Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A. Nature. 2015 Sep 17;525(7569):339-44. PMID: 26344197 


1990                 B.S. Microbiology & Immunology. McGill University, Montreal, QC Canada

1993                 Master of Science. Banting & Best Dept Medical Research University of Toronto, Toronto, ON Canada

1996                 Ph.D. Molecular and Medical Genetics. University of Toronto, Toronto, ON Canada

1997-2000        Post-Doctoral Fellowship - Human Biology. Lee Hartwell. Fred Hutchinson Cancer Center, Seattle, WA

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.