Curriculum vitae Patrick O’Donoghue, Ph.D....Curriculum vitae Patrick O’Donoghue, Ph.D. 5 26. Stephanie Anagnostou (Chem 4491, 2016-2017)

Curriculum vitae Patrick O’Donoghue, Ph.D.

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Patrick O’Donoghue, Ph.D.

Associate Professor & Canada Research Chair Departments of Chemistry and Biochemistry

Faculty of Science, Schulich School of Medicine & Dentistry The University of Western Ontario

Medical Sciences Building 388 London, Ontario, Canada N6A 5C1

phone: (519) 850-2373 email: [email protected]

I. EXPERTISE & RESEARCH INTERESTS Patrick O’Donoghue is a Canada Research Chair in Chemical Biology and Associate Professor of Chemistry and Biochemistry at The University of Western Ontario (London, Ontario, Canada). He received a bachelor’s degree in Biophysics and a Ph.D. in Chemistry, supervised by Dr. Zan Luthey-Schulten, at The University of Illinois Urbana-Champaign. He was a postdoctoral fellow with Dr. Carl Woese at Illinois and then at Yale University with Dr. Dieter Söll. In 2013, he was appointed Assistant Professor at Western where he was promoted to Associate Professor with tenure in 2019. His research focuses on genetic code evolution and engineering. The O’Donoghue lab develops methods for site-specific insertion of post-translational modifications into proteins and applies these methods to elucidate the role of protein modifications in signaling networks linked to cancer and neurodegenerative diseases. The O’Donoghue lab also investigates the role of protein mistranslation in health and disease. II. EDUCATION & TRAINING Postdoctoral Fellow 6/2006-12/2010 Department of Molecular Biophysics & Biochemistry, Yale University Adviser: Professor Dieter Söll Postdoctoral Fellow 1/2005-5/2006 Institute for Genomic Biology, University of Illinois at Urbana-Champaign Adviser: Professor Carl R. Woese Ph.D. in Chemistry 12/2004 University of Illinois at Urbana-Champaign Adviser: Professor Zaida Luthey-Schulten Graduate Fellow 2000-2004 Department of Chemistry, University of Illinois at Urbana-Champaign Adviser: Professor Zaida Luthey-Schulten Research Assistant 2000 Theoretical Biophysics Group, University of Illinois at Urbana-Champaign B.S. in Biophysics 5/2000


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University of Illinois at Urbana-Champaign III. EMPLOYMENT Associate Professor (tenured) & Canada Research Chair 7/2019-present Departments of Chemistry and Biochemistry, The University of Western Ontario Assistant Professor & Canada Research Chair 9/2013-6/2019 Departments of Chemistry and Biochemistry, The University of Western Ontario Associate Research Scientist 1/2011-8/2013 Department of Molecular Biophysics & Biochemistry, Yale University IV. AWARDS, HONOURS, FELLOWSHIPS Canada Research Chair in Chemical Biology (Tier 2 renewed) 5/2019-5/2024 Canada Research Chair in Chemical Biology (Tier 2) 5/2014-5/2019 National Science Foundation Postdoctoral Fellowship 6/2006-6/2008 PhRMA Foundation Postdoctoral Fellowship in Informatics awarded & declined 12/2005 Institute for Genomic Biology Postdoctoral Fellowship, University of Illinois 5/2005-5/2006 Research Fellowship, NIH Institutional NRSA in Molecular Biophysics 2001-2004 University Fellowship, University of Illinois 2001-2002 Graduate Scholar, Department of Chemistry, University of Illinois 2000-2001 V. HIGHLY QUALIFIED PERSONNEL (HQP) TRAINING (last 6 years) Table 1. Summary of HQP training in my lab Currently Past 6 years

(excluding current year)

Supervised Co-supervised

Supervised Co-supervised

Total

Secondary school 1 4 5 Undergraduate 1 23 24 Master’s 2 5 1 8 Doctoral 2 1 1 1 5 Postdoctoral 1 1 2 Technician 1 1 Total 6 1 35 3 45


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Table 2. Participation in graduate advisory committees and exams at Western

V.1 O’Donoghue lab Trainees at Western since 2013 (total 43) Total MSc/PhD graduated from my lab

• 1 MSc • 4 MSc (non-thesis) • 2 MSc transfers to PhD in 2017 • 1 PhD 5/2019

Current Trainees (7) Graduate students

1. David Wright (PhD candidate)

Start date 5/2016; Expected degree date: 8/2021

2. Jeremy Lant (PhD candidate) Start date 5/2016; Expected degree date: 8/2021

3. Tanara Siddika (PhD candidate, co-supervised with Dr. Heinemann) Start date 9/2019; Expected degree date: 8/2023

4. McShane McKenna (MSc candidate) Start date 9/2017; Expected degree date: 8/2019

5. Peter Rozik (MSc candidate) Start date 9/2019; Expected degree date: 8/2021

Undergraduates 6. Elizabeth Connelly (Biology 4491 honors thesis, 2019-2020) High School Partners in Experiential Learning (PEL) co-op students 7. Baiqi Xing, London Central Secondary School

Graduate Advisory Committee 12 Thesis Defense Exam PhD 9 Thesis Defense Exam MSc 7 Biochemistry Qualifying Examiner 5 Chemistry 1st and 3rd year reports 17 Total 50


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Former Trainees (36) Technician 8. Yumin Bi (2014-2017). Current position: Western University lab technician Postdoc 9. Zaid Altaany (2014-2015). Current position: Assistant Professor of Biochemistry &

Molecular Genetics, Faculty of Medicine, Yarmouk University, Irbid, Jordan Graduates 10. Nileeka Balasuriya, PhD 2019.

Current position: Postdoctoral Fellow, Western University & Robarts Research Institute. 11. Rashmii Kiri, MSc (non-thesis) 2019

Current position: DDS student, University of Toronto. 12. Folawiyo Laditi, MSc (non-thesis) 2018.

Current position: MD student, Yale School of Medicine 13. Ibukan Akinpelu, MSc (non-thesis) 2017.

Current position: Technical Support, Sutherland, Windsor, Ontario. 14. Susanna George, MSc 2016.

Current position: Operational Quality Manager at Sanofi Pasteur, Toronto, Ontario. 15. Kyler Roy, MSc (non-thesis) 2016.

Current position: Staff scientist, Biomine, Sudbury, Ontario. Undergraduates 16. Melanie Offman (Chem 4491, 2018-2019) 17. Katherine Van Belois (Biochemistry, undergraduate researcher 2018) 18. Peter Rozik (Biochemistry, undergraduate researcher 2018)

Current position: MSc candidate, Western University. 19. Tony Nguyen (Biochemistry, undergraduate researcher 2018)

Current position: BSc candidate, Western University. 20. Yasir Al-Dojaily (Biochem 3383, 2016-2017; Biochem 4883 Summer 2017; Biochem 4999

Advanced Research Project student (2017-2018). Current position: Clinical Research Associate, Canadian Surgical Technologies and Advanced Robotics, London, Ontario.

21. Mitchell Salter (Biochem 4999 Advanced Research Project student (2017-2018). 22. Malaz Abd Elrahim (Chem 4491, 2017-2018).

Current position: Research and Administrative Assistant, Fowler Kennedy Sport Medicine Clinic, London, Ontario.

23. Sabrina Wang (NSERC USRA 2017 and 2018). Current position: BSc candidate McMaster and summer USRA student in the O’Donoghue lab at Western.

24. Nishita Sharif (Biochemistry, undergraduate volunteer 2017-2018). Current position: BSc candidate Western University.

25. Margot Treidlinger (Chem 4491, 2016-2017). Current position: Graduate student, Department of Nursing Health Systems, University of Toronto.


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26. Stephanie Anagnostou (Chem 4491, 2016-2017). Current position: Customer Service/Scheduling Representative, Phantom Ontario Screens, Mississauga, Ontario.

27. Folawiyo Laditi (NSERC USRA, Biochem 4483, 2016-2017). Current position: MD student, Yale University School of Medicine

28. Chetan Chana (Biochem 4483, 2016-2017; co-supervised with G. Shaw). Current position: PhD candidate, Biochemistry, University of Toronto.

29. Daniel Sze (Biochem 4483, 2016). Current position: PhD candidate, Biochemistry, Western University.

30. Sydney Legge(Chemistry, NSERC USRA, Summer 2016). Current position: BSc candidate, Chemistry, Western University.

31. Josh Jesin (Chemistry 4491, 2015-2016) Current position: PhD candidate, Biochemistry, University of Toronto.

32. Mahdieh Farahani (Biochemistry, NSERC USRA, Summer 2015) Current position:

33. Zac Alperstein(Chemistry 4491, 2014-2015). Current position: PhD candidate, Biochemistry, University of British Columbia.

34. Sanna Abassi (volunteer 2014). Current position: PhD candidate, Biochemistry, Western University.

35. Vlad Popa (summer researcher 2014). Current position: MESc candidate, Mechanical and Materials Engineering, Western University.

36. Chi-Lan Tran (NSERC USRA 2014). Current position: MD student, Wayne State University School of Medicine.

37. Madeline Jeffery (summer research 2014). Current position: Investments Rotational Analyst, CPP Investment Board, Toronto, Ontario.

38. Anika Rinehold (DAAD summer researcher 2014). Current position: PhD candidate, Biology, Freie Universität Berlin.

High School Partners in Experiential Learning (PEL) co-op students 39. Jazmyn Fuentes (Mother Teresa Catholic Secondary School, PEL co-op 2018) 40. Jin Young Bang (A. B. Lucas Secondary School, PEL co-op 2017) 41. Brooklyn Ball (London Central Secondary School, PEL co-op 2016) 42. Nishita Sharif (A. B. Lucas Secondary School, PEL co-op 2016) 43. Sabrina Wang (London Central Secondary School, PEL co-op 2015) Students recently supervised: My role as principal supervisor of these students includes training in biochemistry, molecular biology, microbiology, scientific presentation and teaching. Bachelor’s 2018 Sabrina Wang (completed)

USRA researcher, The University of Western Ontario; BSc candidate, McMaster. Project Title: Screening human kinase activity with programmed phosphorylation.

Distinction: NSERC Undergraduate Student Research Awards ($9K, 2017, 2018) Publication: co-author publication: George, Wang et al. BBA 2017.


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Master’s non-Thesis 2018-2019 Rashmii Kiri (Complete in Aug 2019)

MSc candidate, The University of Western Ontario. Thesis Title: Live cell reporters for mistranslation.

Master’s Thesis 2017 – 2019 McShane McKenna (In Progress)

MSc candidate, The University of Western Ontario Thesis Title: Genetic code expansion applications in protein phosphorylation and biocontainment Publication: 2nd author publication:

Balasuriya, McKenna et al. Genes 2018. Doctorate 2019 – 2023 Tarana Siddika (In Progress)

PhD candidate, The University of Western Ontario Co-supervised with Dr. Heinemann. Thesis Title: microRNA regulation in health and disease 2016 – 2021 Jeremy Lant (In Progress)

PhD candidate, The University of Western Ontario Thesis Title: Genetic code engineering for programmed phosphorylation and mistranslation.

Distinction: NSERC Postgraduate Scholarships-Doctoral Award ($63K, 2018-2021)

Publication: 1st author publications: Lant et al. RNA Biology 2017. Lant et al. JBC 2019. Berg et al. RNA Biol 2019.

2016 – 2021 David Wright (In Progress)

PhD candidate, The University of Western Ontario Thesis Title: Regulating thioredoxin reductase with programmed modifications. Distinction: NSERC Postgraduate Scholarships-Doctoral Award ($63K, 2019-2022); Ontario Graduate Scholarship ($30K, 2016, 2018) Publication: 1st author publications:

Wright et al. Antioxidant & Redox Signaling 2018 Front cover Wright et al. Structure 2019.

2014 – 2018 Nileeka Balasuriya (Completed)

PhD candidate, The University of Western Ontario Thesis Title: Activating the oncogenic kinase Akt1. Distinction: Ontario Graduate Scholarship ($15K, 2016), QEII Graduate Scholarship ($15K, 2017); Gold award Canadian Student Health Research Forum (2016)


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Publications: 1st author publications: Balasuriya et al. JBC 2018; Balasuriya et al. Genes 2018. Co-authored publication: Chung et al. RNA Biol 2019.

STUDENT AWARDS, HONORS, AND OUTREACH TOTAL VALUE = $217,500 (F = fellowship/scholarship, A = academic/presentation/research award, O = outreach activity) Graduate Students Jeremy Lant (PhD candidate) NSERC Postgraduate Scholarships-Doctoral Award ($63K) 2018-2021 David E. Wright (PhD candidate) NSERC Postgraduate Scholarships-Doctoral Award ($63K) 2019-2022 Ontario Graduate Scholarship ($15K) (F) 2017 Interviewed on thesis research. Gradcast Radio Episode 136 (O) 2017 Ontario Graduate Scholarship ($15K) (F) 2018 Nileeka Balasuriya (PhD candidate) Schulich Graduate Scholarship ($2K) (F) 2015 Schulich Graduate Scholarship ($2K) (F) 2016 Ontario Graduate Scholarship ($15K) (F) 2016 Top 100 poster: London Health Research Day (A) 2016 Gold category award and cash prize, recognized as a top 5% PhD students across the Canadian medical schools Canadian Student Health Research Forum (Winnipeg, Manitoba) (A) 2016 Schulich Graduate Scholarship ($2K) (F) 2017 Queen Elizabeth II Graduate Scholarship ($15K) (F) 2017 Canadian Cancer Society Travel Grant ($2K) (A) 2017 Susanna George (MSc 2016) Graduate Research Scholarship ($4.5K) (F) 2014 Graduate Research Scholarship ($4.5K) (F) 2015 Toronto RNA Enthusiasts Day Poster prize runner-up SickKids Peter Gilgan Centre for Research and Learning Cash award (A) 2016 Undergraduate Students DSM Haines Gold Medal in Biochemistry and Human Pathology, Kaney Ebuzaki Award for Biochemistry 4410, Biochemistry 4415 Course Award Folawiyo Laditi (A) 2017


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Gold Medal in Honors Specialization in Biochemistry and Chemistry Josh Jesin (A) 2016 NSERC Undergraduate Student Research Awardees Sabrina Wang ($4.5K) (F) 2018 Mitchell Salter ($4.5K) (F) 2017 Sabrina Wang ($4.5K) (F) 2017 Sydney Legge ($4.5K) (F) 2016 Folawiyo Laditi ($4.5K) (F) 2016 Mahdieh Farahani ($4.5K) (F) 2015 Chi-Lan Tran ($4.5K) (F) 2014

VI. SCHOLARLY AND PROFESSIONAL ACTIVITIES VI.1 National and International Impact VI.1.1 Presentations as invited speaker 1. P. O’Donoghue. Opening and closing remarks. Chemical biology applications in cells,

molecules, and disease. Canadian Society for Chemistry Conference, Quebec City, QC (6/2019)

2. P. O’Donoghue. tRNAs are agents of genetic code expansion, evolution, and ambiguity. Chemistry Department seminar series, Wayne State University, Detroit, MI. (4/2018)

3. P. O’Donoghue. tRNAs are agents of genetic code expansion, evolution, and ambiguity. Aminoacyl-tRNA Synthetase Conference. Clearwater, FL. (10/2017)

4. P. O’Donoghue. Genetically encoded protein post-translational modification. Dr. Maud L. Menten Memorial Symposium, The University of Western Ontario, London, ON. (6/2017)

5. P. O’Donoghue. Genetically encoded protein phosphorylation. Ohio State University, Department of Microbiology Seminar Series, Columbus, OH. (9/2016)

6. P. O’Donoghue. Genetically encoded protein phosphorylation. Canadian Society for

Chemistry, Chemical Biology division, Halifax, NS. (6/2016)

7. P. O’Donoghue. Genetically encoded protein phosphorylation. 16th annual International Union of Biochemistry and Molecular Biology (IUBMB) Conference 2016, Vancouver, BC. (7/2016)

8. P. O’Donoghue. Genetically encoded protein phosphorylation. Canadian Cancer Society Daffodil Breakfast, Point Edward, ON. (3/2016)


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9. P. O’Donoghue. Genetically encoded protein phosphorylation. Oncology Grand Rounds, London Regional Cancer Program, The University of Western Ontario, London, ON. (2/2016)

10. P. O’Donoghue. Redefining the genetic code by codon reassignment and recoding.

Biochemistry Department seminar series, Université de Montréal, Montréal, QC. (10/2015)

11. P. O’Donoghue. My life in science – why I never left school and you might, too. Presented to High School students at the Gairdner Award Event at The University of Western Ontario, London, ON. (10/2015)

12. P. O’Donoghue. Genetically encoded protein phosphorylation. Dr. Maud L. Menten

Memorial Symposium, The University of Western Ontario, London, ON. (5/2015) 13. P. O’Donoghue. Recoding the entire genetic code with selenocysteine. Chemistry Department

Seminar Series, Oakland University, Rochester, MI. (10/2014)

14. P. O’Donoghue. Recoding the entire genetic code with selenocysteine. RNA Society Satellite meeting and CDMC Symposium: Structure and dynamics of RNA interactions. Université de Montréal. (6/2014)

15. P. O’Donoghue. Expanded, dynamic, and recoded genetic codes. EMBO Workshop: Recoding: Reprogramming genetic decoding. Killarney, Ireland. (5/2014)

16. P. O’Donoghue. Recoding the entire genetic code with selenocysteine. Schulich School of Medicine & Dentistry’s New Faculty Lecture Series. The University of Western Ontario, London, ON. (12/2013)

17. P. O’Donoghue. Nonsense and sense codon reassignment for expanded genetic codes. XXIV

tRNA Conference. Olmué, Chile. (12/2012) 18. P. O’Donoghue. The role of the aminoacyl-tRNA synthetases in the evolution of the genetic

code. Aminoacyl-tRNA Synthetase Conference. Annecy, France. (9/2008) 19. P. O’Donoghue. Probing the roots of the tree of life: origins & evolutionary history of cysteine

coding genes. LUCA, ten years after. Fondation des Treilles, France. (9/2006) 20. P. O’Donoghue. Evolution of structure in the aminoacyl-tRNA synthetases. American

Chemical Society Meeting, Division of Physical Chemistry. Anaheim, CA. (3/2004) 21. P. O’Donoghue. Toward structure prediction of multi-domain proteins. 14th Annual Cell and

Molecular Biology & Molecular Biophysics Symposium. University of Illinois. (11/2001) VI.1.2 Poster Presentations 1. P. O’Donoghue. Manipulating codon meaning with orthogonal translation systems. Gordon

Research Conference in Synthetic Biology. Sunday River, ME. (7/2015)


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2. L. Prat (poster presenter), I. U. Heinemann, P. O’Donoghue (co-supervisor) and D. Söll.

Carbon source dependent encoding of pyrrolysine in bacteria. XXIV tRNA Conference, Olmue, Chile(12/2012)

VI.1.3 Press stories and interviews 1. Featured Researcher P. O’Donoghue (2019). “Lost in translation: researchers discover

translator gene may play a role in disease” by Crystal Mackay; University of Western Ontario press release.

2. Featured Researcher P. O’Donoghue (2019) “Biochemistry faculty awarded CIHR grants: Pathways to Neurodegeneration from Natural Human tRNA Variation” Biochemistry News [knowledge translation and community outreach web publication]. https://www.schulich.uwo.ca/biochem/about_us/news/2019/biochemistry_faculty_awarded_cihr_grants.html

3. Featured Researcher P. O’Donoghue (2019) “Funding: CIHR funds translational

collaborative research” Schulich News [knowledge translation and community outreach web publication]. https://www.schulich.uwo.ca/about/news/2019/july/funding_cihr_funds_translational_collaborative_research_at_western.html

4. Featured Researcher P. O’Donoghue (2019) “Western lands nine new CRCs among latest

round” Western News [knowledge translation and community outreach publication]. https://news.westernu.ca/2019/06/national-research-chairs-western/

5. Featured Researcher P. O’Donoghue (2019) “Announcement: Four new CRCs announced” Schulich School of Medicine and Dentistry News https://www.schulich.uwo.ca/about/news/2019/june/three_new_crcs_announced.html

6. Featured Researchers, I. U. Heinemann, and P. O’Donoghue. (2016) Rapport Magazine,

Schulich School of Medicine & Dentistry [knowledge translation and community outreach publication]

7. Featured Researcher, P. O’Donoghue Schulich School of Medicine and Dentistry News “Patrick O’Donoghue receives Canadian Cancer Society Innovation Grant” 2/2016.

8. Featured Researcher, P. O’Donoghue The Scientist Magazine “Streamlining the E. coli

Genetic Code” by Karen Zusi, Aug 18, 2016. 9. Featured Researcher, P. O’Donoghue CRC announcement: Schulich School of Medicine

and Dentistry News “Congratulations to Patrick O'Donoghue” 10/2014. 10. Featured Researcher, P. O’Donoghue Exchange Magazine “New Canada Research Chair

finds promise from proteins for cancer, neurodegenerative disease” 10/2014.


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11. Featured Researcher, P. O’Donoghue The Scientist Magazine “Recoding Life: Rewriting the genetic code can lead to a better understanding of how living cells work, and spawn new biotechnological applications” By Laasya Samhita 1/2014.

VI.1.4 Editorial Boards and Other Professional Activities Regular peer reviewer for: ACS Synthetic Biology; Biochemistry; Biochimica et Biophysica Acta; Biophysical Journal; BMC Biology; Cell Chemical Biology; Environmental Microbiology Reports; Frontiers in Genetics; Infection, Genetics, and Evolution; Life; Nature Ecology & Evolution; Nucleic Acids Research; PLoS One; PNAS; RNA Biology 2017-2021 Chair of the organizing committee (appointed in 2017): 12th

International Symposium on Aminoacyl-tRNA Synthetases 2021. Ontario, Canada (location TBD)

2017-2020 Counselor of the tRNA Synthetase Society (appointed in 2017): member of the International Symposium on Aminoacyl-tRNA Synthetases scientific advisory board.

2019-2021 Member of the Editorial Board, Genes. 2019 Chair and lead organizer Canadian Society for Chemistry, Symposium

on chemical biology applications in molecules, cells, and disease. Québec City, Canada. 6/2019.

2018 Guest editor of Genes special issue: Synthetic DNA and RNA reprogramming (in preparation) http://www.mdpi.com/journal/genes/special_issues/Synthetic_Programming.

2017 Session Chair, Aminoacyl-tRNA Synthetase Conference. Clearwater, FL. 2016-2017 Scientific Officer: CCSRI Innovation/Innovation to Impact Grant panel Toronto, ON 6/3/2016; 12/9/2016; 6/2018. 2016-2017 Primary and Secondary reviewer: CCSRI Innovation Grant panel Toronto, ON 6/3/2016; 12/9/2016; 6/2018. 2016-2017 Guest editor of Biochimica et Biophysica Acta special issue:

Biochemistry of synthetic biology (17 articles published) Volume 1861, Issue 11, Part B (2017)

2017-2018 Guest editor of RNA Biology special focus double issue: Transfer RNA function and evolution (24 articles published) Volume 15, Issue 4 & Issue 5 (2018)

2001-2003 Committee co-chair, corporate sponsor liaison, Cell and Molecular Biology & Molecular Biophysics Symposium, University of Illinois

2001-2002 Student representative, Molecular Biophysics NIH Training Grant Executive Committee, University of Illinois VI.1.5 Selected Active Research Collaborations


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1. Identifying activating phosphorylations in the oncogenic kinase Akt1: with Alexandra

Newton (UCSD) and Shawn Li (UWO Biochemistry, CRC). I am lead PI and Shawn is Co-PI on an awarded CCSRI Innovation Grant ($200k). This project so far resulted in 3 publications (Balasuriya et al. JBC 2018; Balasuriya et al. Genes 2018; Chung et al. RNA Biol 2019) and two manuscript currently in preparation. A CIHR application (in collaboration with Ilka Heinemann and Shawn Li at UWO) is pending on this project.

2. Elucidating the role of mistranslation in diseases of proteostasis: with Chris Brandl (UWO

Biochemistry) and Martin Duennwald (UWO Pathology). This new collaboration led to a series of publications (Hoffman et al. NAR 2017; Hoffman et al. BBA 2017; Berg et al. Genetics 2017; Lant et al. RNA Biol 2017; Lant et al. JBC 2019; Berg et al. RNA Biol 2019) and a successful Collaborative Research Seed Grant ($61k) supported by the Schulich School of Medicine and Dentistry. A CIHR project grant was awarded: “Pathways to neurodegeneration from human tRNA variation” ($865K; 2019-2024).

3. Investigations into the role of phospho-ubiquitin signaling in neurodegenerative disease:

with Gary Shaw (UWO Biochemistry, CRC). Initial studies led to two publications (George et al. BBA 2017; George et al FEBS Lett 2016) revealing the ability of multiple ubiquitin phosphorylation sites to activate, hyper-activate, or inhibit the disease-linked enzyme parkin.

4. Bio-contained Bacillus subtilis for infection control: with Dr. Ylan Nguyen and CEO Leslie

Drake, Germiphene Corporation (Brantford, Ontario). In this industrial collaboration, the O’Donoghue lab is developing a synthetic auxotrophic strain of B. subtilis that depends on unnatural amino acids for growth. The advance will enable Germiphene Corporation to precisely regulate the growth of the micro-organism that is the active ingredient in their infection control product (Gobble) for dental evacuation systems. I was recently awarded an NSERC Engage Grant ($25k) and an Ontario Centres of Excellence Voucher for Innovation and Productivity ($25k = $20k OCE + $5k from Germiphene) to support this new collaboration.

VI.2 Teaching 1. Chemistry 4415B/Biochemistry 4415B: Course coordinator (2017-present). This course provides an introduction to the emerging fields of Synthetic Biology and Chemical Genetics and how work in these areas is applied to medicine. In this team-taught course, we explore how metabolic pathways are re-engineered in microorganisms to produce drugs, biofuels, and value-added chemicals. The course introduces chemical genetic approaches to define drug targets and focuses on methods for expanding the genetic code with applications in programmed protein modification and site-directed protein labeling. Emerging tools for genome-wide editing and whole genome synthesis are also presented.

This course was introduced as a new undergraduate course first offered in Winter 2015 in an effort to expand the teaching portfolio of the Biochemistry department to include course offerings in the area of synthetic biology. In 2015, as a recent hire with focus on the related and overlapping field of chemical biology, I designed and developed a new module for this course. At


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that time, I attended several planning meetings with Drs. Haniford (course coordinator 2015-2017), Junop, and Li to design the course, map curriculum relationships to other courses, and define learning outcomes. I teach 12 contact hours in this course. I designed all of the content for my portion of the course, including an exam worth 30% of the total mark.

In 2017, I became course coordinator for this course. I prepared and submitted successful Deans: Academic Programs (DAP) proposals to both the Chemistry and Biochemistry departments that were approved at departmental, faculty, and university levels. This effort resulted in an amendment of the pre-requisites for this course so that additional students (particularly 4th year Chemistry students) would be able to access the course. The course now requires prerequisite(s): Either (Biochemistry 3381A and Biochemistry 3382A) or (Biochemistry 2280A and one of Chemistry 3393A/B or Chemistry 4493A/B). Biochemistry/Chemistry 4415b: Summary of teaching scores

Term Students enrolled

Overall effectiveness

(max score = 7)

Course as a learning experience

(max score = 7) Winter 2015 38 6.1 5.8 Winter 2016 37 5.9 5.7 Winter 2017 28 5.6 5.5 Winter 2018 47 6.4 6.3

2. Chemistry/Biochemistry/MMASc 9703 Chemical Biology. Course coordinator (2014-present). This course begins with a broad overview of chemical biology with special emphasis on topics including protein synthesis with non-canonical amino acids, probing cellular functions and protein-protein interactions with small molecules, and chemical genetic approaches to drug discovery. Following the course lectures, student teams have the opportunity to lead a Journal Club and discussion session. Students are engaged in writing 4 brief article reviews and a news and views article, which is an exercise in writing for a lay audience.

I designed and implemented this as a new graduate course in Winter 2014. This course is part of the effort of the Biochemistry Department to introduce chemical and synthetic biology topics in graduate courses. I am the sole instructor in this 0.25 FCE course. Although the course began with a typical number of students (8) for a Biochemistry graduate course, the course has since expanded to ~40 students in Fall 2015 as it is included in the Master of Management and Applied Science (MMASc) degree program. Subsequent course offerings included students from the MMASc, Chemistry, and Biochemistry (including MSc thesis and MSc 1-year course based) graduate programs. This creates a unique training environment for all students, as they interact with their peers from other departments and programs, fostering interdisciplinary collaboration across the university. Chemistry/Biochemistry 9703: Summary of teaching scores

Term Students enrolled

Overall effectiveness

(max score = 7)

Course as a learning experience

(max score = 7)


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Winter 2014 8 6.5 7.0 Fall 2015 37 5.8 5.8 Fall 2016 35 5.5 5.4 Fall 2017 40 6.0 5.1 Fall 2018 34 6.4 5.6

3. Additional teaching: guest lectures in courses

• Chemical Biology. Chemistry of Biological Macromolecules 4493b, UWO. (2014) • Phylogenomics. Mol. Biophysics & Biochemistry 452, Genomics, Yale. (2008, 2009) • Structure-based phylogeny. Mol. and Cell. Biology 432, University of Illinois. (2006)

4. Lecturer, instructor. NIH Workshop on Computational Biophysics, Boston, MA. (9/2004) VI.3 Service VI.3.1 Service at Western 2019-present Graduate committee member (Biochemistry) 2019-present Faculty senate nominations committee member (Chemistry representative) 2019-present Visiting speaker committee, Chemical Biology representative (Chemistry) 2019-present Promotion & tenure committee, member (Chemistry) 2019-present Annual performance evaluation committee, member (Chemistry) 2017-present Co-director, Functional Proteomics Facility (Biochemistry) 2017-present Chair, Menten memorial lecture Committee (Biochemistry) 2017 Chair, lead organizer and host, Dr. Maud L. Menten Fall Symposium 2017-present Strategic planning committee member (Biochemistry) 2016-present Dr. Maud L. Menten lecture host (Biochemistry) 2016-2017 Menten memorial lecture Committee member (Biochemistry Seminars) 2016-2017 Graduate program working Group (Biochemistry) 2015-2018 Joint lab journal club leader (Biochemistry). Bi-weekly journal club emphasizing student presentations and critical discussions of recent literature (Participating labs: Ball, Heinemann, Junop, Litchfield, Li, O’Donoghue) 2015-2017 Graduate recruitment task Group (Biochemistry) 2014-2017 Graduate committee member (Biochemistry) 2014-2018 Scholarship committee member (Chemistry) 2014-2019 Recorder of faculty meeting minutes (Chemistry) 2014-2016 Department representative at McMaster annual southern Ontario graduate

information session (Chemistry) VI.3.2 Community Outreach


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Graduate Information Session hosted at McMaster (1/20/2015; 1/13/2016; 1/21/2017)

• In 2015-2017, I represented Chemistry at the McMaster University Graduate Information Session. I gave a 10-minute oral presentation about the Chemistry graduate program at Western, and then attended a 2-hour session to answer student questions about our program. Audience: Included faculty representatives and undergraduates (2nd-4th year interested in or applying to graduate school) from 15 Canadian Universities: ~250 attendees.

Partners in Experiential Learning (PEL) Cooperative Education

• Since 2014 and continuing I have mentored a total of 5 high school students via the PEL program. This co-op program brings local high school students into the research lab to work part-time during the school year or full time during the summer term. One exceptional PEL student (Sabrina Wang) worked in my lab for the 2015-2016 fall, winter, and summer terms. She was an NSERC USRA awardee in 2017, and now again in 2018, and she is second author of a paper from my lab (George et al. BBA 2017). This is a great program that gets students excited about research early and provides an excellent training opportunity for my graduate students.

• I gave the following 1-hour talk: My life in science – why I never left school and you might, too. Presented to High School students at the Gairdner Award Event at Western University, London, ON. (10/26/2015). This outreach event was to celebrate Canada’s top science prize and to encourage high school students to pursue a career in science. My talk was a ‘warm up’ act for a scientific talk by the Gairdner Award Winner, Lynne Maquat. Audience: ~200 attendees, mainly high school students and science teachers from the London area who were enrolled in Programs in Experiential Learning (PEL).

VII. PUBLICATIONS Total citations: 2072, h-index: 25 (Google Scholar, 47 publications) Impact Factor (IF), *Co-first author, †Corresponding author, Trainees are underlined. Complete publication list: http://scholar.google.ca/citations?hl=en&user=-EbWzyEAAAAJ Table 3. Summary of publications

Published Submitted In preparation Senior/corresponding author 16 First author 17 Since 2013 @ Western 23 Independent @ Western 16 Total Forthcoming 3 Total Published 47


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Note on publications. Below is a list of 47 publications spanning my academic career (17 as 1st author, 16 as corresponding author). My contribution and those of my trainees (or co-supervised trainees) in each publication is indicated by author order: first or co-first author (60-80% effort, principally involved in designing research, conducting research, analyzing data, writing the paper); middle author (20-30% effort, principally involved in conducting research, writing the paper); corresponding or senior author (50-80% effort, principally involved in designing research, analyzing data, writing the paper). My specific contributions to the 20 publications since 2013 are detailed below. Publications forthcoming 1. D. E. Wright & P. O’Donoghue† (2019) “The molecular architecture of unnatural amino

acid translation systems” Structure Accepted, in press. (IF = 4.9) Publications @ Western 2. C. Chung, N. Balasuriya, E. Manni, X. Liu, S.S. Li, P. O’Donoghue, & I. U. Heinemann

(2019) Gld2 activity is regulated by phosphorylation in the N-terminal domain. RNA Biology. doi: 10.1080/15476286.2019.1608754. (IF = 5.2)

My lab contribution (20%) My role: funded research, designed research, analyzed data, trained students, wrote the paper.

3. M. D. Berg, D. J. Giguere, J. S. Dron, J. Lant, J. Genereaux, C. Liao, J. Wang, J. F. Robinson,

R. A. Hegele, P. O’Donoghue, & C. J. Brandl. (2019) “Targeted sequencing reveals expanded genetic diversity of human transfer RNAs.” RNA Biology. doi: 10.1080/ 15476286.2019.1646079. (IF = 5.2)

My lab contribution (40%) My role: co-lead corresponding author, funded research, designed research, analyzed data, designed experiments, trained students, wrote the paper.

4. P. O’Donoghue† & I. U. Heinemann† (2019) Synthetic DNA and RNA programming. Genes 10(7) pii: E523. doi: 10.3390/genes10070523. (IF = 3.2) Front cover feature. My contribution (50%) My role: lead corresponding author, wrote the paper.

5. J. Lant, M. Berg, I. U. Heinemann, C. Brandl, & P. O’Donoghue† (2019) Pathways to disease

from natural variations in human tRNA genes. J Biol Chem. 294(14):5294-5308 (IF = 4.2) My contribution (95%) My role: funded research, designed research, analyzed data, wrote the paper. This review also contains new findings from my lab.


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6. N. Balasuriya, M. McKenna, X. Liu, S. Li, & P. O’Donoghue† (2018) Phosphorylation-dependent inhibition of Akt1. Genes 9(9), 450; doi: 10.3390/genes9090450. (IF = 3.2)

My lab contribution (95%) My role: lead corresponding author, funded research, designed research, analyzed data, designed experiments, trained students, wrote the paper.

7. N. Balasuriya*, M. Kunkel*, X. Liu, K. Biggar, S. Li, A. Newton†, & P. O’Donoghue† (2018)

Genetic code expansion and live cell imaging reveal that Thr308 phosphorylation is irreplaceable and sufficient for Akt1 activity. J Biol Chem. 293(27):10744-10756. (IF = 4.2)


8. P. O’Donoghue†, Jiqiang Ling†, & Dieter Söll†. (2018) Transfer RNA function and evolution. RNA Biology. 15(4-5): 423-426 (IF = 5.2) Front cover feature. My contribution (70%) My role: funded work, performed research, wrote the paper.

9. J. T. Lant, M. D. Berg, D.H.W Sze, K. S. Hoffman, I. C. Akinpelu, T. M. Turk, I. U.

Heinemann, M. L. Duennwald, C. J. Brandl, & P. O’Donoghue†. (2018) Visualizing tRNA-dependent mistranslation in human cells. RNA Biology.15(4-5):567-575. (IF = 5.2)


10. D. E. Wright, Z. Altaany, Y. Bi, Z. Aplerstein, & P. O’Donoghue†. (2017) Acetylation

regulates thioredoxin reductase oligomerization and activity. Antioxidants & Redox Signaling. 29(4): 377-388. (IF = 7.0) Front cover feature. My lab contribution (100%) My role: lead corresponding author, funded research, designed research, analyzed data, designed experiments, trained students, wrote the paper.

11. P. O’Donoghue†, & I. U. Heinemann†. (2017) Biochemistry of synthetic biology – recent developments. Biochim Biophys Acta. 1861(11PB): 2945-2947. (IF = 4.3) Front cover feature. My contribution (50%) My role: lead corresponding author, wrote the paper.


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12. S. George, S. M. Wang, Y. Bi, M. Treidlinger, K. R. Barber, G. S. Shaw, P. O'Donoghue†. Ubiquitin phosphorylated at Ser57 hyper-activates parkin. (2017) Biochim Biophys Acta. 1861:3038-3046. (IF = 4.3)


13. M. D. Berg†, K. S. Hoffman, J. Genereaux, S. Mian, R. S. Trussler, D. B. Haniford, P. O’Donoghue & C. Brandl†. (2017) Evolving mistranslating tRNAs through a phenotypically ambivalent intermediate in Saccharomyces cerevisiae. Genetics. 206:1865-18792. (IF = 6.0) Featured in Genetics Society of America E-news (8/16/17); B. Starr ‘New & Noteworthy’ article feature at Saccharomyces Genome Database: https://www.yeastgenome.org/blog/that-sweet-spot-of-mistranslation (3/8/17). My lab contribution (30%) My role: co-author, designed research, partially funded research, analyzed data, designed experiments, trained students, wrote the paper.

14. K. Hoffman, P. O’Donoghue, & C. Brandl†. (2017) Mistranslation: from adaptations to

applications. Biochimica et Biophysica Acta. 1861: 3070-3080. (IF = 4.3).

My contribution (30%) My role: co-author, wrote the paper.

15. K. Hoffman, M. Berg, B. Shilton, C. Brandl†, & P. O'Donoghue†. (2017) Genetic selection for mistranslation rescues a defective co-chaperone in yeast. Nucleic Acids Research. 45: 3407–3421 (IF = 10.1) My lab contribution (50%) My role: lead corresponding author, partially funded research, designed research, analyzed data, designed experiments, trained students, wrote the paper.

16. S. George*, J.D. Aquirre*, D.E. Spratt, Y. Bi, M. Jeffery, Gary S. Shaw†, & P. O’Donoghue†. (2016) Generation of phospho-ubiquitin variants by orthogonal translation reveals codon skipping. FEBS Lett. 590(10):1530-42. Accepted as ‘prize-worthy’. (IF = 3.2)


17. H. R. Aerni, M. A. Shifman, S. Rogulina, P. O’Donoghue, & J. Rinehart (2015) Revealing the

amino acid composition of proteins within an expanded genetic code. Nucleic Acid Res. 43: e8. (IF = 10.1)

My lab contribution (20%)


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My role: co-author, partially funded research, designed and implemented an algorithm to re-annotate genomes accounting for translation of the UAG codon, wrote the paper.

18. J. Ling*, P. O’Donoghue*, & D. Söll (2015) Genetic code flexibility in microorganisms: novel

mechanisms and impact on bacterial physiology. Nature Reviews Microbiology. 13(11):707-21. (IF = 23.5)

My contribution (45%) My role: first author, wrote the paper.

19. P. O’Donoghue, L. Prat, J. G. Schäfer, M. Kucklick, K. Riedel, J. Rinehart, D. Söll†, & I. U.

Heinemann† (2014) Reducing the genetic code induces massive rearrangement of the proteome. Proc Natl Acad Sci USA. 111: 17206-17211. (IF = 9.7)

My contribution (50%): first author, designed research, partially funded research, analyzed data, designed experiments, trained students, conducted experiments, performed proteomic analysis, provided new strains, wrote the paper.

20. L-T. Guo, Y-S. Wang, A. Nakamura, D. Eiler, J.M. Kavran, M. Wong, L.L. Kiessling, T.A. Steitz, P. O’Donoghue†, & Dieter Söll† (2014) Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. Proc Natl Acad Sci USA. 111: 16724-16729. (IF = 9.7)

My lab contribution (40%) My role: corresponding author, partially funded research, designed research, analyzed data, designed experiments, wrote the paper.

21. M. J. Bröcker, J. M. L. Ho, G. M. Church, D. Söll†, & P. O'Donoghue† (2014) Recoding the

genetic code with selenocysteine. Angewandte Chemie. 53: 319-323. (IF = 11.3) Front cover feature; ChemBiochem commentary (doi: 10.1002/cbic.201300735, 1/2014), featured in The Scientist Magazine (1/2014); Nature Chemical Biology research highlight (2/2014); highlighted as ‘of special interest’ in Metanis et al. Curr Opin Chem Biol (doi: 10.1016/j.cbpa.2014.09.010, 10/2014). My lab contribution (50%) My role: lead corresponding author, partially funded research, designed research, analyzed data, designed experiments, trained students, conducted experiments, provided new reagents/methods, wrote the paper.

22. P. O’Donoghue*, J. Ling*, Y-S. Wang*, & D. Söll (2013). Upgrading protein synthesis for synthetic biology. Nature Chem Biol. 9: 594-598. (IF = 13.0) My contribution (45%) My role: first author, wrote the paper.


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23. M. Englert, S. Gundapalli, M. Hohn, J. Ling, P. O’Donoghue, & D. Söll. (2013). Aminoacylation of tRNA 2'- or 3'-hydroxyl by phosphoseryl- and pyrrolysyl-tRNA syntheses. FEBS Lett. 587: 3360-3364. (IF = 3.2)

My lab contribution (20%) My role: co-author, partially funded research, designed experiments, analyzed data, wrote the paper.

Postdoctoral publications 24. J. H. Campbell*, P. O'Donoghue*, A. G. Campbell, P. Schwientek, A. Sczyrba, T. Woyke, D.

Söll, & M. Podar (2013). UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci USA. 110: 5540-5545. Faculty of 1000 recommended as exceptional. (IF = 9.7)

25. P. O’Donoghue, L. Prat, I. U. Heinemann, J. Ling, K. Odoi, W. R. Liu, & D. Söll (2012).

Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion. FEBS Lett. 586: 3931-3937. (IF = 3.2)

26. L. Prat, I.U. Heinemann, H.R. Aerni, J. Rinehart, P. O’Donoghue†, & D. Söll†. (2012).

Carbon source dependent expansion of the genetic code in bacteria. Proc Natl Acad Sci USA. 109: 21070-21075. (IF = 9.7)

27. I.U. Heinemann, A. Nakamura, P. O’Donoghue, D. Eiler, & D. Söll. (2012) tRNAHis

guanylyltransferase establishes tRNAHis identity. Nucleic Acids Res. 40: 333-344. (IF = 10.1) 28. P. O’Donoghue, K. Sheppard, O. Nureki, & D. Söll. (2011) Rational design of an evolutionary

precursor of glutaminyl-tRNA synthetase. Proc Natl Acad Sci USA. 108: 20485-20490. (IF = 9.7)

29. O. Nureki, P. O’Donoghue, N. Watanabe, A. Ohmori, H. Oshikane, Y. Araiso, K. Sheppard,

D. Söll, & R. Ishitani. (2010) Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. Nucleic Acids Res. 38: 7286-7297. (IF = 9.1)

30. A. Ambrogelly, P. O’Donoghue, D. Söll, & S. Moses. (2010) A bacterial ortholog of class II

lysyl-tRNA synthetase activates lysine. FEBS Lett. 584: 3055-3060. (IF = 3.2) 31. J. Yuan†*, P. O’Donoghue†*, A. Ambrogelly, S. Gundllapalli, R. L. Sherrer, S. Palioura, M.

Simonovic, & D. Söll. (2010). Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems. FEBS Lett. 584: 342-349. (IF = 3.2)

32. I. U. Heinemann, P. O’Donoghue, C. Madinger, J. Benner, L. Randau, C. J. Noren, & D. Söll. (2009). The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution. Proc Natl Acad Sci USA. 106: 21103-21108. (IF = 9.7)


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33. D. Su, M. J. Hohn, S. Palioura, R. L. Sherrer, J. Yuan, D. Söll, & P. O’Donoghue†. (2009)

How an obscure archaeal gene inspired the discovery of selenocysteine biosynthesis in humans. IUBMB Life. 61, 35-39. (IF = 3.1)

34. K. Nozawa*, P. O’Donoghue*, S. Gundllapalli*, Y. Araiso, R. Ishitani, T. Umehara, D. Söll

& O. Nureki. (2009) Pyrrolysyl-tRNA synthetase-tRNAPyl structure reveals the molecular basis of orthogonality. Nature 457, 1163-1167. Faculty of 1000 must read. (IF = 41.5)

35. F. Charriere, P. O’Donoghue, S. Helgadottir, L. Marechal-Drouard, M. Cristodero, E. K. Horn,

D. Söll, & A. Schneider. (2009) Dual targeting of a tRNAAsp requires two different aspartyl-tRNA synthetases in Trypanosoma brucei. J Biol Chem. 284: 16210-16217. (IF = 4.5)

36. R. L. Sherrer, P. O’Donoghue, & D. Söll. (2008) Characterization and evolutionary history of

an archaeal kinase involved in selenocysteinyl-tRNA formation. Nucleic Acids Res. 36: 1247-1259. (IF = 10.1)

37. Y. Araiso, S. Palioura, R. Ishitani, R. L. Sherrer, P. O’Donoghue, J. Yuan, H. Oshikane, N.

Domae, J. Defranco, D. Söll & O. Nureki. (2008) Structural insights into RNA-dependent eukaryal and archaeal, selenocysteine formation. Nucleic Acids Res. 36: 1187-1199. (IF = 10.1)

38. J. M. Kavran, S. Gundllapalli, P. O’Donoghue, M. Englert, D. Söll & T. A. Steitz. (2007)

Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc Natl Acad Sci USA. 104: 11268-11273. (IF = 9.7)

39. S. Herring, A. Ambrogelly, S. Gundllapalli, P. O’Donoghue, C. R. Polycarpo, & D. Söll.

(2007) The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity. FEBS Lett. 581: 3197-3203. (IF = 3.2)

40. J. Yuan, S. Palioura, J. C. Salazar, D. Su, P. O’Donoghue, M. J. Hohn, A. M. Cardoso, W. B.

Whitman, & D. Söll. (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci. USA 103: 18923-18927. (IF = 9.7)

41. M. J. Hohn*, H. S. Park*, P. O’Donoghue*, M. Schnitzbauer, & D. Söll. (2006) Emergence

of the universal genetic code imprinted in an RNA record. Proc Natl Acad Sci USA. 103: 18095-18100. Faculty of 1000 recommended. Featured in Nature Research Highlights (Vol. 444|23 November 2006). (IF = 9.7)

Publications from PhD thesis 42. P. O’Donoghue*, A. Sethi*, C. R. Woese & Z. Luthey-Schulten. (2005) The evolutionary

history of Cys-tRNACys formation. Proc Natl Acad Sci USA. 102: 19003-19008. (IF = 9.7)


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43. Sethi, P. O’Donoghue & Z. Luthey-Schulten. (2005) Evolutionary profiles from the QR factorization of multiple sequence alignments. Proc Natl Acad Sci USA. 102: 4045-4050. Faculty of 1000 recommended. (IF = 9.7)

44. P. O’Donoghue & Z. Luthey-Schulten. (2005) Evolutionary profiles derived from the QR

factorization of multiple structural alignments gives an economy of information. J Mol Biol. 346: 875-894. (IF = 4.3)

45. P. O’Donoghue & Z. Luthey-Schulten. (2003) On the evolution of structure in aminoacyl-

tRNA synthetases. Microbiol Mol Biol Rev. 67: 550-573. (IF = 16.8) 46. P. O’Donoghue, R. E. Amaro & Z. Luthey-Schulten. (2001) The structure of HisH: protein

structure prediction in the context of structural and functional genomics. J Struct Biol. 134: 257-268. (IF = 3.2)

47. P. O’Donoghue & Z. Luthey-Schulten. (2000) Barriers to forced transitions in polysaccharides.

J Phys Chem B. 104: 10398-10405. (IF = 3.3) VIII. RESEARCH FUNDING Total funding awarded since starting 1st independent position at Western: $3,755,368 Research funding awarded as lead PI Total funding as lead PI since starting 1st independent position at Western: $3,244,000 1. Start-Up Funds, Departments of Chemistry and Biochemistry, Western University

Term: 2013-2018; Total Value: $160,000.

2. Western Strategic Support for CIHR success SEED grant, Western University Sense codon recoding in human cells Term: 2014-2016; Total Value: $25,000 ($12,500 per year for 2 years).

3. Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant.

Protein synthesis with multiple non-canonical amino acids Term: 2014-2021; Total Value: $364,000 ($52,000 per year for 7 years).

4. Tier 2 Canada Research Chair in Chemical Biology Hardwiring protein modifications as probes of signalling, epigenetic, and redox networks Term: 2014-2019; Total Value: $500,000 ($100,000 per year for 5 years). 5. Canada Foundation for Innovation & Ontario Research Fund: Leadership Opportunity Fund Hardwiring protein modifications as probes of signalling, epigenetic, and redox networks

Term: 2014-2019; Total Value: $500,000 ($100,000 per year for 5 years).


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6. Canada Foundation for Innovation: Infrastructure Operating Fund Hardwiring protein modifications as probes of signalling, epigenetic, and redox networks Term: 2014-2019; Total Value: $60,000 ($12,000 per year for 5 years).

7. Canadian Cancer Society Research Institute: Innovation Grant Targeting pathological phosphorylation in oncogenic pathways Term: 2016-2018; Total Value: $200,000 ($100,000 per year for 2 years).

8. NSERC Engage Grant. Bio-contained Bacillus subtilis for infection control. Partnered with Germiphene, Inc (Brantford, ON). Term 2018-2019; Total Value; $25,000.

9. Ontario Centres of Excellence Voucher for Innovation and Productivity. Bio-contained Bacillus subtilis for infection control. Partnered with Germiphene, Inc (Brantford, ON). Term 2018-2019; Total Value; $25,000 ($20K OCE + $5K Germiphene).

10. Tier 2 Canada Research Chair Supplement. Hardwiring protein modifications as probes of signalling, epigenetic, and redox networks. Term 2019-2020; Total Value; $20,000. 11. Tier 2 Canada Research Chair in Chemical Biology (renewal) Hardwiring protein modifications as probes of signalling, epigenetic, and redox networks Term: 2019-2024; Total Value: $500,000 ($100,000 per year for 5 years). 12. Canadian Institutes of Health Research Project Grant.

Pathways to neurodegeneration from natural human tRNA variation. co-PIs: C. Brandl, M. Duennwald, A. Moehring Term: 2019-2024; Total Value: $865,000.

Research funding awarded as Co-PI Total funding as co-PI since starting 1st independent position at Western: $511,368 1. Natural Sciences and Engineering Research Council of Canada (NSERC) RTI

A nano-UPLC system for the Q-Exactive mass spectrometer. (G. Lajoie lead PI). Term: 2016; Total Value: $150,000.

2. Natural Sciences and Engineering Research Council of Canada (NSERC) RTI

Delimitation of protein function, interaction networks through peptide arrays (S. Li lead PI). Term: 2016; Total Value: $150,000.

3. Natural Sciences and Engineering Research Council of Canada (NSERC) RTI as co-PI Robotic Instrumentation to Establish Workflows for Systematic Cell-Based Analyses. (D. Litchfield lead-PI). Term: 2017; Total Value: $150,000.


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4. Collaborative Research Seed Grant (CRSG), Western University. tRNA variation in diseases of proteostasis. (C. Brandl lead-PI, R. Hegele co-PI). Term: 2017-2019; Total Value: $61,368.

IX. LEAVES OF ABSENCE Since 2013, I was granted a total of 4 months leave, including two paternal leaves as follows: Leave 1: Dec 1, 2014 – Dec 15, 2014; May 5, 2015 – June 5, 2015 (1.5 months) Leave 2: Nov 12, 2017 – Dec 1, 2017; April 23, 2017 – May 25, 2017 (1.5 months) In addition, I was granted a total of 1-month medical leave: Medical Leave 1: Jan 19, 2015- Feb 19, 2015 (1 month)

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Curriculum vitae Patrick O’Donoghue, Ph.D....Curriculum vitae Patrick O’Donoghue, Ph.D. 5 26. Stephanie Anagnostou (Chem 4491, 2016-2017)