Javier A.Alfaro SOFTWARE DEVELOPER·ALGORITHM DEVELOPER · DATA SCIENTIST · COMPUTATIONAL BIOLOGIST 1/5 Rankin Avenue, Edinburgh, Scotland, United Kingdom (+44)-7444-376002 | [email protected] | PhD, MSc “Technology helps us look into and shape the future. Through biology we learn the deep history of nature’s technology. ” www.proteogenomics.ca

Highlights & Qualifications • Cancer researcher focused on cancer immunology, an�gen processing and immune-evasion • Innova�ve domain expert in computa�onal (MS, structure, global expression, integra�ve -) • Mastery in computa�onal biology, algorithm development, data-science and high-throughput compu�ng • 10 years of experience suppor�ng biologists as a domain expert in bioinforma�cs data analysis • Interna�onally recognized through mul�-disciplinary collabora�on, invited talks and conference presenta�ons • Data science group leader developing computa�onal infrastructure and recrui�ng team members from the ground up Education University Of Toronto PhD in Medical Biophysics Toronto, ON, Canada 2012-2017 Dalhousie University MSc Biochemistry Halifax, NS, Canada 2009-2012 University of Victoria Double Major in Biochemistry Victoria, BC, Canada 2003-2008 and Computer Science Experience Independent Research University of Gdansk Gdansk, Poland Fellow University of Edinburgh Edinburgh, United Kingdom 2018-current • Established and led an interna�onal team of 6 data scien�sts and experimentalists opera�ng between three partner Universi�es: The University of Edinburgh (UK), The University of Gdansk (Poland) and Université Paris Diderot (France). The group was established under the umbrella of the Interna�onal Center for Cancer Vaccine Science in Gdansk, Poland. • Integrated mul�-omic datasets to be�er understand cancer biology, an�gen processing and presenta�on, immune-evasion. Developed computa�onal pipelines to characterize neoan�gens for cancer-vaccine development. • Planned and executed the delivery of the IT infrastructure for the en�re center, including access to high-performance compu�ng, google cloud resources, centralized network storage, and an online repor�ng system. • Interviewed and hired a team of scien�sts with diverse backgrounds and implemented an effec�ve training program to on-board data-scien�sts lacking domain exper�se and biologists lacking data-science exper�se. • Developing a memorandum of understanding (MOU) with interna�onal partners to support collabora�on in key areas of technology and algorithm development for cancer vaccine science. Doctorate project University Of Toronto Toronto, ON, Canada 2012-2017 • Delivered computa�onal exper�se to two world-class cancer biomarker discovery labs. Mastered computa�onal proteomics and integra�ve -omics while developing a pipeline to iden�fy protein muta�ons in clinical samples. • Advised mul�-disciplinary collaborators on project progress and challenges via succinct e-mails and short presenta�ons. Outlined problems and ranked solu�ons so that informed decisions on the project could be made. • Par�cipated in a start-up compe��on for funding wherein I proposed a company that would make my thesis work available to the community as a profitable enterprise. Placed as a finalist in the compe��on. This solidified an my interest in transla�ng transferring emerging technologies to the clinic. • Thesis en�tled: Detec�ng protein variants within datasets: h�p://hdl.handle.net/1807/82952 Masters project Dalhousie University Halifax, NS, Canada 2009-2012 • Worked with a biologist and a sta�s�cian to understand evolu�onary constraints on protein sequences, which is important for protein engineering. Developed a maximum-likelihood model of protein evolu�on incorpora�ng protein structure constraints. Thesis: h�p://hdl.handle.net/10222/54064 Honors project University of Victoria Victoria, BC, Canada 2008-2008 • Analyzed the diffrac�on data from many crystallography experiments in order to characterize the poorly understood structure and func�on of the ABO blood group enzyme. Results supported an interna�onal collabora�ve research effort that clarified important aspects of the enzyme’s func�on. Data scientist University of Victoria Victoria, BC, Canada 2008-2008 • Employed a machine learning approach to intelligently dis�nguish between protein structures of two classes of enzymes carrying out different types of reac�ons. Gained insights into glycosyltransferase enzyme family mechanisms.

July 17, 2019 JAVIER A. ALFARO RÉSUMÉ 1/4 Technician/Analyst Dept. Bioc., UVIC Victoria, BC, Canada 2005-2009 • Purified proteins and analyzed the results of x-ray crystallography experiments. Work resulted in a first author and several co-author publica�ons (see back for full list). Home care aide Cridge Brain Injury Center Victoria, BC, Canada 2007-2008 • Assisted ten head-injured pa�ents at a permanent residence with their personal needs and overall wellness. Improved resident lifestyles by engaging in a�er-work social ac�vi�es. • To help a visually impaired resident connect with family, developed a program (Python) to help find and dial the number of contacts. Resident used the program o�en, resul�ng in reduced feelings of isola�on and greater social independence. Forestry data technician Pacific Forestry Center Victoria, BC, Canada 2003-2003 • Worked in a two man team for four months in a remote region of Bri�sh Columbia collec�ng data on an insect infesta- �on for use in models predic�ng outbreaks. Careful planning, dedica�on and long hours ensured that a very high quality dataset was collected. Publications 1. Kalathiya U, Padariya M, Pawlicka K, Hupp T, Verma C, Houston D and Alfaro JA. Structural consequences of cancer muta�ons at the UPF2 and ATP-binding site of NMD factor UPF1. 2019. Scien�fic Reports. Submi�ed. 2. Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T and Boutros PC. The Proteogenomic Landscape of Curable Prostate Cancer. 2019. Cancer Cell. 35(3):414-427.e6. 3. Sinha A, Principe S, Alfaro JA, Ignatchenko A, Ignatchenko V, and Kislinger, T. Proteomic profiling of secreted proteins, exosomes, and microvesicles in cell culture condi�oned media. 2018. In The Surfaceome (pp. 91-102). Humana Press, New York, NY. 4. Alfaro JA, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC and Kislinger T. Detec�ng protein variants by mass-spec- trometry: A comprehensive study in cancer cell-lines. 2017. Genome Medicine. 9:62. 5. Sinha A, Alfaro JA, and Kislinger T. Characteriza�on of protein content present in exosomes isolated from condi�oned media and urine. 2017. Current Protocols in Protein Science. 87:24.9.1-24.9.12. 6. Alfaro JA, Sinha A, Kislinger T and Boutros PC. Onco-proteogenomics: cancer proteomics joins forces with . 2014. Nature Methods. 11(11):1107-13. 7. Weinreb I, Piscuoglio S, Martelo�o LG, Waggo� D, Ng CK, Perez-Ordonez B, Harding NJ, Alfaro JA, et al. Hotspot ac�vat- ing PRKD1 soma�c muta�ons in polymorphous low-grade adenocarcinomas of the salivary glands. 2014. Nature Genet- ics. 46(11):1166-9. 8. Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD and Batada NN. Aber- rant DNA methyla�on reprogramming during induced pluripotent stem cell genera�on is dependent on the choice of reprogramming factors. 2014. Cell Regenera�on. 3(1):1. 9. Johal AR, Blackler RJ, Alfaro JA, Schuman B, Borisova S and Evans SV. pH-induced conforma�onal changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrosta�c interac�ons in the forma�on of the semi-closed state. 2014. Glycobiology. 24(3):237-46. 10. Johal AR, Schuman B, Alfaro JA, Borisova S, Seto NOL and Evans SV. Sequence-dependent effects of cryoprotectants on the ac�ve sites of the human ABO(H) blood group A and B glycosyltransferases. 2012. Acta Cryst. D68, 268–276. 11. Alfaro JA, Zheng RB, Persson M, Le�s JA, Polakowski R, Bai Y, Borisova SN, Seto NO, Lowary TL, Palcic MM and Evans SV. ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conforma�onal changes. 2008. J Biol Chem. 283(15):10097-10108. Additional Training 1. Genomics: GATK Variant Calling Workshop. (2019). Copenhagen, Denmark. • 4 day workshop covered best-prac�ces from the Broad in single-nucleo�de and copy-number variant calling from exome sequencing and whole genome sequencing datasets 2. Biology: EMBO Workshop: An�gen processing and presenta�on 10. (2019). Paris, France. • 4 days of detailed lectures on the biology of an�gen processing and presenta�on across the spectrum of MHC and MHC-like molecules 3. Mass Spectrometry School in Biotechnology and Medicine. (2019). Dubrovnik Croa�a • 6 day workshop covering all aspects of mass-spectrometry. Topics include sample prepara�on for proteomics, lipidom- ics and , separa�on by liquid , ion-mobility separa�on, different instrument setups, mass analyzers and computa�onal proteomics. I lectured on computa�onal proteomics.

July 17, 2019 JAVIER A. ALFARO · RÉSUMÉ 2/4 Posters, Presentations & Lectures 1. Lecturer: Didac�c lecture in computa�onal proteomics + 2 hands on workshops. Course instructor. Mass Spectrometry in Biotechnology and Medicine. 2019. Dubrovnik, Croa�a. 2. Presenta�on: Bedran G, Mayordomo MY, Pawlika K, Saxena S, Prakash A, Goodle� D and Alfaro JA*. Characterizing an�gen at the cell surface, a computa�onal perspec�ve.Invited Speaker. Center for Advanced Academic Studies. 2019. Dubrovnik, Croa�a. 3. Presenta�on: Bedran G, Mayordomo MY, Pawlika K, Saxena S, Prakash A, Goodle� D and Alfaro JA*. Comprehensively characterizing immunopep�dome landscapes. Invited Speaker. University of Maryland. Faculty of Den�stry. 2019. Bal�more, United States. 4. Presenta�on and conference poster: Bedran G, Mayordomo MY, Pawlika K, Saxena S, Prakash A, Goodle� D and Alfaro JA*. Bioinforma�cs strategies for comprehensively characterizing immunopep�dome landscapes. Conference on An�gen Processing and Presenta�on. 2019. Paris, France. 5. Presenta�on: Alfaro JA*, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC and Kislinger T. Detec�ng protein variants by mass-spectrometry: A comprehensive study in cancer cell-lines. Conference on Single Molecule Protein Sequencing. 2017. Del�, Netherlands. 6. Conference Poster: Alfaro JA*, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC and Kislinger T. Detec�ng protein variants by mass-spectrometry: A comprehensive study in cancer cell-lines. 2017. Toronto, Canada. 7. Lecturer: Machine learning applied to cancer biology. 2016. São Paulo, Brazil. 1 day of sta�s�cs at the workshop. 8. Conference Poster: Alfaro JA*, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC and Kislinger T. Onco- proteogenomics: Exploring the complexity of the cancer genome at the level. Canadian Cancer Research Conference. 2015. Montreal, Canada. 9. Wright Keynote: Alfaro JA*, Susko E., Roger A. A site-independent structurally constrained phylogene�c model of protein evolu�on. Mechanisms of Protein Evolu�on. 2011. Denver, USA. 10. Conference Poster 3DSIG: Alfaro JA*, Susko E., Roger A. Applica�ons of structurally constrained models of protein evolu�on to problems in structural bioinforma�cs. 2010. Boston, USA. Committees and Defenses 1. PhD Defense: Unraveling Proteins at the Single Molecule Level Using Nanopores. PhD Examiner. (2019). Del�, Nether- lands. 2. Commi�ee: Commercializa�on push: Industry needs and biomedical research in Poland. (2019) Krakow. Poland. • Par�cipated in a mee�ng with execu�ves from major pharmaceu�cal companies to discuss industry needs in poland. Honors & Awards 2017-2017 $8500 University of Toronto Doctoral Comple�on Award Internal 2017-2017 $1000 Medical Biophysics Travel Award Internal 2016-2017 $20,000 Scace Graduate Fellowship in Prostate Cancer Research Internal 2013-2016 $105,000 Alexander Graham Bell Canada Graduate Scholarships-Doctoral Program External 2011-2012 $16,824 Nova Sco�a Health Research Award External 2016-2017 $9,134 Medical Biophysics Excellence UTF Scholarship Internal 2012-2013 $9,134 Medical Biophysics Excellence UTF Scholarship Internal Departmental Committees 2017-2017 Senior student representa�ve, Commi�ee for Improved Student Experience 2016-2017 Social commi�ee member, Medical Biophysics Graduate Student Associa�on 2012-2013 Department retreat organizer, Geneva Park Departmental Retreat Commi�ee

Technical Skills Wri�ng Edi�ng, reviewing and wri�ng manuscripts, centralized wri�ng Bioinforma�cs Integra�ve -omics, computa�onal proteomics, computa�onal molecular evolu�on Analy�cal Machine learning, algorithm design, mathema�cs and sta�s�cs Programming Perl (5 yr), Python (4 yr), C/C++ (3 yr), Java (3 yr), R (10 yr), LaTeX (5 yr) Visualiza�on La�ce, ggplot, plo�ng.general, d3.js, Adobe Illustrator, Adobe Photoshop Environments Sun Grid Engine (cluster compu�ng), SLURM (cluster compu�ng), Windows, UNIX, Mac OS Languages English, Spanish

July 17, 2019 JAVIER A. ALFARO · RÉSUMÉ 3/4 Javier A.Alfaro SOFTWARE DEVELOPER·ALGORITHM DEVELOPER · DATA SCIENTIST · COMPUTATIONAL BIOLOGIST 1/5 Rankin Avenue, Edinburgh, Scotland, United Kingdom (+44)-7444-376002 | [email protected] | PhD, MSc

The following professors have generously agreed to provide letters of support for this application upon request. These referees cover the breadth of my experience as a researcher. I recommend Dr. Paul Boutros, Dr. Edward Susko and Dr. Andrew Roger for questions regarding the more computational aspect of my work. I recommend Dr. Ted Hupp, Dr. Thomas Kislinger, Dr. Andrew Roger and Dr. Stephen Evans to gain insight on biological or clinical questions I’ve had experience with. Dr. Chirlmin Joo has a unique perspective on my capacity as an independent-researcher through our early-stage collaboration.

Thanks for your consideration, Javier A. Alfaro

Referees Independent Research University of Gdansk Gdansk, Poland Fellow University of Edinburgh Edinburgh, United Kingdom 2018-current Prof. Ted Hupp Prof. Chirlmin Joo Director of ICCVS (University of Gdansk) Director Kavli Institute of NanoScience and Chair of Cancer Research (University of Edinburgh) Prof. Department of BioNanoScience Edinburgh Cancer Research Center TU-Delft University of Edinburgh [email protected] [email protected] Emerging -Omics technologies

Doctorate project University Of Toronto Toronto, ON, Canada 2012-2017 Detecting variant proteins by mass spectrometry Dr. Thomas Kislinger Dr. Paul Boutros Professor and Chair Professor and Director of Cancer Data Science Department of Medical Biophysics University of California University of Toronto Los Angeles [email protected] [email protected] Clinical proteomics, mass-spectrometry Cancer genomics, integrative -omics Masters project Dalhousie University Halifax, NS, Canada 2009-2012 Capturing the dynamics of protein sequence evolution through site-independent structurally constrained phylogenetic models Dr. Andrew Roger Dr. Edward Susko Professor and Director Professor and Statistician Center for and Department of statistics Evolutionary [email protected] [email protected] Statistical modelling Evolutionary genomics, integrative -omics, Statistical models of evolution Honors project University of Victoria Victoria, BC, Canada 2008-2008 Structure and function of the ABO(H) blood group glycosyltransferases Dr. Stephen Evans Professor and Associate Dean of Graduate Studies Department of Biochemistry University of Victoria [email protected]

July 17, 2019 JAVIER A. ALFARO RÉSUMÉ 4/4