Postdoctoral Fellow

Alina Chan

Alina Chan

Human Frontier Science Program Postdoctoral Fellow

I am a postdoc from Canada directing various mammalian synthetic biology projects in the Silver lab, including de novo human artificial chromosomes (HACs), protein fusion therapeutics, and human-to-virus interactions. Our work regarding the delivery of synthetic genomes to human cells via yeast has been published in Nucleic Acids Research; the open access article is available here. Additionally, we are now a part of Genome Project-write: A Grand Challenge, which is an international research project to engineer and test large genomes in cell lines in order to understand the blueprint of life discovered in the original Human Genome Project. The white paper describes our pilot project to create a new generation of HACs.

I also created the Silver lab website and am the resident photographer for the lab.

I obtained my doctorate degree in 2014 at the University of British Columbia in the yeast genetics laboratory of Philip Hieter (APOYG!). I am thrilled to have the support of a Human Frontier Science Program Postdoctoral Fellowship.

Research focus: Human genome engineering

Ph. D., Biochemistry and Molecular Biology 2009-2014

University of British Columbia, Vancouver, BC

Roman M. Babicki Fellow and NSERC Doctoral Scholar

B. Sc. (Honours), Biochemistry and Molecular Biology 2005-2009

University of British Columbia, Vancouver, BC

Science Scholar and Dean’s Honour List

Postdoctoral 2015

Human Frontier Science Program Long Term Postdoctoral Fellowship

Natural Sciences and Engineering Research Council (NSERC) of Canada Postdoctoral Fellowship – gratefully declined

Doctoral 2009-2014

Roman M. Babicki Fellowship in Medical Research

NSERC Alexander Graham Bell Postgraduate Scholarship Doctoral

NSERC Alexander Graham Bell Canada Graduate Scholarship Master’s

Harry and Florence Dennison Fellowship in Medical Research

William and Dorothy Gilbert Graduate Scholarship in Biomedical Sciences

DeLill Nasser Travel Award for Professional Development in Genetics

Federation of European Microbiological Societies (FEMS) Meeting Grant

Peer Reviewed Journal Articles

Brown DM, Chan YA, Desai PJ, Grzesik P, Oldfield LM, Vashee S, Way JC, Silver PA, Glass JI. 2016. Efficient size-independent chromosome delivery from yeast to cultured cell lines. Nucleic Acids Research. PMID: 27980064 Download PDF

Chan YA, Hieter P, Stirling PC. 2014. Mechanisms of genome instability induced by RNA processing defects. Trends in Genetics. 30(6):245-253. PMID: 24794811

Chan YA*, Aristizabal MJ*, Leung PYT, Luo Z, Hamza A, Kobor MS, Stirling PC, Hieter P. 2014. Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genetics. 10(4): e1004288. *Authors contributed equally. PMID: 24743342

Braberg H, Jin H, Moehle E, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qui C, Hu F, Tang LK, Fraser JS, Holstege FCP, Kornberg R, Hieter P, Guthrie C, Kaplan CD, Krogan NJ. 2013. From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II. Cell. 154(4):775-788. PMID: 23932120

Stirling PC*, Chan YA*, Minaker SW*, Aristizabal MJ, Barrett I, Sipahimalani P, Kobor MS, Hieter P. 2012. R loop-mediated genome instability in mRNA cleavage and polyadenylation mutants. Genes & Development. 26(2): 163-175. *Authors contributed equally. PMID: 22279048

Auweter SD, Bhavsar AP, de Hoog CL, Li Y, Chan YA, van der Heijden J, Lowden MJ, Coombes BK, Rogers LD, Stoynov N, Foster LJ, Finlay BB. 2011. Quantitative mass spectrometry catalogues Salmonella pathogenicity island-2 effectors and identifies their cognate host binding partners. The Journal of Biological Chemistry. 286(27): 24023-24035. PMID: 21566117

 

International Conferences

Invited speaker

Prototyping Shuttle Human Artificial Chromosomes. Wyss Institute Retreat. Boston, USA, 2016.

HAC’ing Hs2.0. The 5th Annual Sc2.0 and Synthetic Genomes Conference. Edinburgh, UK, 2016.

De novo chromosomes that shuttle between yeast and mammalian systems. HGP-write: A Grand Challenge. Testing Large Genomes in Cells. Boston, USA, 2016.

Invited seminar

HAC’ing mammalian synthetic biology. The UK Centre for Mammalian Synthetic Biology Research. Edinburgh, UK, 2016.

De novo human artificial chromosomes for the advancement of mammalian synthetic biology. National University of Singapore, Department of Biochemistry. Singapore, 2016.

Plenary Speaker

Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. 26th International Conference on Yeast Genetics and Molecular Biology. Frankfurt, Germany. 2013.

Posters

Hacking mammalian synbio with artificial chromosomes and memory devices. The Third International Workshop on Mammalian Synthetic Biology. Cambridge, USA, 2016.

Interferon memory devices and human artificial chromosomes for programmable organoids. Synberc Meeting. Cambridge, USA, 2015.

Genomic DNA:RNA hybrids arise from DNA replication and kinetochore defects. Yeast Genetics Meeting. Seattle, USA. 2014. Honorable mention.

Genomic RNA:DNA hybrids arise from various defective RNA biogenesis, DNA repair and kinetochore processes. Mutagenesis Gordon Research Conference. Newport, USA. 2012.

R loop-mediated genome instability in mRNA cleavage and polyadenylation mutants. Canadian Institute for Advanced Research Genetic Networks Meeting. New York, USA. 2011.

Harvard Medical School, Dr. Pamela Silver, Department of Systems Biology    

Postdoctoral Fellow, October 2014 – Present

  • Designing and constructing de novo human artificial chromosomes, transcription-mediated epigenetic devices in mammalian systems, interferon-responsive memory devices for programmable organoids, and anti-STING yeast

University of British Columbia, Dr. Philip Hieter, Medical Genetics Laboratory         

Ph. D. in Biochemistry, September 2009 – April 2014

  • Investigating connections between RNA processing, DNA:RNA hybrids and genomic instability in yeast as a model organism

University of British Columbia, International Genetically Engineered Machines (iGEM)

Graduate Student Advisor, Team 2010, Team 2011 and Team 2012

  • Supervised a team of undergraduate science and engineering students to construct and computationally model biological systems for bacterial biofilm degradation (2010), mass production of monoterpenes (2011) or pathway distribution in microbial consortia (2012)

National University of Singapore, Dr. Paul Matsudaira, Department of Biological Sciences

Research Assistant, June 2009 – August 2009

  • Performed preliminary study of canal water ecogenetics and microbe visualization

University of British Columbia, Dr. Brett Finlay, Microbiology & Immunology Laboratory  

Undergraduate Honours Thesis in Biochemistry, July 2008 – April 2009

  • Researched Salmonella effectors and host interaction partners required for pathogenesis

 University of British Columbia, Dr. Yossef Av-Gay, Infectious Diseases Laboratory  

Undergraduate Research Student, May 2007 – May 2008

  • Researched Mycobacterium protein effectors and interactions

Program Development Committee Member for the Canadian Science Policy Conference 2017

  • I am helping to shape the content of CSPC by coordinating the call for panel proposals, reviewing, and evaluating the panel proposals based on the established criteria, liaising with panel organizers, and coordinating the panels according to conference objectives.

Organizer of HMS Systems Biology Department Meeting for Tissue Culture Scientists

  • I initiated and organized the first departmental meeting for tissue culture research (meeting minutes here), and am facilitating the creation of a department-wide database and mailing list for tissue culture-specific resources.

Harvard Synthetic Biology Bootcamp Mentor 2016 and 2017

  • Mentors designed the curriculum and teaching materials, including laboratory experiments, for a 10 day bootcamp for 20 undergraduate students. The bootcamp covered a range of topics including key principles of biology and genetics, synthetic biology design, and experimental design.

International Genetically Engineered Machines (iGEM) Competition Judge 2014 UBC iGEM Graduate Advisor, Teams 2010, 2011 and 2012

  • Gold Medals in 2011 and 2012, Best Model in North America in 2011
  • iGEM is the premiere undergraduate synthetic biology research competition, in which student teams worldwide design and conduct their own research plans over the summer and compete at the Massachusetts Institute of Technology. These research projects encompass laboratory experiments, computational modeling and community outreach, and address key issues pertinent to the environment, healthcare and industry. As a graduate advisor, I mentored approximately ten undergraduate students each year to brainstorm and plan their experiments. Being a part of the UBC iGEM team exposed me to diverse research areas as well as unique synthetic biology approaches. We collaborated with many research groups at UBC and other universities that aided us in our research in microbial biofilms (2010), engineered microbial consortia (2011) and monoterpene synthesis (2012). I actively supervised the students in the laboratory, in the design of their computational models, and in their outreach activities, which included delivering workshops at Science World in Vancouver. I also trained the team to present their work effectively at the competition. The UBC iGEM team has been very successful at the international competitions, winning several gold medals, as well as special awards for their computational models. More importantly, many of our iGEM team members gain valuable research and transferrable skills from this experience and several have gone on to become outstanding graduate and medical students. Ultimately, this experience broadened my horizons and inspired me to attain a postdoctoral position with Pamela Silver, a leading synthetic biology researcher at the Harvard Medical School. I look forward to running a lab in future that addresses important questions using a broad range of innovative approaches and skill sets.

UBC Biochemistry 203 Teaching Assistant 2013-2014

  • I assisted in the development of the new second year biochemistry course, BIOC 203 Fundamentals of Biochemistry, specifically in the design of the teaching material, problem sets and writing assignment. The course aimed to inculcate research skills in second year students and required them to write a professional review of a specific hemoglobin variant including original figures to explain structural differences and their significance. I created and delivered hourly tutorials six times a week, ran several review sessions, and graded student written assignments and exams. This was much more intensive compared to the average teaching assistant experience since I was able to provide input at every level of the course and regularly interact with every student in each cohort of over 100 students. It was a great opportunity for me to implement teaching tools that I had learnt about in science education courses and instructional workshops at UBC, such as providing students with lesson objectives, lessons that link real life problems to their course material, and clear grading criteria for their written project. I encouraged my students to seek out research opportunities at UBC and advised several of them one-to-one on their academic and career pursuits. I am very happy to see that many of my students have embarked on productive involvements as research students in laboratories at UBC. I hope to continue teaching and nurturing students as a university professor in future.

Let’s Talk Science UBC Teacher Partnership Program Coordinator 2010-2013

  • Let’s Talk Science (LTS) is a national charitable outreach organization that aims to create learning programs to engage youth and educators in science, technology, engineering and math. The Teacher Partnership Program is the core of LTS at UBC and is the most popular program for volunteers, teachers and students. As the Partnership Program Coordinator, I recruited and trained over 100 graduate students each year in partnership with schools across Vancouver. Graduate students work with teachers throughout the year to organize multiple lessons that focus on critical thinking and problem-solving through hands-on activities. This allows elementary and high school students to meet real scientists and help teachers supplement their science curriculum at no cost. During my three years as program coordinator, I interacted with and assisted hundreds of graduate students at UBC to plan and supply their lessons using my experience and LTS resources. This experience was vital to my development as a scientist. I was able to bridge scientific research and science literacy at the level of classroom visits as a volunteer, a coordinator and a mentor.

Since joining the Silver lab in October 2014, I have taken charge of and co-written several grants for different projects, often in collaboration with other labs and institutes, in applications to the NIH, DARPASynberc, and IARPA.

We have successfully obtained 2015-2016 funding for human artificial chromosomes from DARPA and Synberc, and 2017 funding for investigating viral factors from IARPA.

Education

 

Ph. D., Biochemistry & Molecular Biology

2009-2014

Philip Hieter Medical Genetics Laboratory

University of British Columbia, Vancouver, BC

 

Conference Talks

 

Invited speaker

HAC’ing Hs2.0. The 5th Annual Sc2.0 and Synthetic Genomes Conference. Edinburgh, UK, 2016.

De novo chromosomes that shuttle between yeast and mammalian systems. HGP2: A Grand Challenge. Synthesis of the human genome in order to understand life. Boston, USA, 2016.

 

Postdoctoral Awards

 

Human Frontier Science Program Long Term Postdoctoral Fellowship

Natural Sciences and Engineering Research Council (NSERC) of Canada Postdoctoral Fellowship

 

Leadership & Teaching

 

Harvard Systems Biology Meeting for Tissue Culture Organizer 2016

Harvard Synbio Bootcamp Mentor 2016

International Genetically Engineered Machines (iGEM) Competition Judge 2014

UBC iGEM Graduate Advisor 2010-2012

UBC Faculty of Medicine Research Council Graduate Student Member 2013-2014

UBC Biochemistry Teaching Assistant 2013-2014

Let’s Talk Science Partnership Program Coordinator 2010-2013

Research Experience

 

Human genome and epigenetic engineering, Pamela Silver Laboratory, Harvard, Postdoctoral Fellow, 2014 – Present

DNA:RNA hybrids, Philip Hieter Laboratory, UBC, PhD, 2009-2014

Ecogenetics, Paul Matsudaira Laboratory, National University of Singapore, Research Assistant, 2009

Salmonella pathogenesis, Brett Finlay Laboratory, UBC, Undergraduate Honours Thesis, 2008-2009

Mycobacterium pathogenesis, Yossef Av-Gay Laboratory, UBC, Undergraduate Research Student, 2007-2008