Master of Science, Bioinformatics Sept.2014 – May.2017
University of British Columbia, Vancouver, BC
Funded by CIHR and the CGS-M (see Awards section)
Thesis project (see Projects section)
Bachelor of Science, Biochemistry Sept.2008 – May.2013
University of British Columbia, Vancouver, BC
Completed the Co-operative Education Program
2016 CEEHRC Travel Award recipient
↳ Awarded $1,000 for the cost of travel to present at the ISMB 2016 conference in Orlando, Florida.
2016 John Bosdet Memorial Fund
2015 Canada Graduate Scholarship Master’s Award (CGS-M) recipient
↳ Administered by the Tri-Council Agencies (NSERC, SSHRC, CIHR), the CGS-M is a one year, non-renewable research training award valued at $17,500 to support students who demonstrate a high standard of achievement in undergraduate and early graduate studies.
2014 CIHR Strategic Training in Health Research Award recipient
↳ Awarded a two-year ($22,000/year) funding for M.Sc. training in Bioinformatics.
2013 NSERC Undergraduate Student Research Award
2008 UBC President’s Entrance Scholarship
↳ This one-time funding of $2,000 is to support academically qualified students who show an interest in joining the UBC community.
Co-authored in:
Siu et al. (2017) Characterization of the human thyroid epigenome. Journal of Endocrinology, 235(2):153-165. doi:10.1530/JOE-17-0145
Lever et al. (2017) A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics, 34(4):652-659. doi:10.1093/bioinformatics/btx613
Wang et al. (2017) Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes. Nature genetics, 49(49):856-865. doi:10.1038/ng.3849
Wong et al. (2017) Management of PET diagnosed thyroid incidentalomas in British Columbia Canada: Critical importance of the PET report. The American Journal of Surgery, 213(5):950-957.
doi:10.1016/j.amjsurg.2017.03.015
McPherson et al. (2016) Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nature Genetics. doi:10.1038/ng.3573
Eirew et al. (2015) Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature, 518(7539):422-6. doi: 10.1038/nature13952
Leon et al. (2012) Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text. Bioinformatics, 28(22):2963-70. doi: 10.1093/bioinformatics/bts542
Acknowledged in:
Zoubarev et al. (2012) Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics, 28(17):2272-3. doi: 10.1093/bioinformatics/bts430
Poster presentation, Intelligent Systems for Molecular Biology (ISMB) 2016 Conference July 9 & 10, 2016
Poster presentation, BTP/IOP/GSAT 2016 Retreat March 11, 2016
Oral presentation, Bioinformatics Research Rotation Presentation July 24, 2015
Oral presentation, Bioinformatics Research Rotation Presentation March 27, 2015
Oral presentation, Bioinformatics Research Rotation Presentation November 28, 2014
100 Days of Code Feb.2017 – Jun.2017
See my technical blog: http://csiu.github.io/blog/tag/100daysofcode
Formulated models using machine learning methods from Scikit-learn to enter Kaggle competitions
Setup and used PostgreSQL databases to gain experience with SQL and learn new technologies
Analyzed data using Python (eg. Pandas, Matplotlib, BeautifulSoup, Nltk, Theano), R, D3, & APIs
Characterization of the human thyroid epigenome Sept.2015 – May.2017
Jones Lab, Michael Smith Genome Sciences Centre
Modelled chromatin states from epigenetic features using hidden Markov models to produce 26 candidate models
Developed a new model selection criterion
Used Makefiles to create pipelines, organize code, and rerun analyses
Master’s Thesis:
Siu, C. (2017). Characterization of the human thyroid epigenome (T). University of British Columbia. Retrieved from https://open.library.ubc.ca/collections/ubctheses/24/items/1.0343360
Literature-based knowledge discovery of biomedical text May.2015 – Aug.2015
Jones Lab, Michael Smith Genome Sciences Centre
Contributed to the development of text mining and machine learning approaches to prioritize therapeutics from Medline abstracts and the full-text of open access papers
Visualized the output of MySQL database queries in R and D3
miRNA promoter recognition with CAGE and sRNA-seq Jan.2015 – Apr.2015
Wasserman Lab, Centre for Molecular Medicine and Therapeutics
Modified a miRNA promoter recognition method to include a new feature in Python
Evaluated a semi supervised statistical model trained on CAGE data, DNA sequence features, and sRNA-sequencing data
Primer Data Extraction & Blast API Sept.2014 – Dec.2014
Daley Lab, Centre for Heart Lung Innovation
Used data mining to extract primers sequences from academic papers
Made API calls to programmatically submit BLAST searches of primer sequences
Visier Inc. May.2017 – Present
Business Intelligence Consultant II (Aug.2020 – Present)
Guided data discovery consultation meetings with customers to educate, explore options, and gather requirements for delivering value on their business use cases
Created internal and customer-facing assets including best practice documentations in Confluence and ServiceNow
Sr. Data Management Engineer, Lead (Jul.2019 – Aug.2020)
Reviewed new customer onboarding activities and business logic customizations by assessing requirements, evaluating technical implementation design proposals, and doing code reviews
Followed the Scrum agile framework for managing sprint planning in JIRA and leading sprint review and retrospective meetings
Data Management Engineer II, Lead (Jul.2018 – Jul.2019)
Coached, mentored, and trained up junior and new staff
Gave presentations to small and large groups during training sessions, workshops, team all hands meetings, and new hire info sessions
Data Management Engineer I (May.2017 – Jul.2018)
Extracted, transformed, and loaded large amounts of customer HR data into the Visier application using Mercurial/Git and proprietary DSL
BCCRC | The University of British Columbia Jan.2014 – Aug.2014
Bioinformatics Research Assistant at the Shah Lab
Wrote Bash, Python, and R scripts for downstream analysis and pipeline development
Produced figures and limited text suitable for scientific manuscripts
Optimized analyses by leveraging parallel computing on compute clusters
BCCRC | Provincial Health Services Authority Sept.2013 – Dec.2013
Bioinformatics Research Intern at the Shah Lab
Ran automated analysis pipelines for data processing and data generation
Wrote scripts to rename files, parse data, and wrap third party software
Documented protocols, results, and comments on platforms such as the Atlassian Confluence wiki and Jira issue tracker
NSERC Undergraduate Student Research Award May.2013 – Aug.2013
Undergraduate Summer Research Student in the UBC Department of Statistics
Contributed to the collaborative development of an R package using Git and Github
Validated code integrity by writing and running unit tests
UBC Centre for High-throughput Biology May.2012 – Aug.2012
System Administrator Assistant
Produced and updated protocols for internal use and for end users
Setup user accounts on desktops, servers, and wikis
Monitored, backed up, and performed various system administrative tasks using Nagios, Bacula, CFengine, and Request Tracker
UBC Centre for High-throughput Biology Sept.2011 – Apr.2012
Bioinformatics Research Assistant at the Pavlidis Lab
Annotated Gene Expression Omnibus datasets that were to be imported with ontology terms
Evaluated software across multiple operating systems and reported issues on BugZilla
Assessed the quality of microarray data for the FishManOmics project headed by the Department of Fisheries and Oceans Canada
Biofine International Inc. May.2011 – Aug.2011
Organic Chemistry Synthesis Laboratory Assistant
Verbally communicated with supervisors to receive instructions for the execution of experiments
Researched, experimented, and evaluated the method of Marfey’s reaction for enantiomeric resolution of amino acids
Multitasked in coordination between executing experiments, keeping records, restocking supplies, and cleaning glassware
A&W Food Services of Canada July.2007 – Oct.2010
Cashier
Provided excellent customer service by responding in a timely manner, listening to what the customer has to say, and keeping an upbeat positive attitude
Took initiative to find extra tasks when scheduled duties were completed
Pacific National Exhibition Fair time
Concessions Attendant at Triple-O’s in August 2006, 2007, 2008, and 2009
Maintained high standards of customer service during high-volume, fast-paced operations
Handled currency and credit transactions quickly and accurately
Conference Volunteer, VR/AR Global Summit Sept.2018
Greeted guests/speakers/exhibitors, provided directions, and made sure things go according to plan
Judge, Technovation Challenge May.2018
Inspired the next generation of innovators by motivating girls ages 10-18 to learn and improve their skills by providing constructive feedback to continue to develop their product
Event Organizer, Hackseq: https://www.hackseq.com Oct.2017
Organized a genomics hackathon to bring individuals with diverse backgrounds together to collaborate in person and online on scientific questions and problems in genomics
Authored a Medium article to jounnal the event (https://medium.com/@celiassiu/hackseq17-661060a64bb1)
Helper, Software Carpentry workshop Oct.2016 & Feb.2017
Troubleshot and helped students learn Git, GitHub, Bash, Python, and Jupyter Notebook
Wayfinder & Healthy Heart Resource Centre Clerk, St. Paul’s Hospital Feb.2013 – Aug.2013
Approached, greeted, and helped patients and visitors find their way
Welcomed and provided information and assistance to visitors of the resource centre