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who i am

I use code to solve big biological data problems. tools: deep learning, network analysis, non-parametric and Bayesian statistics. domain expertise in life sciences: molecular biology, microbiology, genetics and genomics, and a bit of ecology.

education

peer-reviewed publications

I have published scholarly articles in peer-reviewed journals. I believe in open science, and have posted pre-prints of work that I personally led.

  1. Ma, E. J. et. al. Reticulate evolution is favored in influenza niche switching. PNAS (2016) (1st author) (link, pdf, preprint)
  2. Hill, N. J. et al. Switching transmission strategies is key to infecting a mobile host: Influenza A virus across the annual cycle of wild birds. Ecology Letters (2016) (2nd author) (link, pdf)
  3. Hussein, I. T. M. et al. New England harbor seal H3N8 influenza virus retains avian-like receptor specificity and replicates in human lung cells. Scientific Reports (2016) (3rd author) (link, pdf)
  4. Bahl, J et. al. Ecosystem interactions and reassortment dynamics underlie the emergence of influenza A viruses with pandemic potential. PLoS Pathogens (2016) (5th author) (link, pdf)
  5. Hussein, I. T. M. et. al. A point mutation in the polymerase protein PB2 alleviates the restriction on a wild reassortant H9N2 influenza isolate, enabling replication in human cells. Infection, Genetics & Evolution (2016) (2nd author) (link, pdf)
  6. Bui, V. N. et al. Genetic characterization of a rare H12N3 avian influenza virus isolated from a green-winged teal in Japan. Virus Genes (2015). (8th author) (link, pdf)

funding

In collaboration with colleagues, we have won funding for research that I have been involved in.

  1. Broad Next10, 1 Jan 2017 - 1 Jan 2018. PI. Title: Data science for genomic surveillance: predicting and evaluating pathogen risk from genomic data. $40,000 (proposal)
  2. Broad Next10, 1 Jun 2016 - 1 Jun 2017. Co-PI. Title: Scalable mapping of viral polymerase genotype to phenotype. $40,000 ( proposal)
  3. CIHR/MSFHR Training Program in Transplantation, 1 June 2009 - 31 August 2009. Rapid whole cell biosensors for sensitive transplantation diagnostics. $6000 (proposal)

academic teaching

I have led and assisted with classes at MIT.

  1. 20.506 - BE Stats for Grads, 2016 Winter @ MIT. Co-taught basic probability, hypothesis testing and inference. (notebooks)
  2. 20.106 - Systems Microbiology, 2015 Fall @ MIT. Co-taught one module on machine learning, bayesian statistics, and phylogenetic inference in infectious disease. (notebooks)
  3. 20.109 - Biological Engineering Laboratory, 2012 Fall @ MIT. Served as Teaching Assistant in the synthetic biology module. (webpage)

workshops

I have led workshops at community and technical conferences. My workshop material can be found on the projects page.

  1. PyCon 2017 @ Portland, OR. Tutorial Leader: Network Analysis Made Simple (video)
  2. PyCon 2017 @ Portland, OR. Tutorial Leader: Best Testing Practices for Data Science (video)
  3. SciPy 2016 @ Austin, TX. Tutorial Leader: Network Science and Statistics: Fundamentals and Applications (video)
  4. PyCon 2016 @ Portland, OR. Tutorial Leader: Practical Network Analysis Made Simple (video)
  5. Open Data Science Conference 2016 @ Boston, MA. Workshop Leader: Network Analysis Fundamentals
  6. Broad Institute NextGen Workshops 2016 @ Cambridge, MA. Tutorial Leader: Machine Learning with scikit-learn
  7. PyData 2015 @ New York, NY. Tutorial Leader: Network Analysis Fundamentals (video)
  8. Data Science for Social Good Conference 2015 @ Boston, MA. Tutorial Leader: Network Analysis Fundamentals
  9. PyCon 2015 @ Montreal, QC. Tutorial Leader: Practical Network/Graph Analysis Made Simple (video)
  10. PyCon 2014 @ Montreal, QC. Tutorial Leader: How to formulate a (science) problem and analyze it using Python code (video)

individual mentorship

These are the students whom I have individually mentored over the years.

  1. Vivian Zhong, MIT Biological Engineering.
  2. Justin Zabilansky, MIT Biological Engineering. Currently at AeroFarms. (linkedin)
  3. Andrea Nickerson, MIT Biological Engineering. Currently at Silver Creek Pharmaceuticals. (linkedin)

talks

Throughout my undergraduate and graduate career, I have given talks on my research and shared my experience as a mentor to junior students.

  1. PyCon 2017 @ Portland, OR. Bayesian Statistical Analysis with Python (video, repository)
  2. Thesis Defence @ MIT, Cambridge, MA. Identification of Reassortant Influenza Viruses At Scale - Algorithm and Applications (slides, video)
  3. Quantitative Systems Pharmacology Day @ Cambridge, MA. Deep Learning Methods for Learning Phenotype from Genotype (slides)
  4. Big Data Boston Meetup @ Boston, MA. networks, networks everywhere! (slides)
  5. IMED 2016 Hackathon @ Vienna, Austria. Animal Village: Sharing Local Knowledge Globally (slides, video (one of 6 highlighted hackathon pitches))
  6. UBC Science One Seminar Series 2016 @ UBC Vancouver. What Science One did to my brain. (slides, figshare, slides source)
  7. Center of Excellence for Influenza Research and Surveillance (CEIRS) Annual Meeting 2015 @ Rochester NY. Speaker: Reticulate evolution primes a pathogen to cross host phylogenetic barriers (slides)
  8. Broad Institute Infectious Disease Initiative (IDI) weekly seminar. (Invited) 12 Feb 2016. Reassortment is favoured in influenza niche switching. (chalk talk, no slides)
  9. SciPy 2015 Lightning Talks. Test All Your Data! (video)
  10. Boston Python Lightning Talks. Test All Your Data! (slides)
  11. CSB Seminar Series. Reticulate evolution primes influenza to cross host barriers. (Invited) (slides)
  12. UBC Multidisciplinary Undergraduate Research Conference (MURC) 2009 @ Vancouver BC. Talk Presenter: T Cells Aggravate Intestinal Fibrosis (Conference Talk Prize)

posters

I have had the privilege of presenting my research work at poster sessions around the world.

  1. Quantitative Systems Pharmacology Day @ Cambridge, MA. Deep Learning Methods for Learning Phenotype from Genotype (Poster Winner) (poster)
  2. Computational Aspects of Biological Information, 2016 @ Cambridge, MA. Interpretable deep learning models to predict protein phenotype from genotype (poster)
  3. International Meeting on Emerging Diseases, 2016 @ Vienna, Austria: A real-time surveillance dashboard for monitoring viral phenotype from sequence. (poster)
  4. Center for Environmental & Health Sciences Poster Session, 2016 @ Cambridge, MA: Interpretable deep learning models to predict protein phenotype from genotype (poster)
  5. Broad Institute Annual Retreat 2015 @ Boston, MA: Reassortment is favoured in influenza niche switching (Poster Winner) (poster)
  6. Center for Environmental & Health Sciences Poster Session, 2015 @ Cambridge, MA: Reassortment primes in uenza for host group switches (poster)
  7. Gordon Research Conference on Ecological and Evolutionary Genomics 2015 @ Biddeford, ME: Reticulate evolution primes a pathogen to cross host phylogenetic barriers (poster)
  8. SciPy 2015 @ Austin, TX: Reassortment primes influenza for host group switches (poster)
  9. Center for Environmental & Health Sciences Poster Session, 2014 @ Cambridge, MA: Network-based methods for identifying reassortant influenza viruses (Poster Winner) (poster)
  10. Rising Stars of Research 2008 @ Vancouver, BC. Poster Presenter: The Role of T Cells in Intestinal Fibrosis (Poster Winner)

community service

  1. PLOS Computational Biology. I have reviewed one paper for PCB.
  2. SciPy 2016 Financial Aid Committee. I served as one of two co-chairs (myself & Dr. Scott Colis, ANL) for the SciPy 2016. Together with the Diversity Chair (Celia Cintas, Universidad Nacional del Sur), we ensured that a broad range of qualified applicants received partial or full funding, disbursing $30,000 in financial scholarships. (website)
  3. SciPy 2016 Program Committee. I helped evaluate talks in the Life Sciences track.
  4. PyCon 2016 Program Committee. I pitched in with evaluating and championing talks that I thought would be beneficial for the community. In particular, I pushed for scientific applications of Python.
  5. Boston Python Tutorial Lead. I have assumed the role of helping put together workshops/tutorial sessions for the Boston Python community, led by community instructors.
  6. Boston Python Co-Organizer. I occasionally stand in for Ned Batchelder as the guy who hollers at the Project Night crowd to help people find other people to talk with.

certifications

  1. Software Carpentry Instructor, 2016 (certificate)
  2. Data Carpentry Instructor, 2016 (certificate)

awards

  1. 1st Place Poster Prize, Quantitative Systems Pharmacology Day @ MIT, 2017.
  2. Graduate Student Council Travel Grant @ MIT, 2016.
  3. Distinguished Poster Award, 11th Annual Broad Institute Retreat @ MIT, 2015. (certificate)
  4. Best Graduate Student Poster, CEHS Poster Session @ MIT, 2014. (certificate)
  5. Best Student Presentation, Multidisciplinary Undergraduate Research Conference @ UBC, 2009.
  6. Best Student Poster, FINDER Division, Rising Stars of Research @ UBC, 2008.

scholarships & fellowships

  1. SciPy 2015 Conference Attendance Scholarship @ SciPy Conference, 2015.
  2. Viterbi Fellowship @ MIT, 2011
  3. Charles and Jane Banks Scholarship @ UBC, 2010
  4. Dean of Science Scholarship @ UBC, 2010
  5. Arthur Whitehead Science One Memorial Scholarship @ UBC, 2007
  6. UBC President's Entrance Scholarship @ UBC, 2006