Eric J. Ma
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. find me online at http://www.ericmjl.com/.
experience
- Novartis Institutes for Biomedical Research, 2017-Present
- Investigator II, Data Science & Statistical Learning (2018-Present)
- Investigator I, Data Science & Statistical Learning (2017-2018)
education
- Sc.D.: Biological Engineering, MIT, 2017
- Advisor: J. A. Runstadler, PhD, DVM
- Committee: M. Bathe, PhD (Chair), J-P. Onnela, PhD
- Thesis (in writing): Identification of Reassortant Influenza Viruses At Scale - Algorithm and Applications
- B.Sc.: Integrated Sciences, UBC, 2010 (with Distinction)
- Advisors: B. B. Finlay, PhD; G. A. Grassl, PhD
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.
- Ma, E. J. et. al. Reticulate evolution is favored in influenza niche switching. PNAS (2016) (1st author)
- 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)
- 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)
- Bahl, J et. al. Ecosystem interactions and reassortment dynamics underlie the emergence of influenza A viruses with pandemic potential. PLoS Pathogens (2016) (5th author)
- 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)
- 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)
funding
In collaboration with colleagues, we have won funding for research that I have been involved in.
- 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
- Broad Next10, 1 Jun 2016 - 1 Jun 2017. Co-PI. Title: Scalable mapping of viral polymerase genotype to phenotype. $40,000
- CIHR/MSFHR Training Program in Transplantation, 1 June 2009 - 31 August 2009. Rapid whole cell biosensors for sensitive transplantation diagnostics. $6000
academic teaching
- 20.506 - BE Stats for Grads, 2016 Winter @ MIT. Co-taught basic probability, hypothesis testing and inference.
- 20.106 - Systems Microbiology, 2015 Fall @ MIT. Co-taught one module on machine learning, bayesian statistics, and phylogenetic inference in infectious disease.
- 20.109 - Biological Engineering Laboratory, 2012 Fall @ MIT. Served as Teaching Assistant in the synthetic biology module.
workshops
- PyCon 2017 @ Portland, OR. Tutorial Leader: Network Analysis Made Simple
- PyCon 2017 @ Portland, OR. Tutorial Leader: Best Testing Practices for Data Science
- SciPy 2016 @ Austin, TX. Tutorial Leader: Network Science and Statistics: Fundamentals and Applications
- PyCon 2016 @ Portland, OR. Tutorial Leader: Practical Network Analysis Made Simple
- Open Data Science Conference 2016 @ Boston, MA. Workshop Leader: Network Analysis Fundamentals
- Broad Institute NextGen Workshops 2016 @ Cambridge, MA. Tutorial Leader: Machine Learning with
scikit-learn
- PyData 2015 @ New York, NY. Tutorial Leader: Network Analysis Fundamentals
- Data Science for Social Good Conference 2015 @ Boston, MA. Tutorial Leader: Network Analysis Fundamentals
- PyCon 2015 @ Montreal, QC. Tutorial Leader: Practical Network/Graph Analysis Made Simple
- PyCon 2014 @ Montreal, QC. Tutorial Leader: How to formulate a (science) problem and analyze it using Python code
mentorship
- Vivian Zhong, MIT Biological Engineering. Went on to be a UROP in the Alm lab at MIT.
- Justin Zabilansky, MIT Biological Engineering. Went on to work at AeroFarms.
- Andrea Nickerson, MIT Biological Engineering. Went on to work at Silver Creek Pharmaceuticals.
talks
- PyCon 2017 @ Portland, OR. * Bayesian Statistical Analysis with Python* (accepted)
- Big Data Boston Meetup @ Boston, MA. networks, networks everywhere!
- IMED 2016 Hackathon @ Vienna, Austria. Animal Village: Sharing Local Knowledge Globally, (one of 6 highlighted hackathon pitches)
- UBC Science One Seminar Series 2016 @ UBC Vancouver. What Science One did to my brain. 1. 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
- Broad Institute Infectious Disease Initiative (IDI) weekly seminar. (Invited) 12 Feb 2016. Reassortment is favoured in influenza niche switching. (chalk talk, no slides)
- SciPy 2015 Lightning Talks. Test All Your Data!
- Boston Python Lightning Talks. Test All Your Data!
- CSB Seminar Series. Reticulate evolution primes influenza to cross host barriers. (Invited)
- UBC Multidisciplinary Undergraduate Research Conference (MURC) 2009 @ Vancouver BC. Talk Presenter: T Cells Aggravate Intestinal Fibrosis (Conference Talk Prize)
posters
- Computational Aspects of Biological Information, 2016 @ Cambridge, MA. Interpretable deep learning models to predict protein phenotype from genotype
- International Meeting on Emerging Diseases, 2016 @ Vienna, Austria: A real-time surveillance dashboard for monitoring viral phenotype from sequence.
- Center for Environmental & Health Sciences Poster Session, 2016 @ Cambridge, MA: Interpretable deep learning models to predict protein phenotype from genotype
- Broad Institute Annual Retreat 2015 @ Boston, MA: Reassortment is favoured in influenza niche switching (Poster Winner)
- Center for Environmental & Health Sciences Poster Session, 2015 @ Cambridge, MA: Reassortment primes in uenza for host group switches
- Gordon Research Conference on Ecological and Evolutionary Genomics 2015 @ Biddeford, ME: Reticulate evolution primes a pathogen to cross host phylogenetic barriers
- SciPy 2015 @ Austin, TX: Reassortment primes influenza for host group switches
- Center for Environmental & Health Sciences Poster Session, 2014 @ Cambridge, MA: Network-based methods for identifying reassortant influenza viruses (Poster Winner)
- Rising Stars of Research 2008 @ Vancouver, BC. Poster Presenter: The Role of T Cells in Intestinal Fibrosis (Poster Winner)
- SciPy 2017 Financial Aid Committee. I served a second year as one of the two co-chairs with Dr. Scott Collis for the Financial Aid committee.
- PLOS Computational Biology. I have reviewed one paper for PCB.
- SciPy 2016 Financial Aid Committee. I served as one of two co-chairs (myself & Dr. Scott Collis), 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.
- SciPy 2016 Program Committee. I helped evaluate talks in the Life Sciences track.
- 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.
- 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.
- 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
- Software Carpentry Instructor, 2016
- Data Carpentry Instructor, 2016
awards
- Graduate Student Council Travel Grant @ MIT, 2016
- Distinguished Poster Award, 11th Annual Broad Institute Retreat @ MIT, 2015.
- Best Graduate Student Poster, CEHS Poster Session @ MIT, 2014.
- Best Student Presentation, Multidisciplinary Undergraduate Research Conference @ UBC, 2009.
- Best Student Poster, FINDER Division, Rising Stars of Research @ UBC, 2008.
scholarships & fellowships
- SciPy 2017 Conference Attendance Scholarship @ SciPy Conference, 2017.
- SciPy 2015 Conference Attendance Scholarship @ SciPy Conference, 2015.
- Viterbi Fellowship @ MIT, 2011
- Charles and Jane Banks Scholarship @ UBC, 2010
- Dean of Science Scholarship @ UBC, 2010
- Arthur Whitehead Science One Memorial Scholarship @ UBC, 2007
- UBC President’s Entrance Scholarship @ UBC, 2006