Senior data scientist and clinician working on AI applied to Drug Discovery. Background in biomedical engineering and bioinformatics.
Machine learning, python and data engineering architecture - delivering production-grade analysis pipeline to computational biology, statistical genetics and early discovery groups.
Leading academic/industrial research collaborations, communicating across disciplines, managing multi-year scientific projects, writing funding grants, leading product decisions in a software team.
Analysis of clinical trial data - current and retrospective analysis up to Phase 2b
Drug target identification and prioritization - Genetics, integrative and network-based approaches
Sequencing analysis - QC pipelines and statistical analysis of 16S and RNA-seq experiments
Machine learning for biomarker identification - human microbiome and immune cells subpopulations
Medicine - anesthesia, genetics, general medicine
Python - ipython, scikit-learn, numpy, matplotlib, seaborne, pandas, lxml, NLTK, requests, sqlite3.
Cloud ops - Docker, Kubernetes, Google Cloud, AWS
R - applied ML packages; ggplot2, knitr, shiny.
Web development - HTML/CSS/JS, D3, dc.js, crossfilter.
Linux - Git, bash/zsh, sge/torque/pbs
Worked in and led teams using kanban, scrum and test-driven development practices.
Feb2017 - now
Senior Data Scientist, Translational Advanced Analytics, Biogen
Feb2016 - Feb2017
Manager, Digital Health Technology & Data Science, Biogen
Concurrent projects: 1) Advanced analytics & scientific computing
I employ my knowledge of machine learning, python and data engineering architecture to deliver production-grade analysis pipeline to Biogen’s computational biology group, statistical genetics group and early discovery groups. This includes models based on RF, SVM, xgboost (scikit-learn), vowpal wabbit applied on biomarker and genomics data, as well as applied deep learning approaches (Keras, Tensorflow) applied on MEDLINE data (22m records) plus clinical trial literature and data.
2) Open Targets liaison
Working on computational biology and genomics analysis which leverage large scale human data sets with the goal of identify and prioritize new drug targets. Manage and influence Open Targets scientific program, working in partnership with the Wellcome Trust Sanger Institute, the European Bioinformatics Institute, and GSK. This work has resulted in several collaborations approved and funded by Open Targets that benefit Biogen. I routinely represent Biogen externally, including speaking invitations at informatics and scientific venues.
3) Development of the Open Targets Platform
I am one of the team lead, responsible to plan and manage the work of 2 Biogen and 4 EBI engineers including weekly planning and engineering duties. I manage the long-range planning and decision-making, including creating and owning the de facto Open Targets informatics platform roadmap, and making sure the team adopts the tool and process. This has directly resulted in new features important to Biogen in 2016’s Open Targets informatics platform releases.
4) Biogen’s principal liaison for the and Genomics England discovery forum
Participated and contributed to the Genomics England GENE consortium together with VPs and Directors from AZ, GSK, Takeda, Abbvie, Alexion and others.
- Statistical analysis of microbiome communities during fecal transplant delivery by capsule
- Project consulting for large pharmaceutical to analyze prevalence of drug resistant genes in the general population
- Retrospective analysis of Phase 2b trial results and additional microbiome sequencing to measure efficacy
Chief Scientist, Klappo/um.ai, London,UK
- Building a recommendations engine to craft context-aware suggestions for every meal.
- Normalization and concept mapping used to organize natural language data related to food onto a structured ontology
- Data analysis and visualization
- Management team responsible for the business plan and investor relations
- Medical and scientific direction
Junior doctor, Imperial College NHS Trust, London, UK
- Care of the elderly, palliative care
Theoretical System Biology group, Prof. M. Stumpf, Imperial College
- Integrating Chip-seq, RNAseq and transcriptomics data describing nitrogen stress response in e.coli
- Organized query with a relational db, structured ontology and visualization
- Bayesian model selection of potential e.coli nitrogen stress pathways
May 2012 - Dec 2012
Consultant, SERES Health, Cambridge, MA
- Selection and fitness prediction of synthetic microbial communities intended for therapeutic transplantation using unsupervised/supervised learning.
- Provided strategic input and scientific advice.
Alm Laboratory for Microbiology, Prof. Eric J. Alm, MIT
- Supervised classification of microbiome samples from pediatric IBD patients
- Feature extraction using ecological and phylogenetic information
- Quality control and downstream analysis of Human Microbiome Project sequencing pipeline
Founder, Enumeral biomedical, Cambridge, MA
- MIT $100K Entrepeneurship competition semifinalist
- Contributed to the development of the microfluidic platform at the core of the company intellectual property
Laboratory of Hidde L. Ploegh, Whitehead Institute, MIT
- Unsupervised learning to map affinity and isotype of secreted antibodies in individual primary B cells.
- Describing immune response progression by statistical modelling of the B cell population
- Created a cluster pipeline to automate image analysis of fluorescence microscopy data
MBBS, Imperial College London
Medicine & Surgery
Ph.D, Harvard/MIT Health Science & Technology Institute
Medical Engineering & Medical Physics
S.M., Massachusets Institute of Technology
BASc (Honors), University of Toronto
Engineering Science, Biomedical Option
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S,
Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, et al.
Open Targets: a platform for therapeutic target identification and validation.
Nucleic Acids Res. 2017 Jan 4;45(D1):D985-D994.
doi: 10.1093/nar/gkw1055. PMC5210543.
Fischer M, Bittar M, Papa E, Kassam Z, Smith M.
Can You Cause Inflammatory Bowel Disease with Fecal Transplantation? A 31-Patient Case-Series of Fecal Transplantation Using Stool from a Donor Who Later Developed Crohn’s disease
Gut Microbes 2017 Jan 19:0. doi: 10.1080/19490976.2017.1283469
Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, Alm EJ.
Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.
PLoS ONE 2012;7(6):e39242.
White R, Miyata S, Papa E, Spooner E, Gounaris K, Selkirk M, Artavanis-Tsakonas K.
Characterisation of the Trichinella spiralis deubiquitinating enzyme, TsUCH37, an evolutionarily conserved proteasome interaction partner.
PLoS Negl Trop Dis. 2011 Oct;5(10):e1340.
Artavanis-Tsakonas K, Kasperkovitz PV, Papa E, Cardenas ML, Khan NS, Van der Veen AG, Ploegh HL, Vyas JM.
The Tetraspanin CD82 is Specifically Recruited to Fungal and Bacterial Phagosomes Prior to Acidification.
Infection and Immunity 2011 79(3):1098-106\
Adebola Ogunniyi A, Craig Story CM, Papa E, Guillen E, Love JC.
Screening Individual Hybridomas by Microengraving to Discover Monoclonal Antibodies.
Nature Protocols 2009 4(5):767-82
Ronan JL, Story CM, Papa E, Love JC.
Optimization of the surfaces used to capture antibodies from single hybridomas reduces the time required for microengraving.
Journal of Immunological Methods 2009, 340(2):164-9\
Papa E, Story CM◇, Hu CC, Ronan JL, Herlihy K, Ploegh HL, Love JC.
Profiling Antibody Responses by Multiparametric Analysis of Single B Cells.
PNAS 2008 105(46):17902-7
Composition of an Array of Microwells with an Integrated Microfluidic System, US8569046B2
NSERC Postgraduate D Scholarship, Canada
Poitras pre-doctoral fellowship, MIT
Martino Scholar, Harvard/MIT Health Science & Tech. Inst.
Martha Gray Prizes for Excellence in Research, Annual Forum, Harvard/MIT Health Science & Tech. Inst.
Competition Semifinalist, MIT 100k Business Plan
Uganda Field operative, AISPO, San Raffaele Foundation. Milan, Italy
Conference delegate, Engineers Without Borders