Senior data scientist and clinician working in Drug Discovery, with a background in biomedical engineering
Machine learning, python and data engineering architecture - delivering production-grade machine learning pipelines to computational biology, statistical genetics and early discovery groups.
Leading academic/industrial research collaborations, 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
Feb2017 - now
Senior Data Scientist, Translational Advanced Analytics, Biogen
Feb2016 - Feb2017
Manager, Digital Health Technology & Data Science, Biogen
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. Development follows an iterative and agile process, done in collaboration with scientist at all levels of the organization, and which requires a deep understanding of the domain as well as the technologies available. My broad background (medicine, ML, biomedical engineering) helps me to bridge these diverse skill sets and communicate across disciplines.
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. Direct interactions with Open Targets members (the Wellcome Trust Sanger Institute, the European Bioinformatics Institute, and GSK) and Biogen scientists. Manage and influence the scientific program working to enhance its quality and matching the Open Targets capabilities to Biogen needs. 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 6 EBI software 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
Advised Genomics England industrial strategy as part of the 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 pharma organization 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,North West London, UK
- General Practice
- Care of Elderly, orthopaedic outreach
- Anaesthetics & ITU
- Gastroenterology & Acute medical take
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
Consultant, SERES Health, Cambridge, MA (remote)
- Computationally designed and predicted fitness 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 diagnostics, Cambridge, MA
- MIT $100K Entrepeneurship competition semifinalist
- Developed high-throughput data acquisition and analysis platforms, scaling the technology to production levels.
- 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
- Murine antibody cloning and expression; fluorescence tagging
- Real time fluorescence microcopy; advanced image analysis
Biomedical Nanotechnology Group, Prof. W C. Chan, University of Toronto
- Nanoparticles cytotoxicity
- Quantum Dots characterization (TEM, Absorption, PL, X-IRD)
- Real time fluorescence microscopy, single molecule spectroscopy and biophysics.
Biomaterials Group, Prof. M.C.Tanzi, Politecnico di Milano, Italy
- Morphological, mechanical and functional characterization of polyurethane scaffolds for tissue engineering applications.
MBBS, Imperial College London
Medicine & Surgery
Ph.D, Harvard Medical School/Massachusets Institute of Technology
- Medical Engineering & Medical Physics, Harvard/MIT HST Institute
- Thesis: High-throughput experimental and computational tools for exploring immunity and the microbiome
Sc.M., Massachusets Institute of Technology
BASc (Honors), University of Toronto
Engineering Science, Biomedical Option
Python - jupyter, scikit-learn, numpy, matplotlib, seaborne, pandas, lxml, NLTK, requests, sqlite3. R - ML view: gbm, lasso, randomforest, etc.; ggplot2, knitr, shiny. Cloud ops - Docker, Kubernetes, Google Cloud, AWS Web development - working knowledge of HTML/CSS/JS, D3, dc.js, crossfilter. Strong experience with REST APIs. Linux - Git, bash/zsh, sge/torque/pbs, ansible. Elasticsearch, SQL, Clickhouse
Worked and led teams using kanban, scrum and test-driven development practices.
Fellowships & Awards
Bursary recipient, Exploring Human Host-Microbiome Interactions in Health and Disease, Wellcome Trust Scientific Conferences
Postgraduate D Scholarship, National Science Engineering Research Council, Canada
Poitras pre-doctoral fellowship
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
Postgraduate M Scholarship, National Science Engineering Research Council, Canada
University of Toronto Life Sciences Award, University of Toronto
NSERC Summer Research Award, National Science Engineering Research Council, Canada
OUA Academic Achievement Award, Ontario, Canada
#2 Canadian Army University Course Undergrad Scholarship,University of Toronto
Silver T – academic athletic excellence, University of Toronto
Ontario Scholar, Government of Ontario, Canada
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, Platt T […] Birney E, Barrett J, Dunham I.
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. PubMed PMID: 27899665; PubMed Central PMCID:
Fischer M, Bittar M, Papa E, Kassam Z, Smith M.
Can You Cause Inflammatory Bowel Disease with Fecal Transplantation?
Gut Microbes 2017 Jan 19:0. doi: 10.1080/19490976.2017.1283469
Eliseo Papa, Michael Docktor, Christopher Smillie, Sarah Weber, Sarah Pacocha Preheim,Dirk Gevers,Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Jay Ingram, David B Schauer, Doyle V Ward, Joshua R Korzenik, Ramnik J Xavier, Athos Bousvaros, Eric J Alm.
Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.
PLoS ONE 2012;7(6):e39242.
Rhiannon White, Sachiko Miyata, Eliseo Papa, Eric Spooner, Kleoniki Gounaris, Murray Selkirk, Katerina Artavanis-Tsakonas.
Characterisation of the Trichinella spiralis deubiquitinating enzyme, TsUCH37, an evolutionarily conserved proteasome interaction partner.
PLoS Negl Trop Dis. 2011 Oct;5(10):e1340.
Katerina Artavanis-Tsakonas, Pia V Kasperkovitz, Eliseo Papa, Michael L Cardenas, Nida S Khan, Annemarthe G Van der Veen, Hidde L Ploegh and Jatin M Vyas.
The Tetraspanin CD82 is Specifically Recruited to Fungal and Bacterial Phagosomes Prior to Acidification.
Infection and Immunity 2011 79(3):1098-106\
Adebola Ogunniyi, Craig Story, Eliseo Papa, Eduardo Guillen, J. Christopher Love.
Screening Individual Hybridomas by Microengraving to Discover Monoclonal Antibodies.
Nature Protocols 2009 4(5):767-82
Jehnna L. Ronan, Craig Story, Eliseo Papa, J. Christopher Love.
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\
Craig Story*, Eliseo Papa* (co-author), Chih-Chi Andrew Hu, Jehnna L Ronan, Hidde L Ploegh, J.Christopher Love.
Profiling Antibody Responses by Multiparametric Analysis of Single B Cells.
PNAS 2008 105(46):17902-7
Hans Fischer, Eli Papa, Lichuan Liu, K. Sandy Pang, Warren C. W. Chan.
Preliminary Results: Exploring the Interactions of Quantum Dots with Whole Blood Components.
SPIE Proceedings 2005 5969,54
Wen Jiang, Eli Papa, Hans Fischer, Sawitri Mardyani, Warren C.W. Chan.
Semiconductor quantum dots as contrast agents for whole animal imaging.
Trends in Biotechnology 2004 22:12
Eliseo Papa, Andrea Pierleoni, Gautier Koscielny, Naruemon Pratanwanich, Oliver Stegle, Jeffrey Barrett, Ian Dunham, and the Open Targets Team
Open Targets : a platform for therapeutic target identification and validation
Miguel Pignatelli, Denise Carvalho-Silva, Jennifer Cham, Luca Fumis, Samiul Hasan,
Nikiforos Karamanis, Gautier Koscielny , Michael Maguire, William Newell, Eliseo Papa, Andrea Pierleoni, Francis Rowland, Sirarat Sarntivijal, Oliver Stegle, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham and the Open Targets team
Target Validation Platform: A New Drug Target Identification and Prioritisation Web Platform
Genome informatics 2016
Monika Fischer, Mohamad Bittar, Eliseo Papa, Zain Kassam, Mark Smith
Can you cause IBD with fecal transplantation?: 31-patient case series of fecal transplantation using stool from a donor who later developed Crohn’s disease
Digestive Disease Week 2016
Jessica Allegretti, Monika Fischer, Eliseo Papa, Ryan Elliot, M. Jane Klank, Gina Mendolia, Elaine Vo, Zain Kassam, Mark Smith
Fecal Microbiota Transplantation Delivered via Oral Capsules Achieves Microbial Engraftment Similar to Traditional
Delivery Modalities: Safety, Efficacy and Engraftment Results From a Multi-Center Cluster Randomized Dose-Finding Study
Digestive Disease Week 2016
White RR, Morrow M, Miyata S, Papa E, Spooner E, Selkirk M, Gounaris K, Das C, Artavanis-Tsakonas K
Characterisation of the Trichinella Spiralis Deubiquitinating Enzyme, TsUCH37
Molecular and Cellular Biology of Helminth Parasites VII
Eliseo Papa, Michael Docktor, Christopher Smillie, Sarah Weber, Sarah P. Preheim, Dirk Gevers, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Jay Ingram, David B Schauer, Doyle V Ward, Joshua R Korzenik, Ramnik J Xavier, Athos Bousvaros, Eric J Alm.
Diagnosing IBD from the fecal microbiome
Exploring Human Host-Microbiome Interactions in Health and Disease, Wellcome Trust Scientific Conferences
High-Throughput and High-Content Screening of Antibody Responses from Single Cells
AIChE annual meeting, Nanoscale Science Engineering Forum
Applying Ligands to B Cell Receptors by Microfluidics
AIChE annual meeting, Engineering Fundamentals in Life Sciences
Microengraving for high-throughput affinity mapping of humoral responses
Harvard/MIT HST Forum
Multi-variate profiling of B cell immune responses
Novartis Vaccine Symposium
Composition of an Array of Microwells with an Integrated Microfluidic System, USA Serial No. 12/390279
Field Operative, AISPO, San Raffaele del Monte Tabor Foundation. Milan, Italy
- Streamlined diagnostic routines, Kampala’s Hospital & Gulu’s outpost, Uganda
- Consulted regarding the infrastructure, human resources and logistics of the Kampala’s hospital
Engineers Without Borders.
- University of Toronto Conference delegate