Eliseo Papa

Senior data scientist and clinician working in Drug Discovery, with a background in biomedical engineering

| elipapa.github.io | LinkedIn | GitHub

Experienced in

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

Professional Experience

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.

2015-2016 ML Scientist, OpenBiome / Finch Therapeutics Cambridge,MA (remote)

2014-2015 Chief Scientist, Klappo/um.ai, London,UK

2014 Junior Doctor, Imperial College NHS Trust,North West London, UK

2013 Theoretical System Biology group, Prof. M. Stumpf, Imperial College

2012 Consultant, SERES Health, Cambridge, MA (remote)

2009-2013 Alm Laboratory for Microbiology, Prof. Eric J. Alm, MIT

2009 Founder, Enumeral diagnostics, Cambridge, MA

2006-2009 Laboratory of Hidde L. Ploegh, Whitehead Institute, MIT

2004-2005 Biomedical Nanotechnology Group, Prof. W C. Chan, University of Toronto

2003 Biomaterials Group, Prof. M.C.Tanzi, Politecnico di Milano, Italy

Education

2013 MBBS, Imperial College London Medicine & Surgery

2006-2012 Ph.D, Harvard Medical School/Massachusets Institute of Technology

2008 Sc.M., Massachusets Institute of Technology Mechanical Engineering

2005 BASc (Honors), University of Toronto Engineering Science, Biomedical Option

Computing

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.

Contributor to open source projects: open targets , kubernetes, luigi

Fellowships & Awards

2012 Bursary recipient, Exploring Human Host-Microbiome Interactions in Health and Disease, Wellcome Trust Scientific Conferences

2010-2011 Postgraduate D Scholarship, National Science Engineering Research Council, Canada

2008-2009 Poitras pre-doctoral fellowship

2007 Martino Scholar, Harvard/MIT Health Science Tech. Inst.

2008 Martha Gray Prizes for Excellence in Research, Annual Forum, Harvard/MIT Health Science Tech. Inst.

2008 Competition Semifinalist, MIT 100k Business Plan

2005-2008 Postgraduate M Scholarship, National Science Engineering Research Council, Canada

2004 University of Toronto Life Sciences Award, University of Toronto

2004 NSERC Summer Research Award, National Science Engineering Research Council, Canada

2003 OUA Academic Achievement Award, Ontario, Canada

2003 #2 Canadian Army University Course Undergrad Scholarship,University of Toronto

2002-04 Silver T – academic athletic excellence, University of Toronto

2001 Ontario Scholar, Government of Ontario, Canada

Publications

Journals

2017 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: PMC5210543.

2017 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

2012 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.

2011 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.

2011 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\

2009 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

2009 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\

2008 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

2005 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

2004 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

Posters

2016 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 MASAMB 2016

2016 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

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

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

2012 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

2012 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

2008 High-Throughput and High-Content Screening of Antibody Responses from Single Cells AIChE annual meeting, Nanoscale Science Engineering Forum

2008 Applying Ligands to B Cell Receptors by Microfluidics AIChE annual meeting, Engineering Fundamentals in Life Sciences

2008 Microengraving for high-throughput affinity mapping of humoral responses Harvard/MIT HST Forum

2008 Multi-variate profiling of B cell immune responses Novartis Vaccine Symposium

Patents

2009 Composition of an Array of Microwells with an Integrated Microfluidic System, USA Serial No. 12/390279

Volunteering

2005 Field Operative, AISPO, San Raffaele del Monte Tabor Foundation. Milan, Italy

2004 Engineers Without Borders.