Eliseo Papa

Senior data scientist and clinician working on AI applied to Drug Discovery. Background in biomedical engineering and bioinformatics.

| elipapa.github.io | LinkedIn | GitHub | Medium

Experienced in

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.

Knowledge graph learning from text

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

Computing

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
SQL

Worked in and led teams using kanban, scrum and test-driven development practices.

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

Work

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.

Apr2015 - Feb2016 ML Analyst, OpenBiome / Finch Therapeutics Cambridge,MA (remote)

Sep2014-Jun2016 Chief Scientist, Klappo/um.ai, London,UK

Aug2013-Dec2014 Junior doctor, Imperial College NHS Trust, London, UK

Jun2013 Theoretical System Biology group, Prof. M. Stumpf, Imperial College

May 2012 - Dec 2012 Consultant, SERES Health, Cambridge, MA

2009-Jun2012 Alm Laboratory for Microbiology, Prof. Eric J. Alm, MIT

2009 Founder, Enumeral biomedical, Cambridge, MA

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

Education

2013 MBBS, Imperial College London Medicine & Surgery

2012 Ph.D, Harvard/MIT Health Science & Technology Institute Medical Engineering & Medical Physics

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

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

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, 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.

2017 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

2012 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.

2011 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.

2011 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\

2009 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

2009 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\

2008 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

Patents

2009 Composition of an Array of Microwells with an Integrated Microfluidic System, US8569046B2

Fellowships

2010-2011 NSERC Postgraduate D Scholarship, Canada

2008-2009 Poitras pre-doctoral fellowship, MIT

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

Awards

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

2008 Competition Semifinalist, MIT 100k Business Plan

Volunteering

2005 Uganda Field operative, AISPO, San Raffaele Foundation. Milan, Italy

2004 Conference delegate, Engineers Without Borders