Eliseo Papa

| elipapa.github.io | LinkedIn

Interested in

Opportunities at the intersection of data science, artificial intelligence and medicine.

Experienced in

Computational biology, machine learning, sequencing pipelines (16S, NGS), human microbiome, medicine, immunology.

Computing

Python - ipython,scikit-learn, numpy, matplotlib, seaborne, pandas, lxml, NLTK, requests, sqlite3.
R - ML view: gbm, lasso, randomforest, etc.; ggplot2, knitr, shiny.
Web development - working knowledge of HTML/CSS/JS, D3, dc.js, crossfilter. Strong experience with REST APIs. Linux - Git, bash/zsh, sge/torque/pbs, docker, CI(travis/wercker), vagrant, ansible.
Elasticsearch, SQL, Hadoop

Familiar with agile and test-driven development.

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

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

Professional Experience

2016-present Digital Health Technology & Data Science, Biogen

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

2014-2015 Chief Scientist, Klappo, London,UK

2014 Doctor, Senior house officer, Imperial College NHS Trust, Ealing Hospital, London, UK

2013-2014 Doctor, House officer, Imperial College NHS Trust, Hillingdon Hospital, Uxbridge, Middlesex, 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

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

Computing skills

Python - ipython, scikit-learn, numpy, matplotlib, seaborne, pandas, lxml, NLTK, requests, sqlite3.
R - gbm, lasso, randomforest, etc.; ggplot2, knitr, shiny.
Web development - HTML/CSS/JS, D3, dc.js, crossfilter.
Linux - Git, bash/zsh, sge/torque/pbs, docker/vagrant. Cloud computing - AWS, Google cloud
DevOps - Kubernetes, Ansible
Familiar with agile and test-driven development.

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, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O’Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, 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? 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 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.