# Eliseo Papa Biomedical Engineer, Computational Biologist, Data Scientist
[elipapa@alum.mit.edu](mailto:elipapa@alum.mit.edu) | [eliseopapa.org](http://eliseopapa.org) | [LinkedIn](http://uk.linkedin.com/in/eliseopapa)
## Current position MBBS Candidate, Graduate Entry Medicine, Imperial College London Researcher, [Alm lab](http://almlab.mit.edu), MIT ### Specialized in Medical Engineering, Analysis of large data sets, Microbiome, Machine learning, Immunology, Optics, Nano/microfabrication, Phylogenetics. ### Research interests Host-pathogen interactions at the level of microbiome and single cells. Human Microbiome Project. High-throughput diagnostics. Electronic health records. Emerging properties of networks in a biological and social context. Self-organized systems. ## Languages Italian: Mother tongue English: Perfect oral & written fluency French: Working knowledge ## Education `2009-now` __Imperial College London__ : MBBS Graduate Entry Medicine Programme `2006-2012` __Harvard Medical School & Massachusets Institute of Technology__ : PhD, Biomedical Engineering, [Harvard/MIT Health Science & Technology Institute](http://hst.mit.edu) Thesis: [High-throughput experimental and computational tools for exploring immunity and the microbiome](https://speakerdeck.com/u/elipapa/p/phd-defense-talk-1) Representative courses: _Harvard Medical School_ - pathology, renal pathophysiology, respiratory pathophysiology, cardiac pathophysiology. _MIT_ - biomechanics, statistical learning, systems microbiology, forces fields and flows in biological systems, fluid mechanics, heat transfer, numerical modeling. `2006-2008` __Massachusets Institute of Technology__ : SM in Mechanical Engineering `2001-2005` __University of Toronto__ : BASc (Honors) Engineering Science (Biomedical Option) ## Fellowships `2010-2011` NSERC Postgraduate D Scholarship, National Science Engineering Research Council, Canada `2008-2009` Poitras pre-doctoral fellowship `2007` Martino Scholar, Harvard/MIT Health Science Tech. Inst. `2005-2008` NSERC Postgraduate M Scholarship, National Science Engineering Research Council, Canada `2005` OGS Postgraduate Scholarship (declined), Ontario Government, Canada `2004` NSERC Summer Research Award, National Science Engineering Research Council, Canada `2003` \#2 Canadian Army University Course Undergrad Scholarship,University of Toronto ## Awards `2012` Bursary recipient, *Exploring Human Host-Microbiome Interactions in Health and Disease*, Wellcome Trust Scientific Conferences `2008` Martha Gray Prizes for Excellence in Research, Annual Forum, Harvard/MIT Health Science Tech. Inst. `2008` Competition Semifinalist, MIT 100k Business Plan `2004` University of Toronto Life Sciences Award, University of Toronto `2002-04` Silver T – academic athletic excellence, University of Toronto `2003` OUA Academic Achievement Award, Ontario, Canada `2001` Ontario Scholar, Government of Ontario, Canada ## Publications ### Journals `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.](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039242) **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 `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](http://eliseopapa.org/downloads/documents/ibdML-poster.pdf) *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 ## Research `2009-now` __Alm Laboratory for Microbiology, Prof. Eric J. Alm__, MIT - Human Microbiome Project - Bioinformatic analysis of large datasets - Microbial evolution, phylogenetics `2006-2009` __Laboratory of Hidde L. Ploegh__, Whitehead Institute, MIT - Affinity and isotype mapping of antibody secretion in individual primary B cells. - Development of computational and statistical tools to monitor and predict evolution of immune responses - Murine antibody cloning and expression; fluorescence tagging - Real time fluorescence microcopy; advanced image analysis `2004-2005` __Biomedical Nanotechnology Group, Prof. W C. Chan__, University of Toronto - Nanoparticles cytotoxicity - Quantum Dots synthesis and characterization (TEM, Absorption, PL, X-IRD) - Real time fluorescence microscopy, single molecule spectroscopy and biophysics. `2003` __Biomaterials Group, Prof. M.C.Tanzi__, Politecnico di Milano, Italy - Synthesis of biocompatible polymeric scaffolds for tissue engineering applications. - Morphological, mechanical and functional characterization of polyurethane scaffolds. ## Other employment `2006` __ESL Teacher, Inlingua Language School,__ Brescia, Italy - Teaching approx. 12hrs/week on individual basis and to large groups - Provided on site focussed training for companies `2004-2005` __Residence Don, St.Michael’s College Residence,__ University of Toronto, Canada - Mediate conflicts and provide academic or personal consulting. - Trained in cultural competence and conflict resolution - Responsible to enforce rules and to foster an accepting community `2000-2002` __IT Consultant System Admin, Ital Engineering s.a.s.,__ Brescia, Italy - Interviewed the customer and performed an organizational analysis - Regularly performed formal presentations to the management `2000` __Graphic Designer, Photo Image Studio,__ Brescia, Italy - Assisted photographers in the preparation of gallery exhibitions and openings ## Extracurricular `2006-2008` __Collegiate Cycling. [MIT Cycling Team](http://cycling.mit.edu/www/home)__ - National Collegiate Road Champions - Eastern Collegiate Cycling Conference Road Champions - *Captain*, Cyclocross, 2nd US National Championship - Eastern Collegiate Cycling Conference Road Champions - Cyclocross, US National Champions `2006` __Competitive Triathlon. Team Atletica Desenzano__ - 9th cat. at ITU Bardolino’s International Triathlon `2003-2004` __Competitive Sailing. Italian sailing federation (FIV).__ - 12th at European IMS Sailing Championship - 6th at Canadian J105 Championship `2004` __Engineers Without Borders.__ - University of Toronto Conference delegate `2002` __University of Toronto Varsity Waterpolo.__ - OUA Conference Champions `1998-2001` __Nuoto Club Brescia Swimming Club__ - Regional level competitions ## Volunteering `2005` __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 ## Interests Jazz music. International relations. Semiotics and its implications on mass psychology. Buddhism, Zen and oriental philosophies. Reading classics of Italian and English literature. Travelled by kayak along the major European rivers. Rock Climbing.