From 81d94cb0991b70c9a8ce6ff2815b747f6842f25c Mon Sep 17 00:00:00 2001 From: eliseo papa Date: Thu, 25 Oct 2012 15:07:44 +0100 Subject: using master branch to push to gh-pages directly --- cv_eliseo_papa.md | 326 ------------------------------------------------------ index.md | 326 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 326 insertions(+), 326 deletions(-) delete mode 100644 cv_eliseo_papa.md create mode 100644 index.md diff --git a/cv_eliseo_papa.md b/cv_eliseo_papa.md deleted file mode 100644 index 1a0c8ad..0000000 --- a/cv_eliseo_papa.md +++ /dev/null @@ -1,326 +0,0 @@ ---- -layout: cv ---- -# 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. - - - - diff --git a/index.md b/index.md new file mode 100644 index 0000000..1a0c8ad --- /dev/null +++ b/index.md @@ -0,0 +1,326 @@ +--- +layout: cv +--- +# 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. + + + + -- cgit v1.2.3