Resume

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Postgraduate Experience

Currently (since 2013)

Postdoctoral researcher at the European Molecular Biology Laboratory (EMBL) with Peer Bork.

2012

Postdoctoral researcher at the Institute for Molecular Medicine (IMM), Lisbon, with Musa Mhlanga.

Education

Ph.D. in Computational Biology, 2006–2011

Carnegie Mellon University, Pittsburgh.

Dissertation topic: Modeling the Space of Subcellular Location Patterns Using Images and Other Sources of Information, advised by Prof. Robert F. Murphy.

MS in computer science, Instituto Superior Técnico (Technical University Lisbon), 2006

Dissertation topic: Bayesian Network Parameter Estimation Using Noisy Observations or Soft Evidence, advised by Prof. Arlindo Oliveira.

BS in computer science, Instituto Superior Técnico (Technical University Lisbon), 2004

Finished top of my class.

Spent one year at Technical University of Vienna (Austria) as international exchange student.

Scholarships & Awards

  • Siebel Scholar 2012.

  • Portugal's Science and Research Foundation Ph.D. scholarship 2007-2011

  • Outstanding Research Accomplishment

    Award for Research Excellence in the Joint CMU-University of Pittsburgh Ph.D. Program in Computational Biology (2007).

  • Academic Excellency

    Diploma of Merit from Instituto Superior Técnico for academic excellency in the academic year 1999/2000. Award for Academy Excellence in the Joint CMU-University of Pittsburgh Ph.D. Program in Computational Biology (2007).

  • Fulbright Fellowship for Ph.D. Study in the US, 2006/07.

  • Portugal's Science and Research Foundation research scholarship from December 2004 through July 2006.

  • Fiction Writing

    Second Price in the literature contest Lisboa à Letra 2004 for fiction.

  • Abitur

    Letter of recognition of excellency in German Final Secondary Exam (Abitur).

Research Highlights

Proteome-wide Study of Subcellular Location in Mouse Fibroblasts

I developed new methods for learning from both a very large collection of images of fluorescently tagged proteins and other forms of data (sequence information, database information). This work builds on my past work. A manuscript describing it is in preparation.

Unsupervised Subcellular Pattern Unmixing

Many proteins are located in more than one organelle simultaneously, a phenomenon known as a mixed pattern (the pattern corresponding to a single organelle being a pure pattern). Recovering the organelle structure from image data where mixed patterns are present is known as the unsupervised unmixing problem in subcellular location. We developed new models for solving this problem. Our solution was chosen as one of the highlights of 2010 in computational biology by the journal Nature Biotechnology

More information on unsupervised unmixing

Structured Literature Image Finder (SLIF)

SLIF is a search engine that indexes biomedical papers with their images. In this project, I was responsible for the computer vision aspects of the processing pipeline. I also handled much of the integration effort of the several components and coordinated the preparation of the multi-author publications that resulted from the effort. This project was a finalist in the Elsevier Grand Challenge (4 teams out of 70 were chosen for the final). I represented our team in both the semi-final and the final of this competition.

More information on SLIF

Selected Publications

  1. Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F. Murphy, Determining the subcellular location of new proteins from microscope images using local features in Bioinformatics, 2013 [DOI] [Video Abstract]
  2. Luis Pedro Coelho, Tao Peng, and Robert F. Murphy, Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing in Bioinformatics, vol. 26(12), pp. i7-i12 [online version]
  3. Luis Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, and Robert F. Murphy, Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature in Lecture Notes in Bioinformatics vol. 6004 [PDF version]
  4. Luis Pedro Coelho, Aabid Shariff, and Robert F. Murphy; Nuclear segmentation in microscope cell images: A hand-segmented dataset and comparison of algorithms ISBI 2009 [online version]
  5. Luis Pedro Coelho and Arlindo Oliveira; Dotted Suffix Trees: A Structure for Approximate Text Indexing SPIRE (2006)

See also my full annotated list of publications

Invited Talks

  • Proteome-scale analysis and modeling of subcellular location, Luis Pedro Coelho, 4th CeBiTec Symposium BioImaging, Bielefeld, Germany 25-27 August 2009
  • Unsupervised Mixture Pattern Unmixing, University of Bielefeld International Graduate School of Bioinformatics and Genome Research, July 2008.
  • Studying the subcellular location space with bioimages and other data modalities, University of Delaware, Computer and Information Sciences Department, September 2011
  • Bioimage Informatics: Computer Vision for Biology*, EMBO Practical Course on Microscopy: from single molecules to animals, Pretoria, November 2011
  • Learning Subcellular Location from Images and Other Sources of Information, KDBIO (Knowledge Discovery and Bioinformatics) seminar, Lisbon, February 2012
  • Modeling Subcellular Location from Images and Other Sources of Information, EAO Seminar (Instituto Gulbenkian da Ciência), Oeiras, March 2012
  • Modeling Subcellular Location from Images and Other Sources of Information, Luxembourg Centre for Systems Biology, July 2012

Other Talks

  1. Determining Resolvable Subcellular Location Categories as a Function of Image Resolution, Luis Pedro Coelho & Robert F. Murphy, 24th ISAC Congress, Budapest, May 2008.
  2. Rita Reis and Luis Pedro Coelho Using Theatre to Fight HIV/AIDS in Mozambique, National Conference of the Association for Theatre in Higher Education, Chicago 2011

Languages

  • Bilingual: Portuguese and English
  • Fluent oral and good written German (attended a German-speaking school, grades 5 through 12; spent a year at the Technical University of Austria).
  • Fluent oral and good written French
  • Basic knowledge of Spanish and Luxembourgish

Work Experience

Teaching

Designed and taught a course in computer programming for the sciences (Programming for Scientists). This was a semester-long course taught at Carnegie Mellon University in Spring 2009 (as a student-taught course). In 2012, I taught a shortened version of this at IMM as a two-and-a-half day workshop.

Teaching Assistant for Decision Support Systems at Technical University of Lisbon (Spring 2005). Co-designed and co-taught a Computer Initiation Course for Adults in a social housing project (pro-bono). Teaching Assistant for Laboratory Methods for Computational Biology at Carnegie Mellon University (Spring 2008).

Webdesign

Designed the website for ICSV12 (Twelfth International Congress on Sound and Vibration) and administered the website for the Portuguese non-profit Medicos Pela Escolha (pro bono).

Local Committee for Portuguese-American Postgraduate Society National Forum

I headed the local organising committee for the 2010 edition of this annual event. It took place in Pittsburgh and included, as speakers, cabinet-level Portuguese government officials, renowned researchers, artists, as well as participants from all around the US.

Producer for IST Theatre Group

I served as the producer for the IST Theatre Group, which is one of the top university theatre groups in Portugal. We participated in several festivals, including international festivals. As producer, my activities included fund-raising and management.

Open Source Programming

I was a member of the kde project from 2000 through 2006. I was maintainer of the application kghostview.

I publish and maintainx many open source projects of interest to his research, such as image processing or machine learning code. See the full list in my github page.

Article filed in categories: Personal