A long-form CV is available as a PDF Version.

A narrative version is available as my scientific biography.

Luis Pedro Coelho


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.

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.

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.

Selected Publications

  1. Shinichi Sunagawa,* Luis Pedro Coelho*, Samuel Chaffron*, Jens Roat Kultima, Karine Labadie, Guillem Salazar, Bardya Djahanschiri, Georg Zeller, Daniel R. Mende, Adriana Alberti, Francisco M. Cornejo-Castillo, Paul I. Costea, Corinne Cruaud, Francesco d’Ovidio, Stefan Engelen, Isabel Ferrera, Josep M. Gasol, Lionel Guidi, Falk Hildebrand, Florian Kokoszka, Cyrille Lepoivre, Gipsi Lima-Mendez, Julie Poulain, Bonnie T. Poulos, Marta Royo-Llonch, Hugo Sarmento, Sara Vieira-Silva, Céline Dimier, Marc Picheral, Sarah Searson, Stefanie Kandels-Lewis, Tara Oceans coordinators, Chris Bowler, Colomban de Vargas, Gabriel Gorsky, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Fabrice Not, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Jean Weissenbach, Patrick Wincker, Eric Karsenti, Jeroen Raes, Silvia G. Acinas, Peer Bork, Structure and function of the global ocean microbiome in Science (2015) [DOI].
  2. 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, Sep 15;29(18):2343-9 [DOI] [Video Abstract] [open access version]
  3. 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]
  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]

See also my full annotated list of publications or my full length CV.


  • 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


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. I am a certified software carpentry instructor

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).

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.

Open Source Programming

I publish and maintainx many open source projects of interest to his research, such as image processing or machine learning code. In particular mahotas (ca. 6,000 downloads per month) is a computer vision library in Python.

See the full list of projects in my github page.