Who am I?
I am a computational biologist. I work at the European Molecular Biology Laboratory (EMBL) in Peer Bork's group in microbial community analysis using metagenomics. I have a PhD from Carnegie Mellon University (2011), where I worked on bioimage informatics for subcellular location analysis with Bob Murphy.
Technical version: I am interested in combining meta'omics (methods that obtain high-throughput information on microbial communities such as metagenomics and metatranscriptomics) analysis with machine learning approaches to learn about microbial communities in different environments.
My work is a mix of of method development and applications. In methodological terms, I worry a lot about correct evaluation of methods and avoiding over-inflated measures of performance. I also work in scaling up methods to work on large-scale problems.
Not-so technical version: With modern technology, namely robotic instruments, it is easy to acquire a lot of microscopic pictures. It is also possible to acquire large sequence datasets with the DNA of many organisms. I use these two families of technologies to investigate what is happening in mixed microbial communities such as the one in our guts, the microbiome.
In order to be able to use these data, I also need to develop new computer methods (software) for these tasks. Thus my work is a mix of solving biological problems and tackling the software issues that stand in the way of doing so.
This is what I published in 2014-2016:
- Jens Roat Kultima, Luis Pedro Coelho, Kristoffer Forslund, Jaime Huerta-Cepas, Simone S. Li, Marja Driessen, Anita Yvonne Voigt, Georg Zeller, Shinichi Sunagawa and Peer Bork; MOCAT2: a metagenomic assembly, annotation and profiling framework in Bioinformatics (2016) [DOI]
- Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, Simon Roux, Youssef Darzi, Stephane Audic, Léo Berline, Jennifer Brum, Luis Pedro Coelho, Julio Cesar Ignacio Espinoza, Shruti Malviya, Shinichi Sunagawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Julie Poulain, Sarah Searson, Tara Oceans Consortium Coordinators, Lars Stemmann, Fabrice Not, Pascal Hingamp, Sabrina Speich, Mick Follows, Lee Karp-Boss, Emmanuel Boss, Hiroyuki Ogata, Stephane Pesant, Jean Weissenbach, Patrick Wincker, Silvia G. Acinas, Peer Bork, Colomban de Vargas, Daniele Iudicone, Matthew B. Sullivan, Jeroen Raes, Eric Karsenti, Chris Bowler & Gabriel Gorsky; Plankton networks driving carbon export in the oligotrophic ocean in Nature (2016) [DOI]
- Renato Pinheiro-Silva, Lara Borges, Luís Pedro Coelho, Alejandro Cabezas-Cruz, James J. Valdés, Virgílio do Rosário, José de la Fuente4 and Ana Domingos, Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection in Parasites & Vectors (2015) [DOI]
- 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] [Request reprint].
- Luis Pedro Coelho, Catarina Pato, Ana Friães, Ariane Neumann , Maren von Köckritz-Blickwede Mário Ramirez , João André Carriço, Automatic Determination of NET (Neutrophil Extracellular Traps) Coverage in Fluorescent Microscopy Images in Bioinformatics (2015), [DOI] [Request reprint].
- Ana C. Pena, Mafalda R. Pimentel, Helena Manso, Rita Vaz-Drago, Daniel Neves, Francisco Aresta-Branco, Filipa R. Ferreira, Fabien Guegan, Luis Pedro Coelho, Maria Carmo-Fonseca, Nuno L. Barbosa-Morais, Luisa M. Figueiredo Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo in Molecular Microbiology (2014) [DOI].
- Kristoffer Forslund, Shinichi Sunagawa, Luis P. Coelho, Peer Bork, Metagenomic insights into the human gut resistome and the forces that shape it in Bioessays (2014). [DOI] [Preprint]
- Peter Liehl, Vanessa Zuzarte-Luís, Jennie Chan, Thomas Zillinger, Fernanda Baptista, Daniel Carapau, Madlen Konert, Kirsten K Hanson, Céline Carret, Caroline Lassnig, Mathias Müller, Ulrich Kalinke, Mohsan Saeed, Angelo Ferreira Chora, Douglas T Golenbock, Birgit Strobl, Miguel Prudêncio, Luis P Coelho, Stefan H Kappe, Giulio Superti-Furga, Andreas Pichlmair, Ana M Vigário, Charles M Rice, Katherine A Fitzgerald, Winfried Barchet, and Maria M Mota, Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection in Nature Medicine 20, 47–53 (2014) [DOI]
Upcoming Travels & Talks
Email me if you want to set up meetings at any of these opportunities (or to invite me for other opportunities).
(See above for papers)
23-25 November 2016 I visited Zurich (Switzerland) for the course Machine learning for bioinformatics and computational biology
7 March 2016 I am now an Associate Editor of the Journal of Open Research Software
22-25 August 2015 Visiting Tallinn (Estonia)
17 August 2015 The project ngless is now open source
16 July 2015 I will be teaching at the Lisbon Machine Learning School
15-17 June 2015 I will be in beautiful San Sebastian (Spain) for a software carpentry workshop (and some holiday time).
March 31-April 2 I attended the International Human Microbiome Congress (IHMC) in Luxembourg
February 2015 I was in Granada for the 2015 Aquatic Sciences Meeting, giving a talk on the 26th on our metagenomics work
November 2014 I am the lead organizer for a software carpentry workshop at EMBL.
July 2014 Progression (in which I played the character Luis) has been released at New Filmmakers in NYC. See the film at the Big Bear Film festival
February 2014 I'm now a certified Software Carpentry instructor