Who am I?

Luis Pedro Coelho

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.

I blog about science at metarabbit.wordpress.com and tweet (mostly about sciency things) as @luispedrocoelho. I co-wrote Building Machine Learning Systems with Python.

My Erdös-Bacon number is 7.

In November 2014, I am organizing a Software Carpentry Workshop at EMBL. Apply to learn best practices of computer usage by scientists.

Research Interests

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 bioimage informatics using machine learning approaches. In particular, in obtaining biological knowledge by exploiting large-scale datasets of mixed communities by a sequencing and imaging to be able to derive observations about the relationship between the genotypes and phenotypes. This research can answer questions such as do the measures of genomic biodiversity agree with measures of phenotypic biodiversity?

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 environments.

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.

I work both on developing new computer methods (software) for these tasks as well as on specific biological problems.

Recent Publications

This is what I published in 2013/2014:

  1. 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 [DOI].
  1. 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]
  1. 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) [Abstract] [DOI]
  1. Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis & Peer Bork, Metagenomic species profiling using universal phylogenetic marker genes in Nature Methods 10, 1196–1199 (2013) [Abstract] [DOI]
  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] [preprint] [mendeley]
  1. Luis Pedro Coelho, Mahotas: Open source software for scriptable computer vision, Journal of Open Research Software, vol. 1 (2013) [DOI] [mendeley].

All publications...

Upcoming Travels & Talks

September 15-17 I will be at TGAC.

September 27-28 I will be in San Sebastian for Python San Sebastien

October 8-10 I will be in Leuven for Bioimage Informatics

October 22 Virtual trip for an O'Reilly webcast on Penalised Regression in Python

Email me if you want to set up meetings at any of these opportunities.

Other News

(See above for papers & travels)

November 2014 I am the lead organizer for a software carpentry workshop at EMBL.

July 2014 Progression (in which I starred in) 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

November 2013 I'm a member of the programme committee for DILS 2014 (10th International Conference on Data Integration in the Life Sciences)

July 2013 I got a prize in the ICSB Computational Biology Wikipedia Competition for work on the Bioimage Informatics page

July 2013 My book Building Machine Learning Systems with Python is now published

older news items ...

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