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.

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 2014/2015:

  1. 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].
  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]

All publications...

Upcoming Travels & Talks

March 31-April 2 I will be in Luxembourg at the International Human Microbiome Congress (IHMC)

15-17 June 2015 I will be in beautiful San Sebastian (Spain) for a software carpentry workshop (and some holiday time).

16 July 2015 I will be teaching at the Lisbon Machine Learning School

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

Other News

(See above for papers)

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.

September 2014 Keynote talk in Python San Sebastien [Online talk]

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

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 ...