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 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.
This is what I published in 2014/2015:
- 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 [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]
- 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]
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.
(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.
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
July 2013 My book Building Machine Learning Systems with Python is now published