Who am I?
Moving to Fudan University: I will be starting my own research group at Fudan University (Shanghai) in mid-2018.
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.
More 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. I wish to answer basic questions on what determines the structure of a microbial community in a given environment and what are the differences/similarities between different environments.
My work is a mix of of method and tool development with applications. In methodological terms, I worry a lot about correct evaluation of methods and avoiding over-inflated measures of performance. A large fraction of my time is spent scaling up algorithms and pipelines to work on very-large 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.
Upcoming Travels & Talks
Email me if you want to set up meetings at any of these opportunities (or to invite me for other opportunities).
Publications in 2015-2018:
- Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language (PREPRINT)
- Luis Pedro Coelho, Jens Kultima, Paul Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Hayward, Sofia K. Forslund, Patrick Descombes, Janet Jackson, Qinghong Li, and Peer Bork Similarity of the dog and human gut microbiomes in gene content and response to diet in Microbiome (2018) [DOI]
- Katri Korpela, Paul Igor Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I Boomsma, Nicola Segata, and Peer Bork Selective maternal seeding and environment shape the human gut microbiome in Genome Research (2018) [DOI]
- Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork Subspecies in the global human gut microbiome in Molecular Systems Biology (2017) [DOI]
- Luis Pedro Coelho Jug: Software for parallel reproducible computation in Python in the Journal for Open Research Software (2017) [DOI]
- Sebastien Colin*, Luis Pedro Coelho*, Shinichi Sunagawa, Chris Bowler, Eric Karsenti, Peer Bork, Rainer Pepperkok, Colomban de Vargas, Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes in eLife (2017) [DOI]
- Paul I Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris-Elias Jung, Jens Roat Kultima, Matthew R Hayward, Luis Pedro Coelho, Emma Allen-Vercoe, Laurie Bertrand, Michael Blaut, Jillian R M Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle Daigneault, Muriel Derrien, Anne Druesne, Willem M de Vos, B Brett Finlay, Harry J Flint, Francisco Guarner, Masahira Hattori, Hans Heilig, Ruth Ann Luna, Johan van Hylckama Vlieg, Jana Junick, Ingeborg Klymiuk, Philippe Langella, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C Martin, Clémentine Mery, Hidetoshi Morita, Paul W O'Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, Milena Popova, Anne Salonen, Delphine Saulnier, Karen P Scott, Bhagirath Singh, Kathleen Slezak, Patrick Veiga, James Versalovic, Liping Zhao, Erwin G Zoetendal, S Dusko Ehrlich, Joel Dore, and Peer Bork Towards standards for human fecal sample processing in metagenomic studies in Nature Biotechnology (2017) [DOI] [PDF
- Paul Igor Costea*, Robin Munch*, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork metaSNV: A tool for metagenomic strain level analysis in PLoS One (2017) [DOI]
- Jaime Huerta-Cepas*, Kristoffer Forslund*, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, and Peer Bork Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper in Molecular Biology & Evolution (2017) [DOI]
- Janis Rebecca Bedarf, Falk Hildebrand, Luis Pedro Coelho, Shinichi Sunagawa, Mohammad Bahram, Felix Goeser, Peer Bork, Ullrich Wüllner Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA naive Parkinson's Disease patients in Genome Medicine (2017) [DOI]
- 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] [PDF]
- 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] [PDF]
- 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] [PDF].
(See above for papers)
I will start the Big Data Biology Lab at Fudan University.
June 14: I taugh the Introduction to Python lecture at the Lisbon (Portugal) Machine Learning Summer School
Nov 22-24 I was in Schwarzenber, Switzerland for the Autumn School "Machine Learning applied to Systems Biology". I also visited the University of Bern and presented my scientific work.
Sept 12-13 I was in Delft 12-13** for a workshop on data-driven cell factory and community design
July 20 2017 I was in Lisbon on July 20 for LxMLS 2017
July 9-13 2017 I was in Valencia for FEMS 2017
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