Who am I?
I am the principal investigator of the Big Data Biology Lab at Fudan University (Shanghai) since September 2018. Our group works in computational biology, with a focus on the very large-scale.
Previously, I worked 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
April 16-18 2019 I will be in Utrecht (Netherlands) for the International Conference on One Health Antimicrobial Resistance (ICOHAR)
Email me if you want to set up meetings at any of these opportunities (or to invite me for other opportunities).
Publications since 2017 (updated 05 Mar 2019; full list):
- Alessio Milanese*, Daniel R Mende*, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis Pedro Coelho, Thomas S B Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller# & Shinichi Sunagawa#. Microbial abundance, activity and population genomic profiling with mOTUs2 Nature Communications 10, Article number: 1014 (2019).
- Thomas SB Schmidt*, Matthew R Hayward*, Luis Pedro Coelho, Simone S Li, Paul I Costea, Anita Y Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato J Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz-Buschart, Shinichi Sunagawa, Georg Zeller, Paul Wilmes, Peer Bork Extensive Transmission of Microbes along the Gastrointestinal Tract in eLife (2019) [DOI]
- Luigi Caputi*, Quentin Carradec*, Damien Eveillard*, Amos Kirilovsky*, Eric Pelletier*, ..., Luis Pedro Coelho, ..., Chris Bowler*, Daniele Iudicone* Community‐Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems in Global Biogeochemical Cycles (2019) [DOI]
- Albert Palleja*, Kristian H. Mikkelsen*, Sofia K. Forslund*, Alireza Kashani, Kristine H. Allin, Trine Nielsen, Tue H. Hansen, Suisha Liang, Qiang Feng, Chenchen Zhang, Paul Theodor Pyl, Luis Pedro Coelho, Huanming Yang, Jian Wang, Athanasios Typas, Morten F. Nielsen, Henrik Bjorn Nielsen, Peer Bork, Jun Wang, Tina Vilsbøll, Torben Hansen, Filip K. Knop, Manimozhiyan Arumugam & Oluf Pedersen Recovery of gut microbiota of healthy adults following antibiotic exposure in Nature Microbiology (2018) [DOI]
- Mohammad Bahram*, Falk Hildebrand*, Sofia K Forslund, Jennifer L Anderson, Nadejda A Soudzilovskaia, Peter M Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H Medema, Mia R Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork Structure and function of the global topsoil microbiome in Nature (2018) [DOI]
- 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]
(See above for papers)
Sep 16-19 2018 I was in Heidelberg for the Human Microbiome Conference
Oct 4 2018 I was in Paris talking about single cell approaches
June 14: I taught 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