I am currently looking for postdocs to join my group in Shanghai. Come work with me on metagenomics, antimicrobial resistance, algorithms, or just propose your own project.
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 large-scale microbiome analyses.
Previously, I worked at the European Molecular Biology Laboratory (EMBL) in Peer Bork's group. I have a PhD from Carnegie Mellon University (2011), where I worked on bioimage informatics for subcellular location analysis with Bob Murphy.
Upcoming Travels & Talks
2023 Jan 9-13 At the University of Warwick
Email me if you want to set up meetings at any of these opportunities (or to invite me for other opportunities).
If you want to chat with me about science and such, you can use my calendly link.
Research Interests
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.
Recent Publications
Recent(ish) publications (last 5 years; see full list):
33. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing by Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in bioRxiv (PREPRINT) (2023).
32. metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies by Senying Lai, Shaojun Pan, Chuqing Sun, Luis Pedro Coelho, Wei-Hua Chen, Xing-Ming Zhao in Genome Biology (2022).
31. Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide with implications for heart and kidney disorders by Petros Andrikopoulos, Judith Aron-Wisnewsky, Rima Chakaroun, ..., Luis Pedro Coelho, ..., Karine Clément, Marc-Emmanuel Dumas, MetaCardis Consortium in medRXiv (PREPRINT) (2022).
30. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics by Rémi Gschwind, Svetlana Ugarcina Perovic, Marie Petitjean, Julie Lao, Luis Pedro Coelho, Etienne Ruppé in bioRxiv (PREPRINT) (2022).
29. EXPERT: Transfer Learning-enabled context-aware microbial source tracking by Hui Chong, Yuguo Zha, Qingyang Yu, ..., Weihua Chen, Luis Pedro Coelho, Kang Ning in Briefings in Bioinformatics (2022).
28. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation by Thomas SB Schmidt, Simone S Li, Oleksandr M Maistrenko, ..., Luis Pedro Coelho, ..., Anna Glazek, Rajna Hercog, Hilde Herrema in Nature Medicine (2022).
27. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments by Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao, Luis Pedro Coelho in Nature Communications (2022).
26. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes by Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, ..., Luis Pedro Coelho, ..., Thomas S B Schmidt, Orsolya Barabas, Peer Bork in Nucleic Acids Research (2022).
25. Software testing in microbial bioinformatics: a call to action by Boas C.L. van der Putten, C. I. Mendes, Brooke M. Talbot, ..., Luis Pedro Coelho, ..., Christopher A. Gulvik, Lee S. Katz, The ASM NGS 2020 Hackathon participants in Microbial Genomics (2022).
24. Microbiome and metabolome features of the cardiometabolic disease spectrum by Sebastien Fromentin, Sofia K. Forslund, Kanta Chechi, ..., Luis Pedro Coelho, ..., Marc-Emmanuel Dumas, S. Dusko Ehrlich, Oluf Pedersen in Nature Medicine (2022).
23. Functional and evolutionary significance of unknown genes from uncultivated taxa by Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra, ..., Peer Bork, Luis Pedro Coelho, Jaime Huerta-Cepas in biorXiv (PREPRINT) (2022).
22. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism by Eugeni Belda, Lise Voland, Valentina Tremaroli, ..., Luis Pedro Coelho, ..., Jeroen Raes, Karine Clément, The MetaCardis Consortium in Gut (2022).
21. Towards the biogeography of prokaryotic genes by Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, ..., Henrik Bjørn Nielsen, Jaime Huerta-Cepas, Peer Bork in Nature (2021).
20. An open code pledge for the neuroscience community by Cooper Smout, Dawn Liu Holford, Kelly Garner, ..., Naoyuki Sunami, Sina Mansour L., Luis Pedro Coelho in MetaArXiv Preprint (2021).
19. Combinatorial, additive and dose-dependent drug–microbiome associations by Sofia K. Forslund, Rima Chakaroun, Maria Zimmermann-Kogadeeva, ..., Luis Pedro Coelho, ..., Michael Stumvoll, Peer Bork, The MetaCardis Consortium* in Nature (2021).
18. GUNC: detection of chimerism and contamination in prokaryotic genomes by Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, ..., Daniel R Mende, Thomas SB Schmidt, Peer Bork in Genome Biology (2021).
17. MACREL: antimicrobial peptide screening in genomes and metagenomes by Célio Dias Santos-Junior, Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in PeerJ (2020).
16. Metagenomic assessment of the global diversity and distribution of bacteria and fungi by Mohammad Bahram, Tarquin Netherway, Clémence Frioux, ..., Luis Pedro Coelho, ..., Stefan Geisen, Peer Bork, Falk Hildebrand in Environmental Microbiology (2021).
15. Voices of the new generation: science in a state of benign confusion by Luis Pedro Coelho in Nature Reviews Molecular Cell Biology (2020).
14. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis by Sara Vieira-Silva, Gwen Falony, Eugeni Belda, ..., Luis Pedro Coelho, ..., Fredrik Bäckhed, Karine Clément, Jeroen Raes in Nature (2020).
13. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity by Oleksandr M Maistrenko, Daniel R Mende, Mechthild Luetge, ..., Luis Pedro Coelho, ..., Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork in The ISME Journal (2020).
12. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome by Guillem Salazar, Lucas Paoli, Adriana Alberti, ..., Luis Pedro Coelho, ..., Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa in Cell (2019).
11. Global trends in marine plankton diversity across kingdoms of life by Federico M Ibarbalz, Nicolas Henry, Manoela C Brandão, ..., Luis Pedro Coelho, ..., Hisashi Endo, Josep M Gasol, Ann C Gregory in Cell (2019).
10. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes by Daniel R Mende, Ivica Letunic, Oleksandr M Maistrenko, ..., Jaime Huerta-Cepas, Luis Pedro Coelho, Peer Bork in Nucleic acids research (2020).
9. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer by Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, ..., Luis Pedro Coelho, ..., Manimozhiyan Arumugam, Peer Bork, Georg Zeller in Nature medicine (2019).
8. Microbial abundance, activity and population genomic profiling with mOTUs2 by Alessio Milanese, Daniel R Mende, Lucas Paoli, ..., Luis Pedro Coelho, ..., Peer Bork, Georg Zeller, Shinichi Sunagawa in Nature Communications (2019).
7. Community‐Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems by Luigi Caputi, Quentin Carradec, Damien Eveillard, ..., Luis Pedro Coelho, ..., Patrick Wincker, Chris Bowler, Daniele Iudicone in Global Biogeochemical Cycles (2019).
6. Extensive transmission of microbes along the gastrointestinal tract by Thomas Sebastian Benedikt Schmidt, Matthew Robert Hayward, Luis Pedro Coelho, ..., Georg Zeller, Paul Wilmes, Peer Bork in eLife (2019).
5. Recovery of gut microbiota of healthy adults following antibiotic exposure by Albert Palleja, Kristian H Mikkelsen, Sofia K Forslund, ..., Luis Pedro Coelho, ..., Filip K. Knop, Manimozhiyan Arumugam, Oluf Pedersen in Nature microbiology (2018).
4. Structure and function of the global topsoil microbiome by Mohammad Bahram, Falk Hildebrand, Sofia K Forslund, ..., Luis Pedro Coelho, ..., Martin Ryberg, Leho Tedersoo, Peer Bork in Nature (2018).
3. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork in Microbiome (2019).
2. Similarity of the dog and human gut microbiomes in gene content and response to diet by Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, ..., Janet R. Jackson, Qinghong Li, Peer Bork in Microbiome (2018).
1. Selective maternal seeding and environment shape the human gut microbiome by Katri Korpela, Paul Igor Costea, Luis Pedro Coelho, ..., Dorret I Boomsma, Nicola Segata, Peer Bork in Genome Research (2018).
All publications... (Google Scholar profile)
Other News
(See above for papers)
2022
2022 September 17-21 ECCB 2022 I will present in the Quest for Orthologs workshop
2022 September 24-29 I will attend EDAR
2022 June 9: Novozymes Prize Awardee 2021 - Novozymes Prize Symposium
2022 June 2: Open Office Hours
April 6-9: Keystone Symposium Micropeptides: Biogenesis and Function
2020
Jan 6-7 I was in Gotenburg, Sweden for the first meeting of the EMBARK project
2019
November 21-27 I was in Sydney, Australia
July 21-25 2019 I was in Basel for ECCB/ISMB 2019
June 21-26 2019 I was in San Francisco for ASM Microbe 2019
April 10-11 2019 I was in Chengdu (China), visiting the University of Electronic Science and Technology of China.
April 16-18 2019 I was in Utrecht (Netherlands) for the International Conference on One Health Antimicrobial Resistance (ICOHAR) talking about our dog microbiome work
2018
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 26-29: Ireland IHMC2018: International Human Microbiome Consortium
June 14: I taught the Introduction to Python lecture at the Lisbon (Portugal) Machine Learning Summer School
2017
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.
Oct 24-26 I was in Copenhagen teaching people how to use ngless at the Microbiome data interpretation workshop (slides here) and giving a scientific talk on my work.
Sept 12-13 I was in Delft 12-13** for a workshop on data-driven cell factory and community design
July 21-25 I was in Prague for ECCB/ISMB 2017 with a poster on NGLess
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.
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
Copyright (c) 2009-2023. Luis Pedro Coelho. All rights reserved.