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.
I will move to the Centre for Microbiome Research at Queensland University of Technology (QUT) in Brisbane Australia in August 2023.
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
Aug 21-24: Quadram Institute in Norwich (UK).
Nov 12-15: The 22nd International Conference on Bioinformatics (InCoB 2023) in Brisbane. I will present a highlight talk on SemiBin (including SemiBin2).
Oct 15-20: International Peptide Symposium 2023 in Brisbane. I will present the talk A survey of antimicrobial peptides from the global microbiome.
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 cal.com link.
Research Interests
More technical version: I am interested in microbiomes. 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. Towards this, I pursue both method development (e.g. SemiBin or NGLess) and biologically-driven projects. Solving problems related to small proteins (those with fewer than 100 amino acids) is a particular interest of mine.
Not-so technical version: Microbes are all around us (including inside of us), what we call a microbiome. With modern technology, it is possible to sequence the DNA of all the microbes in a sample (be it from a soil sample or from a human gut sample). This allows us to answer questions such as: what are the microbes present in a given sample? How do they differ between samples? What are the functions of these microbes?
However, to achieve this, we need to develop computational methods to analyse these data. My work is focused on both developing these methods and applying them to answer biological questions.
Here is what chatGPT had to say about my research interests:
Luis Pedro Coelho is a computational biologist known for his work in developing bioinformatics tools and algorithms. As of my last update in September 2021, some specific contributions include his work on the development of machine learning algorithms for the analysis of large-scale molecular biology and metagenomics data.
He is the author of several open-source software packages used in bioinformatics. One notable tool he developed is Jug, a task-based parallelization framework that allows users to easily write and run complex, multi-step computational pipelines.
Coelho's research has spanned a range of topics in the field of bioinformatics and computational biology, such as image analysis, microbiome research, and genomics. His research often emphasizes methodological development, creating new tools and techniques that others in the field can use to more effectively analyze biological data.
Recent Publications
Recent(ish) publications (last 5 years; see full list):
33. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource by Thomas S B Schmidt, Anthony Fullam, Pamela Ferretti, ..., Michael Kuhn, Luis Pedro Coelho, Peer Bork in Nucleic Acids Research (2023).
32. Computational exploration of the global microbiome for antibiotic discovery by Célio Dias Santos-Júnior, Marcelo Der Torossian Torres, Yiqian Duan, ..., Jaime Huerta-Cepas, Cesar de la Fuente-Nunez, Luis Pedro Coelho in biorXiv (PREPRINT) (2023).
31. Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs? by Johan Bengtsson-Palme, Anna Abramova, Thomas U. Berendonk, ..., Luis Pedro Coelho, ..., Yngvild Wasteson, Astrid Louise Wester, Rabaab Zahra in Environment International (2023).
30. A global survey of eco-evolutionary pressures acting on horizontal gene transfer by Marija Dmitrijeva, Janko Tackmann, João Matias Rodrigues, Jaime Huerta-Cepas, Luis Pedro Coelho, Christian von Mering in Research Square (PREPRINT) (2023).
29. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics by Rémi Gschwind, Svetlana Ugarcina Perovic, Maja Weiss, Marie Petitjean, Julie Lao, Luis Pedro Coelho, Etienne Ruppé in Nucleic Acids Research (2023).
28. 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 Bioinformatics (2023).
27. 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).
26. 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).
25. 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).
24. 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).
23. 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).
22. 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).
21. 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).
20. 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).
19. 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).
18. 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).
17. 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).
16. 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).
15. 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).
14. 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).
13. MACREL: antimicrobial peptide screening in genomes and metagenomes by Célio Dias Santos-Junior, Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in PeerJ (2020).
12. 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).
11. Voices of the new generation: science in a state of benign confusion by Luis Pedro Coelho in Nature Reviews Molecular Cell Biology (2020).
10. 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).
9. 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).
8. 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).
7. 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).
6. 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).
5. 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).
4. 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).
3. 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).
2. 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).
1. 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).
All publications... (Google Scholar profile)
Past News & Travels
2023
July 27: I was awarded an ARC Future Fellowship to work on small proteins of the global microbiome at QUT.
June 15-18: Vibecamp
May 31-June 2: microProteins 2023 (Copenhagen, Denmark)
April 2-6: Paris (France) for EMBARK and visiting INRAE
Jan 9-13 At the University of Warwick
Copyright (c) 2009-2023. Luis Pedro Coelho. All rights reserved.