I am currently looking for postdocs to [join my group in
Shanghai](https://big-data-biology.org/positions). 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](https://big-data-biology.org) 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](https://www.embl.de/~bork/). I have a PhD from [Carnegie Mellon
University](https://www.compbio.cmu.edu/) (2011), where I worked on [bioimage
informatics](https://en.wikipedia.org/wiki/Bioimage_informatics) for subcellular
location analysis with [Bob Murphy](https://murphylab.web.cmu.edu/).
My [Erdös-Bacon number is 7](/erdos-bacon).
[Publication list](/publications)
# Upcoming Travels & Talks
**2023 Jan 9-13** At the University of Warwick
[Email me](mailto:luis@luispedro.org) 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](https://calendly.com/luis-pedro-coelho/pub-zoom-15).
# 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](https://www.nature.com/nmeth/journal/v10/n12/abs/nmeth.2693.html) and
[tool](https://ngless.embl.de) development with
[applications](https://doi.org/10.1126/science.1261359). In methodological
terms, I worry a lot about [correct evaluation of
methods](https://luispedro.org/projects/gen-classification) and avoiding
over-inflated measures of performance. A large fraction of my time is spent
scaling up algorithms and [pipelines](https://doi.org/10.5334/jors.161) 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](https://en.wikipedia.org/wiki/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](/publications)):
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).
Copyright (c) 2009-2023. Luis Pedro Coelho. All rights reserved.