Who am I?

I am the principal investigator (PI) of the Big Data Biology Lab at the Centre for Microbiome Research at the Queensland University of Technology (Brisbane, Australia) where we study the global microbiome.

Previously, my lab was hosted at Fudan University in Shanghai (2018–2023).

Before becoming a group leader, 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.

My Erdös-Bacon number is 7.

Publication list

Upcoming Travels & Talks

2025

Aug 17-22, 2025 Decoding Microproteins Across Evolution and Disease GRC in Barcelona, Spain

Sep 16-19 I will be at the EMBL Human Microbiome Symposium.

Oct 13-15 I will be in Houston for the SMBE Satellite Meeting: Evolutionary Biochemistry of Insect Antimicrobial Peptides.

Dec 15-18, 2025 I will give a keynote at the 19th International Conference on Data and Text Mining in Biomedical Informatics (DTMBIO 2025) in Muju, Republic of Korea.

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 o3 had to say about my research interests:

I work at the nexus of microbiology, big data, and machine learning: my group mines massively scaled metagenomic datasets—tens of thousands of environmental and host-associated samples—to build global gene catalogs such as GMGC v1, capturing both canonical proteins and the overlooked “small gene” universe of short open-reading frames. Leveraging these resources, we uncover new biology, most recently assembling AMPSphere, the world’s largest collection of candidate antimicrobial peptides, and experimentally validating their therapeutic promise. In parallel, we create open-source, high-performance tools like SemiBin and SemiBin 2, which use self-supervised neural networks to reconstruct high-quality metagenome-assembled genomes from short- and long-read data with minimal computational cost. Together, these efforts aim to chart the diversity, ecology, and functional capacity of the global microbiome—and translate that knowledge into novel antibiotics and other bioactive molecules.

Recent Publications

Recent(ish) publications (last 3 years; see full list):

26. AEMB: a computationally efficient abundance estimation method for metagenomic binning by Shaojun Pan, Ivan Tolstoganov, Kristoffer Sahlin, Marcel Martin, Xing-Ming Zhao, Luis Pedro Coelho in biorXiv (PREPRINT) (2025).

25. Persistence of High-Risk Antimicrobial Resistance Genes in Extracellular DNA Along an Urban Wastewater-River Continuum by John P. Makumbi, Samuel K. Leareng, Oliver K. Bezuidt, Luis Pedro Coelho, Thulani P. Makhalanyane in Sneak Peek (SSRN Preprints) (2025).

24. A census of hidden and discoverable microbial diversity beyond genome-centric approaches by Vishnu Prasoodanan P K, Oleksandr M Maistrenko, Anthony Fullam, ..., Luis Pedro Coelho, ..., Anja Spang, Peer Bork, Thomas S B Schmidt in bioRxiv (PREPRINT) (2025).

23. AI-Driven Antimicrobial Peptide Discovery: Mining and Generation by Paulina Szymczak, Wojciech Zarzecki, Jiejing Wang, ..., Luis Pedro Coelho, Cesar de la Fuente-Nunez, Ewa Szczurek in Accounts of Chemical Research (2025).

22. argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) by Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luis Pedro Coelho in Bioinformatics (2025).

21. Quest for Orthologs in the Era of Biodiversity Genomics by Felix Langschied, Nicola Bordin, Salvatore Cosentino, ..., Luis Pedro Coelho, ..., Paul D Thomas, Christophe Dessimoz, Ingo Ebersberger in Genome Biology and Evolution (2024).

20. A catalog of small proteins from the global microbiome by Yiqian Duan, Célio Dias Santos-Júnior, Thomas Sebastian Schmidt, ..., Xing-Ming Zhao, Peer Bork, Luis Pedro Coelho in Nature Communications (2024).

19. Discovery of antimicrobial peptides in the global microbiome with machine learning by Célio Dias Santos-Júnior, Marcelo D.T. Torres, Yiqian Duan, ..., Jaime Huerta-Cepas, Cesar de la Fuente-Nunez, Luis Pedro Coelho in Cell (2024).

18. For long-term sustainable software in bioinformatics by Luis Pedro Coelho in PLOS Computational Biology (2024).

17. Challenges in computational discovery of bioactive peptides in ’omics data by Luis Pedro Coelho, Célio Dias Santos‐Júnior, Cesar de la Fuente‐Nunez in PROTEOMICS (2024).

16. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer by Marija Dmitrijeva, Janko Tackmann, João Frederico Matias Rodrigues, Jaime Huerta-Cepas, Luis Pedro Coelho, Christian von Mering in Nature Ecology & Evolution (2024).

15. Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean by Lombard Fabien, Guidi Lionel, Manoela C. Brandão, ..., Luis Pedro Coelho, ..., Karsenti Eric, Gorsky Gabriel, Tara Oceans Coordinators in biorXiv (PREPRINT) (2024).

14. Functional and evolutionary significance of unknown genes from uncultivated taxa by Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra, ..., Emilia López-Solanilla, Luis Pedro Coelho, Jaime Huerta-Cepas in Nature (2023).

13. 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).

12. 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).

11. 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).

10. 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).

9. 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).

8. 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).

7. 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).

6. 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).

5. 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).

4. 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).

3. 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).

2. 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).

1. 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).

All publications... (Google Scholar profile)

Past News & Travels

2025

Apr 15 argNorm published at Bioinformatics

Apr 15-18 I will be at the Pakistan Society for Microbiology Conference.

Jul 16-24 I was in London July 15-20 and then in Liverpool for the ISMB/ECCB 2025 – Intelligent Systems for Molecular Biology & European Conference on Computational Biology

2024

Dec 10 & 12: Open office hours. Two sessions at different times of the day, so it works for all timezones. Attendance is free, but registration is required:

Dec 10 @ 9.30am UTC (find your local time): Register now
Dec 12 @ 9.30pm UTC (find your local time): Register now

Nov 11-15 I co-taught a 1 week course on state-of-the-art bioinformatic approaches to analyze metagenomic data. Click here to learn more and register.

Nov 3-6 I will be in Sydney. On the 4th, I will present at the Symposium on Bioinformatics Excellence and Innovation which is part of the ABACBS conference.
Oct 14-24 I will be in Shanghai
Sep 24 I will be presenting online at APBioNet on using machine learning to find antimicrobial peptides in the global microbiome. The talk will be on September 24, 2024 at 5am UTC (1pm SGT). Learn more and register]
Aug 18-23 I was in Cape Town, South Africa for ISME19. I will present at the Night of the Microbes event.
July 19-22: I was in San Francisco
July 12-17: ISMB2024, followed by the Quest for Orthologs meeting in Montreal, Canada. I presented a talk on AMPSphere and on long term sustainable research software (YouTube version).
July 4: ASM (the Australian one), in Brisbane, QLD, Australia
Jun 11 The AMPSphere manuscript was featured in several news outlets, including the BBC (Science in Action), Deutsche Welle, Guardian, El País, Folha de São Paulo as well as mentions as a Nature Research Highlight and in the Science Adviser.
Jun 5 AMPSphere manuscript published in Cell
May 14 New Season of Extremely Open Science. See episode 1 and the sardyne github repository
Apr 27 argNorm v0.3.0 has been released
9 May open office hours (Zoom)
24 April open office hours (Zoom)
23-25 January (2024) Berlin, Germany

2023

Nov 12-15: The 22nd International Conference on Bioinformatics (InCoB 2023) in Brisbane. I presented a highlight talk on SemiBin (including SemiBin2).
Oct 15-20: International Peptide Symposium 2023 in Brisbane. I presented the talk A survey of antimicrobial peptides from the global microbiome.
Aug 21-24: Quadram Institute in Norwich (UK).
July 27: I was awarded an ARC Future Fellowship to work on small proteins of the global microbiome at QUT.
July 23-27: ISMB (Lyon, France) - talk
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

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