Luis Pedro Coelho

Luis Pedro Coelho is the principal investigator (PI) of the Big Data Biology Lab at the Centre for Microbiome Research at the Queensland University of Technology (Brisbane, Australia). Previously, the lab was hosted at Fudan University (Shanghai) and, prior to that, he worked as a postdoctoral researcher in Peer Bork's group at the European Molecular Biology Laboratory (EMBL). He has a PhD from Carnegie Mellon University an MSc from Instituto Superior Técnico in Lisbon.

Personal website: https://luispedro.org

BDB-Lab Projects

1. GMGC: Global Microbial Gene Catalog
2. SEARCHER

BDB-Lab Publications

1. AI-Driven Antimicrobial Peptide Discovery: Mining and Generation
2. argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
3. Quest for Orthologs in the Era of Biodiversity Genomics
4. A catalog of small proteins from the global microbiome
5. Discovery of antimicrobial peptides in the global microbiome with machine learning
6. For long-term sustainable software in bioinformatics
7. Challenges in computational discovery of bioactive peptides in ’omics data
8. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer
9. Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean
10. Functional and evolutionary significance of unknown genes from uncultivated taxa
11. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
12. Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs?
13. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
14. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
15. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies
16. EXPERT: Transfer Learning-enabled context-aware microbial source tracking
17. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation
18. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
19. Software testing in microbial bioinformatics: a call to action
20. Microbiome and metabolome features of the cardiometabolic disease spectrum
21. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism
22. Towards the biogeography of prokaryotic genes
23. Combinatorial, additive and dose-dependent drug–microbiome associations
24. An open code pledge for the neuroscience community
25. GUNC: detection of chimerism and contamination in prokaryotic genomes
26. Metagenomic assessment of the global diversity and distribution of bacteria and fungi
27. Macrel: antimicrobial peptide screening in genomes and metagenomes
28. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
29. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
30. Microbial abundance, activity and population genomic profiling with mOTUs2
31. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
32. Global Trends in Marine Plankton Diversity across Kingdoms of Life
33. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
34. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
35. Extensive transmission of microbes along the gastrointestinal tract
36. Similarity of the dog and human gut microbiomes in gene content and response to diet
37. Structure and function of the global topsoil microbiome