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