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. Long-read metagenomic sequencing reveals novel lineages and functional diversity in urban soil microbiome
2. Persistence of High-Risk Antimicrobial Resistance Genes in Extracellular DNA Along an Urban Wastewater-River Continuum
3. proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
4. Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort
5. AEMB: a computationally efficient abundance estimation method for metagenomic binning
6. A census of hidden and discoverable microbial diversity beyond genome-centric approaches
7. AI-Driven Antimicrobial Peptide Discovery: Mining and Generation
8. argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
9. Quest for Orthologs in the Era of Biodiversity Genomics
10. A catalog of small proteins from the global microbiome
11. Discovery of antimicrobial peptides in the global microbiome with machine learning
12. For long-term sustainable software in bioinformatics
13. Challenges in computational discovery of bioactive peptides in ’omics data
14. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer
15. Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean
16. Functional and evolutionary significance of unknown genes from uncultivated taxa
17. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
18. Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs?
19. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
20. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
21. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies
22. EXPERT: Transfer Learning-enabled context-aware microbial source tracking
23. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation
24. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
25. Software testing in microbial bioinformatics: a call to action
26. Microbiome and metabolome features of the cardiometabolic disease spectrum
27. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism
28. Towards the biogeography of prokaryotic genes
29. Combinatorial, additive and dose-dependent drug–microbiome associations
30. An open code pledge for the neuroscience community
31. GUNC: detection of chimerism and contamination in prokaryotic genomes
32. Metagenomic assessment of the global diversity and distribution of bacteria and fungi
33. Macrel: antimicrobial peptide screening in genomes and metagenomes
34. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
35. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
36. Microbial abundance, activity and population genomic profiling with mOTUs2
37. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
38. Global Trends in Marine Plankton Diversity across Kingdoms of Life
39. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
40. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
41. Extensive transmission of microbes along the gastrointestinal tract
42. Similarity of the dog and human gut microbiomes in gene content and response to diet
43. Structure and function of the global topsoil microbiome