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