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