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