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