Luis Pedro Coelho

Principal Investigator

BDB-Lab Publications

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

Full list of publications on Google Scholar...

Copyright (c) 2018–2024. Luis Pedro Coelho and other group members. All rights reserved.