DEL CAMPO Javier's profile
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DEL CAMPO JavierORCID_LOGO

  • Biodiversity, Institut de Biologia Evolutiva (CSIC - UPF), Barcelona, Spain
  • Bacteria and archaea, Evolutionary genomics, Metagenomics
  • recommender

Recommendation:  1

Reviews:  0

Website https://scholar.google.ca/citations?user=Mty5iQYAAAAJ&hl=ca
Areas of expertise
I am a microbial ecologist and Group Leader at the Institute of Evolutionary Biology (CSIC - UPF) in Barcelona and an Adjunct Assistant Professor at the Rosenstiel School of Marine and Atmospheric Science - University of Miami. I completed my bachelor’s and my Ph.D. in Environmental Microbiology and Biotechnology at the Institute of Marine Science - CSIC (Barcelona), followed by postdoctoral research at the University of Barcelona, the University of British Columbia (Vancouver), and back to the Institute of Marine Science. In February 2019 I joined as Assistant Professor the Rosenstiel School of Marine and Atmospheric Science at the University of Miami and in February 2021 I joined the Institute for Evolutionary Biology. My research has focused on the study of the ecology and evolution of microbial eukaryotes but recently, I have expanded my scope to the prokaryotes in order to have an integrated view of the microbiome. I am currently investigating microbial community ecology in marine animal-associated environments using cutting-edge sequencing technologies and computational biology. I hope that my research can help to have a better understanding of the role that microorganisms play in the response of animals to climate change.

Recommendation:  1

05 Aug 2024
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LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins

Łukasz F. Sobala https://doi.org/10.1101/2024.01.30.577650

A protein database to study the origin of metazoans

Recommended by based on reviews by Giacomo Mutti and 2 anonymous reviewers

Sobala (2024) introduces a new, comprehensive, and curated eukaryotic database. It consolidates information from EukProt (Richter et al. 2022) and various other resources to enhance Metazoa representation in existing protein databases. The preprint is of significant interest to the phylogenomics and comparative genomics communities, and I commend the author for their work.

LukProt, the expanded database, significantly increases the taxon sampling within holozoans. It integrates data from the previously assembled EukProt and AniProtDB (Barreira et al. 2021) databases, with additional datasets from early-diverging animal lineages such as ctenophores, sponges, and cnidarians. This effort will undoubtedly be useful for researchers investigating these clades and their origins, as well as for the broader field of comparative genomics.

The author provides both web-portal and command-line versions of the database, making it accessible to users with varying degrees of bioinformatic proficiency. The curation effort is commendable, and I believe the comparative genomics community, especially those interested in animal origins, will find LukProt to be a valuable resource.

           

References

Barreira SN, Nguyen A-D, Fredriksen MT, Wolfsberg TG, Moreland RT, Baxevanis AD (2021) AniProtDB: A collection of consistently generated metazoan proteomes for comparative genomics studies. Molecular Biology and Evolution 38, 4628–4633. https://doi.org/10.1093/molbev/msab165

Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C (2022) EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community Journal 2, e56. https://doi.org/10.24072/pcjournal.173

Sobala ŁF (2024) LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2024.01.30.577650
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DEL CAMPO JavierORCID_LOGO

  • Biodiversity, Institut de Biologia Evolutiva (CSIC - UPF), Barcelona, Spain
  • Bacteria and archaea, Evolutionary genomics, Metagenomics
  • recommender

Recommendation:  1

Reviews:  0

Website https://scholar.google.ca/citations?user=Mty5iQYAAAAJ&hl=ca
Areas of expertise
I am a microbial ecologist and Group Leader at the Institute of Evolutionary Biology (CSIC - UPF) in Barcelona and an Adjunct Assistant Professor at the Rosenstiel School of Marine and Atmospheric Science - University of Miami. I completed my bachelor’s and my Ph.D. in Environmental Microbiology and Biotechnology at the Institute of Marine Science - CSIC (Barcelona), followed by postdoctoral research at the University of Barcelona, the University of British Columbia (Vancouver), and back to the Institute of Marine Science. In February 2019 I joined as Assistant Professor the Rosenstiel School of Marine and Atmospheric Science at the University of Miami and in February 2021 I joined the Institute for Evolutionary Biology. My research has focused on the study of the ecology and evolution of microbial eukaryotes but recently, I have expanded my scope to the prokaryotes in order to have an integrated view of the microbiome. I am currently investigating microbial community ecology in marine animal-associated environments using cutting-edge sequencing technologies and computational biology. I hope that my research can help to have a better understanding of the role that microorganisms play in the response of animals to climate change.