ORCID Profile
0000-0002-8238-1083
Current Organisation
University of Southampton
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Publisher: Oxford University Press (OUP)
Date: 04-10-2021
DOI: 10.1093/NAR/GKAB883
Abstract: To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many erse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (adlocbio adloc) and as a webserver (padloc.otago.ac.nz).
Publisher: Cold Spring Harbor Laboratory
Date: 26-01-2019
DOI: 10.1101/527796
Abstract: Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and ex les of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the world's countries, and showed that its phylogeography is locally clustered within countries, cities, and in iduals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.
Publisher: Center for Open Science
Date: 16-05-2023
Abstract: Electroencephalography (EEG) studies of dreaming are an integral paradigm in the study of neurocognitive processes of human sleep and consciousness, but they are limited by the number of observations that can be collected per study. Dream studies also involve substantial methodological and conceptual variability which poses problems for the integration of results. To address these issues, we present the DREAM database—an expanding collection of standardized datasets on human sleep EEG combined with dream report data—with an initial release of 18 datasets, totaling 2331 data points. Each datum consists, at minimum, of sleep electroencephalography (≥20 s, ≥100 Hz, ≥2 electrodes) up to the time of waking and a standardized dream report classification of the subject’s reported sleep experience. This database will provide access to a larger pool of data than any single research group can collect and increase the statistical power of studies focusing on the neural correlates of dreaming. It will also provide useful criteria for methodological choices in future dream laboratory research projects.
Location: United Kingdom of Great Britain and Northern Ireland
Location: Netherlands
No related grants have been discovered for Franklin Nóbrega.