About

This laboratory develops computational probabilistic models to understand RNA structure. We also work with models of sequence evolution in order to bring phylogenetic power to the question of remote homology recognition.

Research topics

• Biology
• Genetics
• Computational biology

Selected publications

• Rfam 14: expanded coverage of metagenomic, viral and microRNA families

  Nucleic Acids Research · 2020 · 1123 citations

  • Computational biology
  • Biology
  • Genetics

  Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam families and updating 40. We established a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs. We have also increased the coverage of bacterial and metagenome-based RNA families from the ZWD database. These developments have enabled a significant growth of the database, with the addition of 759 new families in Rfam 14. To facilitate further community contribution to Rfam, expert users are now able to build and submit new families using the newly developed Rfam Cloud family curation system. New Rfam website features include a new sequence similarity search powered by RNAcentral, as well as search and visualisation of families with pseudoknots. Rfam is freely available at https://rfam.org.

  DOI

Recent grants

• NIH Grant R01GM070538

  NIH · $311k · 2009

• Discovery of structural RNAs involved in human health and disease

  NIH · $1.4M · 2022–2027

• An all-in-one web server for RNA structure prediction using evolutionary information

  NIH · $415k · 2023–2025

Frequent coauthors

• Sean R. Eddy

  Harvard University

  28 shared

• Ph. Boucaud

  Centre National de la Recherche Scientifique

  24 shared

• J. L. Cortés

  Universidad de Zaragoza

  13 shared

• J.L. Alonso

  Universidad de Zaragoza

  8 shared

• Eric P. Nawrocki

  National Center for Biotechnology Information

  8 shared

• Jody Clements

  Janelia Research Campus

  6 shared

• José L. Alonso

  Universitat de Miguel Hernández d'Elx

  6 shared

• Anton I. Petrov

  6 shared

Labs

• Rivas LabPI

  Not provided

Similar researchers at Harvard University

• Walter C Willetth-429
• JoAnn E Mansonh-359
• Randy L. Bucknerh-268
• Edward Giovannuccih-267
• Kristen Andersonh-263