Generative power of a protein language model trained on multiple sequence alignments
- Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol, …, Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
- Elife, 10.7554/elife.79854
The gene regulation knowledge commons: the action area of GREEKC
- Martin Kuiper, Joseph Bonello, Jesualdo T Fernández-Breis, …, Steven Vercruysse, Daniel R Zerbino, Astrid Lægreid
- Biochim Biophys Acta Gene Regul Mech, 10.1016/j.bbagrm.2021.194768
The Clustal Omega Multiple Alignment Package
- Fabian Sievers, Desmond G Higgins
- Methods Mol Biol, 10.1007/978-1-0716-1036-7_1
An intrinsically disordered proteins community for ELIXIR
- Norman E Davey, M Madan Babu, Martin Blackledge, …, Bonnie Ann Wallace, Kanin Wichapong, Silvio C E Tosatto
- F1000Res, 10.12688/f1000research.20136.1
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction
- Fabian Sievers, Desmond G Higgins, Fabian Sievers, Desmond G Higgins
- Bioinformatics, 10.1093/bioinformatics/btz552
An Integrated Global Analysis of Compartmentalized HRAS Signaling
- Tapesh Santra, Ana Herrero, Javier Rodriguez, …, Piero Crespo, David Matallanas, Walter Kolch
- Cell Rep, 10.1016/j.celrep.2019.02.038
TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida
- Paul D Donovan, Linda M Holland, Lisa Lombardi, …, Desmond G Higgins, Kenneth H Wolfe, Geraldine Butler
- PLoS Genet, 10.1371/journal.pgen.1007429
The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche Adaptation
- Graham M Hughes, Emma S M Boston, John A Finarelli, William J Murphy, Desmond G Higgins, Emma C Teeling
- Mol Biol Evol, 10.1093/molbev/msy028
Identification of fungi in shotgun metagenomics datasets
- Paul D Donovan, Gabriel Gonzalez, Desmond G Higgins, Geraldine Butler, Kimihito Ito
- PLoS One, 10.1371/journal.pone.0192898
Clustal Omega for making accurate alignments of many protein sequences
- Fabian Sievers, Desmond G Higgins
- Protein Sci, 10.1002/pro.3290
MyD88 is an essential component of retinoic acid-induced differentiation in human pluripotent embryonal carcinoma cells
- Gomaa Sulaiman, Aoife Cooke, Brendan Ffrench, …, Luke O’Neill, John J O’Leary, Michael F Gallagher
- Cell Death Differ, 10.1038/cdd.2017.124
Protein multiple sequence alignment benchmarking through secondary structure prediction
- Quan Le, Fabian Sievers, Desmond G Higgins
- Bioinformatics, 10.1093/bioinformatics/btw840
Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species
- Markus S Schröder, Kontxi Martinez de San Vicente, Tâmara H R Prandini, …, Eduardo Bagagli, Kenneth H Wolfe, Geraldine Butler
- PLoS Genet, 10.1371/journal.pgen.1006404
Identification of Non-Coding RNAs in the Candida parapsilosis Species Group
- Paul D Donovan, Markus S Schröder, Desmond G Higgins, Geraldine Butler
- PLoS One, 10.1371/journal.pone.0163235
Wnt signalling is a bi-directional vulnerability of cancer cells
- David J Duffy, Aleksandar Krstic, Thomas Schwarzl, …, Steffen Bannert, Desmond G Higgins, Walter Kolch
- Oncotarget, 10.18632/oncotarget.11203
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments
- Gearóid Fox, Fabian Sievers, Desmond G Higgins
- Bioinformatics, 10.1093/bioinformatics/btv592