J
José Almeida Cruz
Researcher at University of Strasbourg
Publications - 9
Citations - 1309
José Almeida Cruz is an academic researcher from University of Strasbourg. The author has contributed to research in topics: RNA & Gene. The author has an hindex of 9, co-authored 9 publications receiving 1145 citations. Previous affiliations of José Almeida Cruz include Champalimaud Foundation & Centre national de la recherche scientifique.
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Journal ArticleDOI
The dynamic landscapes of RNA architecture.
José Almeida Cruz,Eric Westhof +1 more
TL;DR: A wealth of information has emerged from analyses of structures and from the use of innovative biophysical tools, and such efforts are opening new vistas on the RNA folding landscape.
Journal ArticleDOI
RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
José Almeida Cruz,Marc Frédérick Blanchet,Michal J. Boniecki,Janusz M. Bujnicki,Janusz M. Bujnicki,Shi-Jie Chen,Song Cao,Rhiju Das,Feng Ding,Nikolay V. Dokholyan,Samuel C. Flores,Lili Huang,Christopher A. Lavender,Véronique Lisi,François Major,Katarzyna Mikolajczak,Dinshaw J. Patel,Anna Philips,Anna Philips,Tomasz Puton,John SantaLucia,Fredrick Sijenyi,Thomas Hermann,Kristian Rother,Magdalena Rother,Alexander Serganov,Marcin Skorupski,Tomasz Sołtysiński,Parin Sripakdeevong,Irina Tuszynska,Kevin M. Weeks,Christina Waldsich,Michael Wildauer,Neocles B. Leontis,Eric Westhof +34 more
TL;DR: A first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles, to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations.
Journal ArticleDOI
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
Zhichao Miao,Ryszard W. Adamiak,Marc Frédérick Blanchet,Michal J. Boniecki,Janusz M. Bujnicki,Janusz M. Bujnicki,Shi-Jie Chen,Clarence Yu Cheng,Grzegorz Chojnowski,Fang-Chieh Chou,Pablo Cordero,José Almeida Cruz,Adrian R. Ferré-D'Amaré,Rhiju Das,Feng Ding,Nikolay V. Dokholyan,Stanislaw Dunin-Horkawicz,Wipapat Kladwang,Andrey Krokhotin,Grzegorz Lach,Marcin Magnus,François Major,Thomas H. Mann,Benoît Masquida,Dorota Matelska,Mélanie Meyer,Alla Peselis,Mariusz Popenda,Katarzyna J. Purzycka,Alexander Serganov,Juliusz Stasiewicz,Marta Szachniuk,Arpit Tandon,Siqi Tian,Jian Wang,Yi Xiao,Xiaojun Xu,Jinwei Zhang,Peinan Zhao,Tomasz Zok,Eric Westhof +40 more
TL;DR: This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction, where seven groups predicted a lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, using state-of-the-art methods.
Journal ArticleDOI
Comparative genomics of emerging pathogens in the Candida glabrata clade
Toni Gabaldón,Tiphaine Martin,Marina Marcet-Houben,Pascal Durrens,Monique Bolotin-Fukuhara,Olivier Lespinet,Sylvie Arnaise,Stéphanie Boisnard,Gabriela Aguileta,Ralitsa Atanasova,Christiane Bouchier,Arnaud Couloux,Sophie Creno,José Almeida Cruz,José Almeida Cruz,Hugo Devillers,Adela Enache-Angoulvant,Juliette Guitard,Laure Jaouen,Laurence Ma,Christian Marck,Cécile Neuvéglise,Eric Pelletier,Amélie Pinard,Julie Poulain,Julien Recoquillay,Eric Westhof,Patrick Wincker,Bernard Dujon,Christophe Hennequin,Cécile Fairhead +30 more
TL;DR: The analyses shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces, and uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens.
Journal ArticleDOI
New metrics for comparing and assessing discrepancies between RNA 3D structures and models.
TL;DR: The results show that there is little correlation between RMSD and interaction network fidelity, and the deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.