Publications by authors named "Blake Sweeney"

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Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.
Pedro Madrigal, Anil S Thanki, Silvie Fexova, Iris D Yu, Arsenios Chatzigeorgiou, Blake Sweeney

Nucleic Acids Res· December 2025

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First full-genome alignment representative for the genus .
Sandra Triebel, Tom Eulenfeld, Nancy Ontiveros-Palacios, Blake Sweeney, Norbert Tautz

RNA· December 2025

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LitSumm: large language models for literature summarization of noncoding RNAs.
Andrew Green, Carlos Eduardo Ribas, Nancy Ontiveros-Palacios, Sam Griffiths-Jones, Anton I Petrov, Blake Sweeney

Database (Oxford)· February 2025

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R2DT: a comprehensive platform for visualizing RNA secondary structure.
Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Blake A Sweeney

Nucleic Acids Res· February 2025

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Rfam 15: RNA families database in 2025.
Nancy Ontiveros-Palacios, Emma Cooke, Eric P Nawrocki, Sandra Triebel, Manja Marz, Blake Sweeney

Nucleic Acids Res· January 2025

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REDIportal: toward an integrated view of the A-to-I editing.
Pietro D'Addabbo, Roni Cohen-Fultheim, Itamar Twersky, Adriano Fonzino, Domenico Alessandro Silvestris, Blake Sweeney

Nucleic Acids Res· January 2025

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Rfam 15: RNA families database in 2025.
Nancy Ontiveros, Emma Cooke, Eric P Nawrocki, Sandra Triebel, Manja Marz, Blake Sweeney

bioRxiv· September 2024

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R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.
Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Blake A Sweeney

bioRxiv· September 2024

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Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.
Sandra Triebel, Kevin Lamkiewicz, Nancy Ontiveros, Blake Sweeney, Peter F Stadler

Sci Rep· July 2024

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When will RNA get its AlphaFold moment?
Bohdan Schneider, Blake Alexander Sweeney, Alex Bateman, Jiri Cerny, Tomasz Zok

Nucleic Acids Res· October 2023

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Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs.
Emil F Khisamutdinov, Blake A Sweeney, Neocles B Leontis

Nucleic Acids Res· September 2021

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R2DT is a framework for predicting and visualising RNA secondary structure using templates.
Blake A Sweeney, David Hoksza, Eric P Nawrocki, Carlos Eduardo Ribas, Fábio Madeira

Nat Commun· June 2021

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Exploring Non-Coding RNAs in RNAcentral.
Blake A Sweeney, Arina A Tagmazian, Carlos E Ribas, Robert D Finn, Alex Bateman

Curr Protoc Bioinformatics· September 2020

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The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.
Lorena G Parlea, Blake A Sweeney, Maryam Hosseini-Asanjan, Craig L Zirbel, Neocles B Leontis

Methods· July 2016

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JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
James Roll, Craig L Zirbel, Blake Sweeney, Anton I Petrov, Neocles Leontis

Nucleic Acids Res· July 2016

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Identifying novel sequence variants of RNA 3D motifs.
Craig L Zirbel, James Roll, Blake A Sweeney, Anton I Petrov, Meg Pirrung

Nucleic Acids Res· September 2015

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An introduction to recurrent nucleotide interactions in RNA.
Blake A Sweeney, Poorna Roy, Neocles B Leontis

Wiley Interdiscip Rev RNA· August 2015

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R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Jamie J Cannone, Blake A Sweeney, Anton I Petrov, Robin R Gutell, Craig L Zirbel

Nucleic Acids Res· July 2015

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The Nucleic Acid Database: new features and capabilities.
Buvaneswari Coimbatore Narayanan, John Westbrook, Saheli Ghosh, Anton I Petrov, Blake Sweeney

Nucleic Acids Res· January 2014

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Conference Scene: Advances in RNA nanotechnology promise to transform medicine.
Neocles Leontis, Blake Sweeney, Farzin Haque, Peixuan Guo

Nanomedicine (Lond)· July 2013

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Exploring the parameter space of complex self-assembly through virus capsid models.
Blake Sweeney, Tiequan Zhang, Russell Schwartz

Biophys J· February 2008

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The spectrum of Trp- mutants isolated as 5-fluoroanthranilate-resistant clones in Saccharomyces bayanus, S. mikatae and S. paradoxus.
Elizabeth W Jones, Peter B Berget, James M Burnette, Candice Anderson, Denise Asafu-Adjei, Blake Sweeney

Yeast· January 2008

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