R2DT is a framework for predicting and visualising RNA secondary structure using templates
Sweeney, Blake A., Hoksza, David, Nawrocki, Eric P., Ribas, Carlos Eduardo, Madeira, Fábio, Cannone, Jamie J., Gutell, Robin, Maddala, Aparna, Meade, Caeden D., Williams, Loren Dean, Petrov, Anton S., Chan, Patricia P., Lowe, Todd M., Finn, Robert D., Petrov, Anton I.
Published in Nature communications (09.06.2021)
Published in Nature communications (09.06.2021)
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Journal Article
Identifying novel sequence variants of RNA 3D motifs
Zirbel, Craig L, Roll, James, Sweeney, Blake A, Petrov, Anton I, Pirrung, Meg, Leontis, Neocles B
Published in Nucleic acids research (03.09.2015)
Published in Nucleic acids research (03.09.2015)
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Journal Article
An introduction to recurrent nucleotide interactions in RNA
Sweeney, Blake A, Roy, Poorna, Leontis, Neocles B
Published in Wiley interdisciplinary reviews. RNA (01.01.2015)
Published in Wiley interdisciplinary reviews. RNA (01.01.2015)
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Journal Article
Exploring Non‐Coding RNAs in RNAcentral
Sweeney, Blake A., Tagmazian, Arina A., Ribas, Carlos E., Finn, Robert D., Bateman, Alex, Petrov, Anton I.
Published in Current Protocols in Bioinformatics (01.09.2020)
Published in Current Protocols in Bioinformatics (01.09.2020)
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Journal Article
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server
Cannone, Jamie J, Sweeney, Blake A, Petrov, Anton I, Gutell, Robin R, Zirbel, Craig L, Leontis, Neocles
Published in Nucleic acids research (01.07.2015)
Published in Nucleic acids research (01.07.2015)
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Journal Article
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
Sweeney, Blake A, Petrov, Anton I, Ribas, Carlos E, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Seemann, Stefan E, Gorodkin, Jan, Cannone, Jamie J, Gutell, Robin R, Kay, Simon, Marygold, Steven, dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M, Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P, Lowe, Todd M, Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Volders, Pieter-Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J, Kalvari, Ioanna, Nawrocki, Eric P, Petrov, Anton S, Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M, Hoksza, David, Lovering, Ruth C, Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, Weinberg, Zasha
Published in Nucleic acids research (08.01.2021)
Published in Nucleic acids research (08.01.2021)
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Journal Article
RNAcentral: a hub of information for non-coding RNA sequences
Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley J F, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, Williams, Kelly P
Published in Nucleic acids research (08.01.2019)
Published in Nucleic acids research (08.01.2019)
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Journal Article
RNAcentral: a hub of information for non-coding RNA sequences
Sweeney, Blake A, Petrov, Anton I, Burkov, Boris, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Gorodkin, Jan, Seemann, Stefan E, Cannone, Jamie J, Gutell, Robin R, Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J, Huntley, Rachael P, Lovering, Ruth C, Frankish, Adam, Chan, Patricia P, Lowe, Todd M, Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M, Boccaletto, Pietro, Blake, Judith A, Bult, Carol J, Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley J F, Shimoyama, Mary, Gillespie, Marc E, Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R, Cherry, J Michael, Team, SILVA, Berardini, Tanya Z, Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F, Williams, Kelly P
Published in Nucleic acids research (08.01.2019)
Published in Nucleic acids research (08.01.2019)
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Journal Article
RNAcentral: a hub of information for non-coding RNA sequences
Sweeney, Blake A., Petrov, Anton I., Burkov, Boris, Finn, Robert D., Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M., Gorodkin, Jan, Seemann, Stefan E., Cannone, Jamie J., Gutell, Robin R., Fey, Petra, Basu, Siddhartha, Kay, Simon, Cochrane, Guy, Billis, Kostantinos, Emmert, David, Marygold, Steven J., Huntley, Rachael P., Lovering, Ruth C., Frankish, Adam, Chan, Patricia P., Lowe, Todd M., Bruford, Elspeth, Seal, Ruth, Vandesompele, Jo, Volders, Pieter-Jan, Paraskevopoulou, Maria, Ma, Lina, Zhang, Zhang, Griffiths-Jones, Sam, Bujnicki, Janusz M., Boccaletto, Pietro, Blake, Judith A., Bult, Carol J., Chen, Runsheng, Zhao, Yi, Wood, Valerie, Rutherford, Kim, Rivas, Elena, Cole, James, Laulederkind, Stanley J. F., Shimoyama, Mary, Gillespie, Marc E., Orlic-Milacic, Marija, Kalvari, Ioanna, Nawrocki, Eric, Engel, Stacia R., Cherry, J. Michael, Team, SILVA, Berardini, Tanya Z., Hatzigeorgiou, Artemis, Karagkouni, Dimitra, Howe, Kevin, Davis, Paul, Dinger, Marcel, He, Shunmin, Yoshihama, Maki, Kenmochi, Naoya, Stadler, Peter F., Williams, Kelly P.
Published in Nucleic acids research (08.12.2018)
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Published in Nucleic acids research (08.12.2018)
Journal Article
R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types
Sweeney, Blake A, Hoksza, David, Nawrocki, Eric P, Ribas, Carlos Eduardo, Madeira, Fábio, Cannone, Jamie J, Gutell, Robin, Maddala, Aparna, Meade, Caeden, Williams, Loren Dean, Petrov, Anton S, Chan, Patricia P, Lowe, Todd M, Finn, Robert D, Petrov, Anton I
Published in bioRxiv (11.09.2020)
Published in bioRxiv (11.09.2020)
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Paper
Analyzing, searching, and annotating recurrent RNA three-dimensional motifs
Published in RNA Structure and Folding
(2013)
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Book Chapter