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RIsearch2 : suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets
Authors: Alkan, F.; Wenzel, A.; Palasca, O.; Kerpedjiev, P.; Rudebeck, A. F.; Stadler, P. F.; Hofacker, I. L.; Gorodkin, J.
Date of Publication (YYYY-MM-DD): 2017
Title of Journal: Nucleic Acids Research
Volume: 45
Issue / Number: 8
Sequence Number of Article: e60
Document Type: Article
ID: 741400.0
Pseudoknots in RNA folding landscapes
Authors: Kucharik, M.; Hofacker, I. L.; Stadler, P. F.; Qin, J.
Date of Publication (YYYY-MM-DD): 2016
Title of Journal: Bioinformatics
Volume: 32
Issue / Number: 2
Start Page: 187
End Page: 194
Document Type: Article
ID: 729131.0
RNA folding with hard and soft constraints
Authors: Lorenz, R.; Hofacker, I. L.; Stadler, P. F.
Date of Publication (YYYY-MM-DD): 2016
Title of Journal: Algorithms for Molecular Biology
Volume: 11
Sequence Number of Article: 8
Document Type: Article
ID: 729088.0
Optimizing RNA structures by sequence extensions using RNAcop
Authors: Hecker, N.; Christensen-Dalsgaard, M.; Seemann, S. E.; Havgaard, J. H.; Stadler, P. F.; Hofacker, I. L.; Nielsen, H.; Gorodkin, J.
Date of Publication (YYYY-MM-DD): 2015
Title of Journal: Nucleic Acids Research
Volume: 43
Issue / Number: 17
Start Page: 8135
End Page: 8145
Document Type: Article
ID: 718490.0
Processed small RNAs in Archaea and BHB elements
Authors: Berkemer, S.; Siederdissen, C. H.; Amman, F.; Wintsche, A.; Will, S.; Hofacker, I. L.; Prohaska, S. J.; Stadler, P. F.
Date of Publication (YYYY-MM-DD): 2015
Title of Journal: Genomics and Computational Biology
Volume: 1
Issue / Number: 1
Sequence Number of Article: e18
Document Type: Article
ID: 718482.0
Product grammars for alignment and folding
Authors: Siederdissen, C. H.; Hofacker, I. L.; Stadler, P. F.
Date of Publication (YYYY-MM-DD): 2015
Title of Journal: IEEE ACM Transactions on Computational Biology and Bioinformatics
Volume: 12
Issue / Number: 3
Start Page: 507
End Page: 519
Document Type: Article
ID: 718530.0
Basin hopping graph : a computational framework to characterize RNA folding landscapes
Authors: Kucharik, M.; Hofacker, I. L.; Stadler, P. F.; Qin, J.
Date of Publication (YYYY-MM-DD): 2014
Title of Journal: Bioinformatics
Volume: 30
Issue / Number: 14
Start Page: 2009
End Page: 2017
Document Type: Article
ID: 708479.0
Challenges in RNA virus bioinformatics
Authors: Marz, M.; Beerenwinkel, N.; Drosten, C.; Fricke, M.; Frishman, D.; Hofacker, I. L.; Hoffmann, D.; Middendorf, M.; Rattei, T.; Stadler, P. F.; Toepfer, A.
Date of Publication (YYYY-MM-DD): 2014
Title of Journal: Bioinformatics
Volume: 30
Issue / Number: 13
Start Page: 1793
End Page: 1799
Document Type: Article
ID: 708487.0
TSSAR : TSS annotation regime for dRNA-seq data
Authors: Amman, F.; Wolfinger, M. T.; Lorenz, R.; Hofacker, I. L.; Stadler, P. F.; Findeiss, S.
Date of Publication (YYYY-MM-DD): 2014
Title of Journal: BMC Bioinformatics
Volume: 15
Sequence Number of Article: 89
Document Type: Article
ID: 708511.0
2D meets 4G : G-Quadruplexes in RNA secondary structure prediction
Authors: Lorenz, R.; Bernhart, S. H.; Qin, J.; Siederdissen, C. H.; Amman, F.; Tanzer, A.; Amman, F.; Hofacker, I. L.; Stadler, P. F.
Date of Publication (YYYY-MM-DD): 2013
Title of Journal: IEEE ACM Transactions on Computational Biology and Bioinformatics
Volume: 10
Issue / Number: 4
Start Page: 832
End Page: 844
Document Type: Article
ID: 688166.0
Entries: 1-10  
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