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Entries: 1-8  
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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
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
RNAsnp : efficient detection of local RNA secondary structure changes induced by SNPs
Authors: Sabarinathan, R.; Tafer, H.; Seemann, S. E.; Hofacker, I. L.; Stadler, P. F.; Gorodkin, J.
Date of Publication (YYYY-MM-DD): 2013
Title of Journal: Human Mutation
Volume: 34
Issue / Number: 4
Start Page: 546
End Page: 556
Document Type: Article
ID: 688082.0
The RNAsnp web server : predicting SNP effects on local RNA secondary structure
Authors: Sabarinathan, R.; Tafer, H.; Seemann, S. E.; Hofacker, I. L.; Stadler, P. F.; Gorodkin, J.
Date of Publication (YYYY-MM-DD): 2013
Title of Journal: Nucleic Acids Research
Volume: 41
Issue / Number: W1
Start Page: W475
End Page: W479
Document Type: Article
ID: 688224.0
Analyses of pig genomes provide insight into porcine demography and evolution
Authors: Groenen, M. A. M.; Archibald, A. L.; Uenishi, H.; Tuggle, C. K.; Takeuchi, Y.; Rothschild, M. F.; Rogel-Gaillard, C.; Park, C.; Milan, D.; Megens, H.-J.; Li, S.; Larkin, D. M.; Kim, H.; Frantz, L. A. F.; Caccamo, M.; Ahn, H.; Aken, B. L.; Anselmo, A.; Anthon, C.; Auvil, L.; Badaoui, B.; Beattie, C. W.; Bendixen, C.; Berman, D.; Blecha, F.; Blomberg, J.; Bolund, L.; Bosse, M.; Botti, S.; Zhan, B.; Bystrom, M.; Capitanu, B.; Carvalho-Silva, D.; Chardon, P.; Chen, C.; Cheng, R.; Choi, S.-H.; Chow, W.; Clark, R. C.; Clee, C.; Crooijmans, R. P. M. A.; Dawson, H. D.; Dehais, P.; De, S. F.; Dibbits, B.; Drou, N.; Du, Z.-Q.; Eversole, K.; Fadista, J.; Fairley, S.; Faraut, T.; Faulkner, G. J.; Fowler, K. E.; Fredholm, M.; Fritz, E.; Gilbert, J. G. R.; Giuffra, E.; Gorodkin, J.; Griffin, D. K.; Harrow, J. L.; Hayward, A.; Howe, K.; Hu, Z.-L.; Humphray, S. J.; Hunt, T.; Hornshoj, H.; Jeon, J.-T.; Jern, P.; Jones, M.; Jurka, J.; Kanamori, H.; Kapetanovic, R.; Kim, J.; Kim, J.-H.; Kim, K.-W.; Kim, T.-H.; Larson, G.; Lee, K.; Lee, K.-T.; Leggett, R.; Lewin, H. A.; Li, Y.; Liu, W.; Loveland, J. E.; Lu, Y.; Lunney, J. K.; Ma, J.; Madsen, O.; Mann, K.; Matthews, L.; McLaren, S.; Morozumi, T.; Murtaugh, M. P.; Narayan, J.; Dinh, T. N.; Ni, P.; Oh, S.-J.; Onteru, S.; Panitz, F.; Park, E.-W.; Park, H.-S.; Pascal, G.; Paudel, Y.; Perez-Enciso, M.; Ramirez-Gonzalez, R.; Reecy, J. M.; Rodriguez-Zas, S.; Rohrer, G. A.; Rund, L.; Sang, Y.; Schachtschneider, K.; Schraiber, J. G.; Schwartz, J.; Scobie, L.; Scott, C.; Searle, S.; Servin, B.; Southey, B. R.; Sperber, G.; Stadler, P. F.; Sweedler, J. V.; Tafer, H.; Thomsen, B.; Wali, R.; Wang, J.; Wang, J.; White, S.; Xu, X.; Yerle, M.; Zhang, G.; Zhang, J.; Zhang, J.; Zhao, S.; Rogers, J.; Churcher, C.; Schook, L. B.
Date of Publication (YYYY-MM-DD): 2012
Title of Journal: Nature
Volume: 491
Issue / Number: 7424
Start Page: 393
End Page: 398
Document Type: Article
ID: 645687.0
deepBlockAlign : a tool for aligning RNA-seq profiles of read block patterns
Authors: Langenberger, D.; Pundhir, S.; Ekstroem, C. T.; Stadler, P. F.; Hoffmann, S.; Gorodkin, J.
Date of Publication (YYYY-MM-DD): 2012
Title of Journal: Bioinformatics
Volume: 28
Issue / Number: 1
Start Page: 17
End Page: 24
Document Type: Article
ID: 645619.0
Fast local fragment chaining using sum-of-pair gap costs
Authors: Otto, C.; Hoffmann, S.; Gorodkin, J.; Stadler, P. F.
Date of Publication (YYYY-MM-DD): 2011
Title of Journal: Algorithms for Molecular Biology
Volume: 6
Issue / Number: 1
Sequence Number of Article: 4
Document Type: Article
ID: 587693.0
maxAlike : maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Authors: Menzel, P.; Stadler, P. F.; Gorodkin, J.
Date of Publication (YYYY-MM-DD): 2011
Title of Journal: Bioinformatics
Volume: 27
Issue / Number: 3
Start Page: 317
End Page: 325
Document Type: Article
ID: 587683.0
Entries: 1-8  
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