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Publications of Sebastian Will

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Publications of Sebastian Will Publications of Sebastian Will (Joint) First and corresponding authors are highlighted. Journal Articles [1] Hosna Jabbari, Ian Wark, Carlo Montemagno, and Sebastian Will∗. Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. Bioinformatics, 34 no. 22 pp. 3849{3856, 2018. [2] Bj¨ornGr¨uning,Ryan Dale, Andreas Sjodin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, and Johannes Koster. Bioconda: sustainable and comprehen- sive software distribution for the life sciences. Nat Methods, 15 no. 7 pp. 475{476, 2018. [3] Martin Raden, Syed M. Ali, Omer S. Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A. Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C. Lott, Mostafa M. Mohamed, Alexander Mattheis, Milad Miladi, Andreas S. Richter, Sebastian Will, Joachim Wolff, Patrick R. Wright, and Rolf Back- ofen. Freiburg RNA tools: a central online resource for RNA-focused research and teaching. NAR, 46 no. W1 pp. W25{W29, 2018. [4] Felix K¨uhnl,Peter F. Stadler, and Sebastian Will∗. Tractable RNA{ligand interaction kinetics. BMC Bioinformatics, 18 no. Suppl 12 pp. 424, 2017. [5] Sven Findeiß, Maja Etzel, Sebastian Will, Mario M¨orl,and Peter F. Stadler. Design of Arti- ficial Riboswitches as Biosensors. Sensors, 17 no. 9 pp. 1990, 2017. [6] J¨orgFallmann, Sebastian Will, Jan Engelhardt, Bj¨ornGr¨uning, Rolf Backofen, and Peter F Stadler. Recent advances in RNA folding. Journal of Biotechnology, 2017. [7] Gesine Domin, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, and Mario M¨orl. Applicability of a computational design approach for synthetic riboswitches. Nucleic acids research, 45 no. 7 pp. 4108{4119, 2017. [8] Bj¨ornA Gr¨uning,J¨orgFallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, B´er´eniceBatut, Pavankumar Videm, Andrea Bagnacani, and others. The RNA workbench: best practices for RNA and high-throughput sequencing bioin- formatics in Galaxy. Nucleic Acids Research, 2017. [9] Francesco Righetti1, Aaron M. Nuss, Christian Twittenhoff, Sascha Beele, Kristina Urban, Sebastian Will, Stephan H. Bernhart, Peter F. Stadler, Petra Dersch, and Franz Narberhaus. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences, 113 no. 26 pp 7237{7242, 2016. [10] Sebastian Will1 and Hosna Jabbari. Sparse RNA folding revisited: space-efficient minimum free energy structure prediction. Algorithms Mol Biol, 11 no. 7 pp. 13, 2016. [11] Sebastian Will1, Christina Otto1, Milad Miladi1, Mathias M¨ohl,and Rolf Backofen∗. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 31 no. 15 pp. 2489{2496, 2015. 1 [12] Christina Otto1, Mathias M¨ohl,Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, and Sebastian Will∗. ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinformatics, 15 no. 1 pp. 404, 2014. [13] Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias M¨ohl,Christina Otto, and Sebastian Will. Local exact pattern matching for non-fixed RNA structures. IEEE/ACM Trans. Comput. Biology Bioinform., 11 no. 1 pp. 219{230, 2014. [14] J´er^omeWaldisp¨uhl1, Charles W. O'Donnell1, Sebastian Will1, Srinivas Devadas, Rolf Back- ofen, and Bonnie Berger∗. Simultaneous Alignment and Folding of Protein Sequences. J Comput Biol, 21 no. 7 pp. 477{491, 2014. [15] Sebastian Will1, Michael Yu1, and Bonnie Berger∗. Structure-based whole genome realignment reveals many novel non-coding RNAs. Genome Res, 23 no. 6 pp. 1018{1027, 2013. [16] Sita J. Lange1, Omer S. Alkhnbashi1, Dominic Rose1, Sebastian Will, and Rolf Backofen. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive im- mune systems. Nucleic Acids Res, 2013. [17] Sebastian Will1, Michael F. Siebauer1, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, and Rolf Backofen∗. LocARNAscan: Incorporating thermodynamic stabil- ity in sequence and structure-based RNA homology search. Algorithms Mol Biol, 8 no. 1 pp. 14, 2013. [18] Sebastian Will1, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen∗. LocARNA- P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18 no. 5 pp. 900{914, 2012. [19] Stefan Washietl1, Sebastian Will1, David A. Hendrix, Loyal A. Goff, John L. Rinn, Bonnie Berger∗, and Manolis Kellis∗. Computational analysis of noncoding RNAs. WIREs RNA, 3 no. 6 pp. 759{778, 2012. [20] Dragos A. Sorescu1, Mathias M¨ohl, Martin Mann, Rolf Backofen, and Sebastian Will∗. CARNA - alignment of RNA structure ensembles. Nucleic Acids Res, 40 no. W1 pp. W49-W53, 2012. [21] Fernando Meyer1, Stefan Kurtz, Rolf Backofen, Sebastian Will∗, and Michael Beckstette∗. Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinformat- ics, 12(1):214, 2011. [22] The modENCODE Consortium. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330(6012):1787{1797, [23] Mathias M¨ohl1, Raheleh Salari1, Sebastian Will1, Rolf Backofen∗, and S. Cenk Sahinalp∗. Sparsification of RNA structure prediction including pseudoknots. Algorithms for Molcular Biology, 5(1):39, 2010. [24] Cameron Smith1, Steffen Heyne1, Andreas S. Richter1, Sebastian Will1, and Rolf Backofen∗. Freiburg RNA tools: A web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acids Research, 38: W373{W377, 2010. [25] Mathias M¨ohl1, Sebastian Will1, and Rolf Backofen∗. Lifting prediction to alignment of RNA pseudoknots. Journal of Computational Biology, 17(3): 429{442, 2010. 2 [26] Steffen Heyne1, Sebastian Will, Michael Beckstette, and Rolf Backofen∗. Lightweight compar- ison of RNAs based on exact sequence-structure matches. Bioinformatics, 25(16):2095{2102, 2009. [27] Martin Mann1, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen∗. CPSP-web-tool : a server for 3D lattice protein studies. Bioinformatics, 25(5):676{677, 2009. [28] Sebastian Will1, Anke Busch, and Rolf Backofen∗. Efficient sequence alignment with side- constraints by cluster tree elimination. Constraints Journal, 13(1):110{129, 2008. [29] Stephan H. Bernhart1, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler∗. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9:474, 2008. [30] Martin Mann1, Sebastian Will, and Rolf Backofen∗. CPSP-tools - exact and complete algo- rithms for high-throughput 3D lattice protein studies. BMC Bioinformatics, 9:230, 2008. [31] Athanasius F. Bompf¨unewerer1, Rolf Backofen, Stephan H. Bernhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, and Sebastian Will. Variations on RNA folding and alignment: lessons from Benasque. Journal of Mathematical Biology, 56(1{2):129{144, 2008. [32] Sebastian Will1, Kristin Reiche1, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen∗. Infer- ring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology, 3(4):e65, 2007. [33] Athanasius F. Bompf¨unewerer Consortium, Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jorg Hackermuller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, and Sebastian Will. RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zoolog B Mol Dev Evol, 308(1):1{25, 2007. [34] Rolf Backofen and Sebastian Will. A constraint-based approach to fast and exact structure prediction in three-dimensional protein models. Journal of Constraints, 11(1):5{30, January 2006. [35] Michael T. Wolfinger1, Sebastian Will1, Ivo L. Hofacker, Rolf Backofen∗, and Peter F. Stadler. Exploring the lower part of discrete polymer model energy landscapes. Europhysics Letters, 74(4):725{732, 2006. [36] Anke Busch1, Sebastian Will, and Rolf Backofen∗. SECISDesign: a server to design SECIS- elements within the coding sequence. Bioinformatics, 21(15):3312{3, 2005. [37] Rolf Backofen and Sebastian Will. Local sequence-structure motifs in RNA. Journal of Bioin- formatics and Computational Biology (JBCB), 2(4):681{698, 2004. [38] Rolf Backofen and Sebastian Will. Excluding symmetries in constraint-based search. Con- straints, 7(3):333{349, 2002. [39] Rolf Backofen, Sebastian Will, and Erich Bornberg-Bauer∗. Application of constraint pro- gramming techniques for structure prediction of lattice proteins with extended alphabets. Bioinformatics, 15(3):234{242, 1999. 3 Refereed Conference Articles [40] Stefan Hammer, Yann Ponty, Wei Wang, and Sebastian Will∗. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. In Proc. of the 22th Annual In- ternational Conferences on Computational Molecular Biology (RECOMB'18), pages 2, 2018. [41] Hosna Jabbari, Ian Wark, Carlo Montemagno, and Sebastian Will∗. Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. In 17th In- ternational Workshop on Algorithms in Bioinformatics (WABI 2017), Leibniz International Proceedings in Informatics (LIPIcs), pages 12:1{12:13, Schloss Dagstuhl{Leibniz-Zentrum fuer Informatik, 2017. [42] Felix K¨uhnl,Peter F. Stadler, and Sebastian Will∗. Tractable Kinetics of RNA{Ligand Inter- action. In Bioinformatics Research and Applications (ISBRA 2016), LNBI, pages 2, Springer International Publishing, 2016. [43] Sebastian Will1 and Hosna Jabbari.
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