TY - CHAP AU - Zuker, M. AU - Mathews, D. H. AU - Turner, D. H. PY - 1999 DA - 1999// TI - Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide BT - RNA Biochemistry and Biotechnology PB - Springer CY - Dordrecht ID - Zuker1999 ER - TY - JOUR AU - McCaskill, J. S. PY - 1990 DA - 1990// TI - The equilibrium partition function and base pair binding probabilities for RNA secondary structure JO - Biopolymers VL - 29 UR - https://doi.org/10.1002/bip.360290621 DO - 10.1002/bip.360290621 ID - McCaskill1990 ER - TY - JOUR AU - Ding, Y. AU - Chan, C. Y. AU - Lawrence, C. E. PY - 2005 DA - 2005// TI - RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble JO - RNA VL - 11 UR - https://doi.org/10.1261/rna.2500605 DO - 10.1261/rna.2500605 ID - Ding2005 ER - TY - JOUR AU - Hofacker, I. L. AU - Fontana, W. AU - Stadler, P. F. AU - Bonhoeffer, L. S. AU - Tacker, M. AU - Schuster, P. PY - 1994 DA - 1994// TI - Fast folding and comparison of RNA secondary structures JO - Monatsh Chem VL - 125 UR - https://doi.org/10.1007/BF00818163 DO - 10.1007/BF00818163 ID - Hofacker1994 ER - TY - JOUR AU - Hamada, M. AU - Kiryu, H. AU - Sato, K. AU - Mituyama, T. AU - Asai, K. PY - 2009 DA - 2009// TI - Prediction of RNA secondary structure using generalized centroid estimators JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn601 DO - 10.1093/bioinformatics/btn601 ID - Hamada2009 ER - TY - JOUR AU - Taneda, A. PY - 2011 DA - 2011// TI - MODENA: a multi-objective RNA inverse folding JO - Adv Appl Bioinform Chem VL - 4 ID - Taneda2011 ER - TY - JOUR AU - Kleinkauf, R. AU - Mann, M. AU - Backofen, R. PY - 2015 DA - 2015// TI - antaRNA: ant colony-based RNA sequence design JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv319 DO - 10.1093/bioinformatics/btv319 ID - Kleinkauf2015 ER - TY - JOUR AU - Dotu, I. AU - Garcia-Martin, J. A. AU - Slinger, B. L. AU - Mechery, V. AU - Meyer, M. M. AU - Clote, P. PY - 2014 DA - 2014// TI - Complete RNA inverse folding: computational design of functional hammerhead ribozymes JO - Nucl Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku740 DO - 10.1093/nar/gku740 ID - Dotu2014 ER - TY - JOUR AU - Wachsmuth, M. AU - Findeiß, S. AU - Weissheimer, N. AU - Stadler, P. F. AU - Mörl, M. PY - 2013 DA - 2013// TI - De novo design of a synthetic riboswitch that regulates transcription termination JO - Nucl Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1330 DO - 10.1093/nar/gks1330 ID - Wachsmuth2013 ER - TY - JOUR AU - Wang, T. AU - Wei, J. J. AU - Sabatini, D. M. AU - Lander, E. S. PY - 2014 DA - 2014// TI - Genetic screens in human cells using the CRISPR-Cas9 system JO - Science VL - 343 UR - https://doi.org/10.1126/science.1246981 DO - 10.1126/science.1246981 ID - Wang2014 ER - TY - JOUR AU - Hofacker, I. L. PY - 2003 DA - 2003// TI - Vienna RNA secondary structure server JO - Nucl Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg599 DO - 10.1093/nar/gkg599 ID - Hofacker2003 ER - TY - JOUR AU - Andronescu, M. AU - Fejes, A. P. AU - Hutter, F. AU - Hoos, H. H. AU - Condon, A. PY - 2004 DA - 2004// TI - A new algorithm for RNA secondary structure design JO - J Mol Biol VL - 336 UR - https://doi.org/10.1016/j.jmb.2003.12.041 DO - 10.1016/j.jmb.2003.12.041 ID - Andronescu2004 ER - TY - JOUR AU - Busch, A. AU - Backofen, R. PY - 2006 DA - 2006// TI - INFO-RNA: a fast approach to inverse RNA folding JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl194 DO - 10.1093/bioinformatics/btl194 ID - Busch2006 ER - TY - JOUR AU - Zadeh, J. N. AU - Steenberg, C. D. AU - Bois, J. S. AU - Wolfe, B. R. AU - Pierce, M. B. AU - Khan, A. R. AU - Dirks, R. M. AU - Pierce, N. A. PY - 2011 DA - 2011// TI - NUPACK: analysis and design of nucleic acid systems JO - J Comput Chem VL - 32 UR - https://doi.org/10.1002/jcc.21596 DO - 10.1002/jcc.21596 ID - Zadeh2011 ER - TY - JOUR AU - Lyngsø, R. B. AU - Anderson, J. W. AU - Sizikova, E. AU - Badugu, A. AU - Hyland, T. AU - Hein, J. PY - 2012 DA - 2012// TI - Frnakenstein: multiple target inverse RNA folding JO - BMC Bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-260 DO - 10.1186/1471-2105-13-260 ID - Lyngsø2012 ER - TY - JOUR AU - Esmaili-Taheri, A. AU - Ganjtabesh, M. AU - Mohammad-Noori, M. PY - 2014 DA - 2014// TI - Evolutionary solution for the RNA design problem JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu001 DO - 10.1093/bioinformatics/btu001 ID - Esmaili-Taheri2014 ER - TY - JOUR AU - Taneda, A. PY - 2015 DA - 2015// TI - Multi-objective optimization for RNA design with multiple target secondary structures JO - BMC Bioinformatics VL - 16 UR - https://doi.org/10.1186/s12859-015-0706-x DO - 10.1186/s12859-015-0706-x ID - Taneda2015 ER - TY - JOUR AU - Reinharz, V. AU - Ponty, Y. AU - Waldispühl, J. PY - 2013 DA - 2013// TI - A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt217 DO - 10.1093/bioinformatics/btt217 ID - Reinharz2013 ER - TY - JOUR AU - Garcia-Martin, J. A. AU - Clote, P. AU - Dotu, I. PY - 2013 DA - 2013// TI - RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design JO - J Bioinform Comput Biol VL - 11 UR - https://doi.org/10.1142/S0219720013500017 DO - 10.1142/S0219720013500017 ID - Garcia-Martin2013 ER - TY - JOUR AU - Janssen, S. AU - Giegerich, R. PY - 2015 DA - 2015// TI - The RNA shapes studio JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu649 DO - 10.1093/bioinformatics/btu649 ID - Janssen2015 ER - TY - JOUR AU - Sato, K. AU - Kato, Y. AU - Hamada, M. AU - Akutsu, T. AU - Asai, K. PY - 2011 DA - 2011// TI - IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr215 DO - 10.1093/bioinformatics/btr215 ID - Sato2011 ER - TY - JOUR AU - Ren, J. AU - Rastegari, B. AU - Condon, A. AU - Hoos, H. H. PY - 2005 DA - 2005// TI - HotKnots: heuristic prediction of RNA secondary structures including pseudoknots JO - RNA VL - 11 UR - https://doi.org/10.1261/rna.7284905 DO - 10.1261/rna.7284905 ID - Ren2005 ER - TY - JOUR AU - Browne, C. B. AU - Powley, E. AU - Whitehouse, D. AU - Lucas, S. M. AU - Cowling, P. I. AU - Rohlfshagen, P. AU - Tavener, S. AU - Perez, D. AU - Samothrakis, S. AU - Colton, S. PY - 2012 DA - 2012// TI - A survey of monte carlo tree search methods JO - IEEE Trans Comput Intell AI Game VL - 4 UR - https://doi.org/10.1109/TCIAIG.2012.2186810 DO - 10.1109/TCIAIG.2012.2186810 ID - Browne2012 ER - TY - JOUR AU - Silver, D. AU - Huang, A. AU - Maddison, C. J. AU - Guez, A. AU - Sifre, L. AU - van den Driessche, G. AU - Schrittwieser, J. AU - Antonoglou, I. AU - Panneershelvam, V. AU - Lanctot, M. PY - 2016 DA - 2016// TI - Mastering the game of go with deep neural networks and tree search JO - Nature VL - 529 UR - https://doi.org/10.1038/nature16961 DO - 10.1038/nature16961 ID - Silver2016 ER - TY - CHAP AU - Edelkamp, S. AU - Tang, Z. PY - 2015 DA - 2015// TI - Monte-carlo tree search for the multiple sequence alignment problem BT - Eighth Annual Symposium on Combinatorial Search. PB - AAAI Press CY - Palo Alto ID - Edelkamp2015 ER - TY - CHAP AU - Tanabe, Y. AU - Yoshizoe, K. AU - Imai, H. PY - 2009 DA - 2009// TI - A study on security evaluation methodology for image-based biometrics authentication systems BT - Biometrics: Theory, Applications, and Systems, 2009. BTAS’09. IEEE 3rd International Conference On PB - IEEE CY - Washington ID - Tanabe2009 ER - TY - JOUR AU - Harcourt, E. M. AU - Kietrys, A. M. AU - Kool, E. T. PY - 2017 DA - 2017// TI - Chemical and structural effects of base modifications in messenger RNA JO - Nature VL - 541 UR - https://doi.org/10.1038/nature21351 DO - 10.1038/nature21351 ID - Harcourt2017 ER - TY - JOUR AU - Auer, P. AU - Cesa-Bianchi, N. AU - Fischer, P. PY - 2002 DA - 2002// TI - Finite-time analysis of the multiarmed bandit problem JO - Mach Learn VL - 47 UR - https://doi.org/10.1023/A:1013689704352 DO - 10.1023/A:1013689704352 ID - Auer2002 ER - TY - CHAP AU - Kocsis, L. AU - Szepesvári, C. PY - 2006 DA - 2006// TI - Bandit based monte-carlo planning BT - European Conference on Machine Learning PB - Springer CY - Berlin ID - Kocsis2006 ER - TY - JOUR AU - Kleinkauf, R. AU - Houwaart, T. AU - Backofen, R. AU - Mann, M. PY - 2015 DA - 2015// TI - antaRNA–multi-objective inverse folding of pseudoknot RNA using ant-colony optimization JO - BMC Bioinformatics VL - 16 UR - https://doi.org/10.1186/s12859-015-0815-6 DO - 10.1186/s12859-015-0815-6 ID - Kleinkauf2015 ER - TY - JOUR AU - Taufer, M. AU - Licon, A. AU - Araiza, R. AU - Mireles, D. AU - Van Batenburg, F. AU - Gultyaev, A. P. AU - Leung, M. Y. PY - 2009 DA - 2009// TI - Pseudobase++: an extension of pseudobase for easy searching, formatting and visualization of pseudoknots JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn806 DO - 10.1093/nar/gkn806 ID - Taufer2009 ER - TY - CHAP AU - Yoshizoe, K. AU - Kishimoto, A. AU - Kaneko, T. AU - Yoshimoto, H. AU - Ishikawa, Y. PY - 2011 DA - 2011// TI - Scalable distributed monte-carlo tree search BT - Fourth Annual Symposium on Combinatorial Search. PB - AAAI Press CY - Palo Alto ID - Yoshizoe2011 ER - TY - JOUR AU - Jindalertudomdee, J. AU - Hayashida, M. AU - Zhao, Y. AU - Akutsu, T. PY - 2016 DA - 2016// TI - Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order JO - BMC Bioinformatics VL - 17 UR - https://doi.org/10.1186/s12859-016-0962-4 DO - 10.1186/s12859-016-0962-4 ID - Jindalertudomdee2016 ER - TY - JOUR AU - Ikebata, H. AU - Yoshida, R. PY - 2015 DA - 2015// TI - Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv017 DO - 10.1093/bioinformatics/btv017 ID - Ikebata2015 ER - TY - JOUR AU - Avihoo, A. AU - Churkin, A. AU - Barash, D. PY - 2011 DA - 2011// TI - RNAexinv: an extended inverse RNA folding from shape and physical attributes to sequences JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-319 DO - 10.1186/1471-2105-12-319 ID - Avihoo2011 ER - TY - JOUR AU - Lee, J. AU - Kladwang, W. AU - Lee, M. AU - Cantu, D. AU - Azizyan, M. AU - Kim, H. AU - Limpaecher, A. AU - Gaikwad, S. AU - Yoon, S. AU - Treuille, A. PY - 2014 DA - 2014// TI - RNA design rules from a massive open laboratory JO - Proc Natl Acad Sci VL - 111 UR - https://doi.org/10.1073/pnas.1313039111 DO - 10.1073/pnas.1313039111 ID - Lee2014 ER - TY - JOUR AU - Zandi, K. AU - Butler, G. AU - Kharma, N. PY - 2016 DA - 2016// TI - An adaptive defect weighted sampling algorithm to design pseudoknotted RNA secondary structures JO - Front Genet VL - 7 UR - https://doi.org/10.3389/fgene.2016.00129 DO - 10.3389/fgene.2016.00129 ID - Zandi2016 ER -