RNA inverse folding using Monte Carlo tree search

[1]  E. Kool,et al.  Chemical and structural effects of base modifications in messenger RNA , 2017, Nature.

[2]  N. Kharma,et al.  An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures , 2016, Front. Genet..

[3]  Tatsuya Akutsu,et al.  Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order , 2016, BMC Bioinformatics.

[4]  Demis Hassabis,et al.  Mastering the game of Go with deep neural networks and tree search , 2016, Nature.

[5]  R. Backofen,et al.  antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization , 2015, BMC Bioinformatics.

[6]  A. Taneda.  Multi-objective optimization for RNA design with multiple target secondary structures , 2015, BMC Bioinformatics.

[7]  Rolf Backofen,et al.  antaRNA: ant colony-based RNA sequence design , 2015, Bioinform..

[8]  Stefan Edelkamp,et al.  Monte-Carlo Tree Search for the Multiple Sequence Alignment Problem , 2015, SOCS.

[9]  R. Rizzo,et al.  Probabilistic topic modeling for the analysis and classification of genomic sequences , 2015, BMC Bioinformatics.

[10]  Ryo Yoshida,et al.  Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets , 2015, Bioinform..

[11]  Robert Giegerich,et al.  The RNA shapes studio , 2014, Bioinform..

[12]  Peter Clote,et al.  Complete RNA inverse folding: computational design of functional hammerhead ribozymes , 2014, Nucleic acids research.

[13]  Mohammad Ganjtabesh,et al.  Evolutionary solution for the RNA design problem , 2014, Bioinform..

[14]  Minjae Lee,et al.  RNA design rules from a massive open laboratory , 2014, Proceedings of the National Academy of Sciences.

[15]  E. Lander,et al.  Genetic Screens in Human Cells Using the CRISPR-Cas9 System , 2013, Science.

[16]  Yann Ponty,et al.  A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution , 2013, Bioinform..

[17]  Peter Clote,et al.  Rnaifold: a Constraint Programming Algorithm for RNA inverse Folding and molecular Design , 2013, J. Bioinform. Comput. Biol..

[18]  P. Stadler,et al.  De novo design of a synthetic riboswitch that regulates transcription termination , 2012, Nucleic acids research.

[19]  James W. J. Anderson,et al.  Frnakenstein: multiple target inverse RNA folding , 2012, BMC Bioinformatics.

[20]  Simon M. Lucas,et al.  A Survey of Monte Carlo Tree Search Methods , 2012, IEEE Transactions on Computational Intelligence and AI in Games.

[21]  Alfredo Benso,et al.  POLITECNICO DI TORINO Repository ISTITUZIONALE Building Gene Expression Profile Classifiers with a Simple and Efficient Rejection Option in R / , 2022 .

[22]  D. Barash,et al.  RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences , 2011, BMC Bioinformatics.

[23]  Akihiro Kishimoto,et al.  Scalable Distributed Monte-Carlo Tree Search , 2011, SOCS.

[24]  Tatsuya Akutsu,et al.  IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming , 2011, Bioinform..

[25]  Michael A. Langston,et al.  The maximum clique enumeration problem: algorithms, applications, and implementations , 2011, BMC Bioinformatics.

[26]  Conrad Steenberg,et al.  NUPACK: Analysis and design of nucleic acid systems , 2011, J. Comput. Chem..

[27]  Akito Taneda,et al.  MODENA: a multi-objective RNA inverse folding , 2010, Advances and applications in bioinformatics and chemistry : AABC.

[28]  Hideki Imai,et al.  A study on security evaluation methodology for image-based biometrics authentication systems , 2009, 2009 IEEE 3rd International Conference on Biometrics: Theory, Applications, and Systems.

[29]  Kiyoshi Asai,et al.  Prediction of RNA secondary structure using generalized centroid estimators , 2009, Bioinform..

[30]  Michela Taufer,et al.  PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots , 2008, Nucleic Acids Res..

[31]  Csaba Szepesvári,et al.  Bandit Based Monte-Carlo Planning , 2006, ECML.

[32]  Rolf Backofen,et al.  INFO-RNA - a fast approach to inverse RNA folding , 2006, Bioinform..

[33]  H. Hoos,et al.  HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. , 2005, RNA.

[34]  C. Lawrence,et al.  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. , 2005, RNA.

[35]  Anne Condon,et al.  A new algorithm for RNA secondary structure design. , 2004, Journal of molecular biology.

[36]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[37]  Peter Auer,et al.  Finite-time Analysis of the Multiarmed Bandit Problem , 2002, Machine Learning.

[38]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[39]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[40]  Michael Zuker,et al.  Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .