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Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and translation.
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R. W. Hamming · 1950
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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
M Zuker and P. Stiegler · 1981
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RNA secondary structures and their prediction
Michael Zuker and David Sankoff · 1984
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An algorithm for comparing multiple rna secondary structures
Bruce A Shapiro · 1988
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Fast Folding and Comparison of RNA Secondary Structures
Ivo Hofacker, Walter Fontana, Peter Stadler, Sebastian Bonhoeffer, Manfred Tacker, and Peter Schuster · 1994
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A New Algorithm for RNA Secondary Structure Design
Mirela Andronescu, Anthony P. Fejes, Frank Hutter, Holger H. Hoos, and Anne Condon · 2003
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An Algorithm for Computing Nucleic Acid Base-Pairing Probabilities Including Pseudoknots
Robert M. Dirks and Niles A. Pierce · 2004
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The ENCODE (encyclopedia of DNA elements) project
ENCODE Project Consortium and others · 2004
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INFO-RNA—a fast approach to inverse RNA folding
Anke Busch and Rolf Backofen · 2006
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Generalized functional ANOVA diagnostics for high-dimensional functions of dependent variables
Giles Hooker · 2007
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Engineering RNA for Targeted siRNA Delivery and Medical Application
Peixuan Guo, Oana Coban, Nicholas M. Snead, Joe Trebley, Steve Hoeprich, Songchuan Guo, and Yi Shu · 2010
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Nupack: Analysis and design of nucleic acid systems
Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, and Niles A. Pierce · 2010
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Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Camille J. Delebecque, Ariel B. Lindner, Pamela A. Silver, and Faisal A. Aldaye · 2011
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MODENA: a multi-objective RNA inverse folding
Akito Taneda · 2011
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Designing and using RNA scaffolds to assemble proteins in vivo
CJ Delebecque, PA Silver, and AB Lindner · 2012
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Towards 3d structure prediction of large rna molecules: an integer programming framework to insert local 3d motifs in rna secondary structure
Vladimir Reinharz, François Major, and Jérôme Waldispühl · 2012
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Automated and fast building of three-dimensional RNA structures
Y Zhao, Y Huang, Z Gong, Y Wang, J Man, and Y Xiao · 2012
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De novo design of a synthetic riboswitch that regulates transcription termination
Manja Wachsmuth, Sven Findeiß, Nadine Weissheimer, Peter F. Stadler, and Mario Mörl · 2013
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Complete RNA inverse folding: computational design of functional hammerhead ribozymes
Ivan Dotu, Juan Antonio Garcia-Martin, Betty L. Slinger, Vinodh Mechery, Michelle M. Meyer, and Peter Clote · 2014
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Evolutionary solution for the RNA design problem
Ali Esmaili-Taheri, Mohammad Ganjtabesh, and Morteza Mohammad-Noori · 2014
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Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases
Ronald Gstir, Simon Schafferer, Marcel Scheideler, Matthias Misslinger, Matthias Griehl, Nina Daschil, Christian Humpel, Gerald J. Obermair, Claudia Schmuckermair, Joerg Striessnig, Bernhard E. Flucher, and Alexander Hüttenhofer · 2014
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An efficient approach for assessing hyperparameter importance
F. Hutter, H. Hoos, and K. Leyton-Brown · 2014
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TensorFlow: Large-scale machine learning on heterogeneous systems, 2015
Martín Abadi, Ashish Agarwal, Paul Barham, Eugene Brevdo, Zhifeng Chen, Craig Citro, Greg S. Corrado, Andy Davis, Jeffrey Dean, Matthieu Devin, Sanjay Ghemawat, Ian Goodfellow, Andrew Harp, Geoffrey Irving, Michael Isard, Yangqing Jia, Rafal Jozefowicz, Lukasz Kaiser, Manjunath Kudlur, Josh Levenberg, Dandelion Mané, Rajat Monga, Sherry Moore, Derek Murray, Chris Olah, Mike Schuster, Jonathon Shlens, Benoit Steiner, Ilya Sutskever, Kunal Talwar, Paul Tucker, Vincent Vanhoucke, Vijay Vasudevan, Fernanda Viégas, Oriol Vinyals, Pete Warden, Martin Wattenberg, Martin Wicke, Yuan Yu, and Xiaoqiang Zheng · 2015
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RNA inverse folding using Monte Carlo tree search
Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, and Koji Tsuda · 2017
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Neural architecture search with reinforcement learning
B. Zoph and Q. V. Le · 2017
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Emergent complexity via multi-agent competition
Trapit Bansal, Jakub Pachocki, Szymon Sidor, Ilya Sutskever, and Igor Mordatch · 2018
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Deepcrispr: optimized crispr guide rna design by deep learning
Guohui Chuai, Hanhui Ma, Jifang Yan, Ming Chen, Nanfang Hong, Dongyu Xue, Chi Zhou, Chenyu Zhu, Ke Chen, Bin Duan, Feng Gu, Sheng Qu, Deshuang Huang, Jia Wei, and Qi Liu · 2018
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Solving the RNA design problem with reinforcement learning
Peter Eastman, Jade Shi, Bharath Ramsundar, and Vijay S Pande · 2018
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Neural Architecture Search: A Survey
Thomas Elsken, Jan Hendrik Metzen, and Frank Hutter · 2018
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Predicting RNA 3D structure using a coarse-grain helix-centered model
P Kerpedjiev, C Höner zu Siederdissen, and IL Hofacker · 2015
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antaRNA–Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization
Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, and Martin Mann · 2015
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Metalearning: a survey of trends and technologies
Christiane Lemke, Marcin Budka, and Bogdan Gabrys · 2015
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Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies
Sarai Meyer, James Chappell, Sitara Sankar, Rebecca Chew, and Julius B. Lucks · 2015
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Principles for predicting RNA secondary structure design difficulty
Jeff Anderson-Lee, Eli Fisker, Vineet Kosaraju, Michelle Wu, Justin Kong, Jeehyung Lee, Minjae Lee, Mathew Zada, Adrien Treuille, and Rhiju Das · 2016
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Neural combinatorial optimization with reinforcement learning
Irwan Bello, Hieu Pham, Quoc V Le, Mohammad Norouzi, and Samy Bengio · 2016
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Towards automatically-tuned neural networks
H. Mendoza, A. Klein, M. Feurer, J. Springenberg, and F. Hutter · 2016
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The conservation and function of RNA secondary structure in plants
Lee E. Vandivier, Stephen J. Anderson, Shawn W. Foley, and Brian D. Gregory · 2016
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BOHB: Robust and efficient hyperparameter optimization at scale
Stefan Falkner, Aaron Klein, and Frank Hutter · 2018
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Hyperparameter optimization
Matthias Feurer and Frank Hutter · 2018
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Design of metalloproteins and novel protein folds using variational autoencoders
Joe G Greener, Lewis Moffat, and David T Jones · 2018
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Feedback gan (fbgan) for dna: a novel feedback-loop architecture for optimizing protein functions
Anvita Gupta and James Zou · 2018
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RNA secondary structure profiling in zebrafish reveals unique regulatory features
Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavprithesh Sethi, Souvik Maiti, Vinod Scaria, and Sridhar Sivasubbu · 2018
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Automatically designing cnn architectures for medical image segmentation
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Sentrna: Improving computational rna design by incorporating a prior of human design strategies
Jade Shi, Rhiju Das, and Vijay S Pande · 2018
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Transfer learning with neural automl
Catherine Wong, Neil Houlsby, Yifeng Lu, and Andrea Gesmundo · 2018
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Towards automated deep learning: Efficient joint neural architecture and hyperparameter search
Arber Zela, Aaron Klein, Stefan Falkner, and Frank Hutter · 2018
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Learning transferable architectures for scalable image recognition
B. Zoph, V. Vasudevan, J. Shlens, and Q. V. Le · 2018
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Automated Machine Learning: Methods, Systems, Challenges
Frank Hutter, Lars Kotthoff, and Joaquin Vanschoren (eds.) · 2019
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Rna folding and combinatory landscapes
Walter Fontana, Peter F. Stadler, Erich G. Bornberg-Bauer, Thomas Griesmacher, Ivo L. Hofacker, Manfred Tacker, Pedro Tarazona, Edward D. Weinberger, and Peter Schuster · 2083
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