When Does Additional Information Improve Accuracy of RNA Secondary Structure Prediction?

David Murrugarra

Logan Rose Luis Sanchez Giraldo Duc Nguyen Matthew Wheeler David Murrugarra When Does Additional Information Improve Accuracy of RNA Secondary Structure Prediction? 10701-10712 2025 65 J. Chem. Inf. Model. 19 https://doi.org/10.1021/acs.jcim.5c01231 db/journals/jcisd/jcisd65.html#RoseGNWM25 streams/journals/jcisd

Elena S. Dimitrova Brandilyn Stigler Claus Kadelka David Murrugarra Revealing the canalizing structure of Boolean functions: Algorithms and applications. 110630 2022 146 Autom. https://doi.org/10.1016/j.automatica.2022.110630 db/journals/automatica/automatica146.html#DimitrovaSKM22

David Murrugarra Alan Veliz-Cuba An information theoretic approach for the inference of Boolean networks and functions from data: BoCSE. 100617 2022 3 Patterns 11 https://doi.org/10.1016/j.patter.2022.100617 db/journals/patterns/patterns3.html#MurrugarraV22

Karthik Chandrasekhar Claus Kadelka Reinhard C. Laubenbacher David Murrugarra Stability of Linear Boolean Networks. 2022 abs/2209.02044 CoRR https://doi.org/10.48550/arXiv.2209.02044 db/journals/corr/corr2209.html#abs-2209-02044

David Murrugarra Elena S. Dimitrova Quantifying the total effect of edge interventions in discrete multistate networks. 109453 2021 125 Autom. https://doi.org/10.1016/j.automatica.2020.109453 db/journals/automatica/automatica125.html#MurrugarraD21

David J. Wooten Jorge Gómez Tejeda Zañudo David Murrugarra Austin M. Perry Anna Dongari-Bagtzoglou Reinhard C. Laubenbacher Clarissa J. Nobile Réka Albert Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies. 2021 17 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1008690 https://www.wikidata.org/entity/Q113746490 db/journals/ploscb/ploscb17.html#WootenZMPDLNA21

Elena S. Dimitrova Brandilyn Stigler Claus Kadelka David Murrugarra Revealing the canalizing structure of Boolean functions: Algorithms and applications. 2021 abs/2106.06580 CoRR https://arxiv.org/abs/2106.06580 db/journals/corr/corr2106.html#abs-2106-06580

David Murrugarra Alan Veliz-Cuba Boris Aguilar Reinhard C. Laubenbacher Identification of control targets in Boolean molecular network models via computational algebra. 94 2016 10 BMC Syst. Biol. https://doi.org/10.1186/s12918-016-0332-x https://www.wikidata.org/entity/Q36143299 db/journals/bmcsb/bmcsb10.html#MurrugarraVAL16

David Murrugarra Elena S. Dimitrova Molecular network control through boolean canalization. 9 2015 2015 EURASIP J. Bioinform. Syst. Biol. https://doi.org/10.1186/s13637-015-0029-2 https://www.wikidata.org/entity/Q41290862 db/journals/ejbsb/ejbsb2015.html#MurrugarraD15

Alan Veliz-Cuba David Murrugarra Reinhard C. Laubenbacher Structure and dynamics of acyclic networks. 647-658 2014 24 Discret. Event Dyn. Syst. 4 https://doi.org/10.1007/s10626-013-0174-2 db/journals/deds/deds24.html#Veliz-CubaML14

Reinhard C. Laubenbacher Franziska Hinkelmann David Murrugarra Alan Veliz-Cuba Algebraic Models and Their Use in Systems Biology. 443-474 2014 Discrete and Topological Models in Molecular Biology https://doi.org/10.1007/978-3-642-40193-0_21 series/ncs/2014JS db/series/ncs/JS2014.html#LaubenbacherHMV14

Yuan Li John O. Adeyeye David Murrugarra Boris Aguilar Reinhard C. Laubenbacher Boolean nested canalizing functions: A comprehensive analysis. 24-36 2013 481 Theor. Comput. Sci. https://doi.org/10.1016/j.tcs.2013.02.020 db/journals/tcs/tcs481.html#LiAMAL13

David Murrugarra Alan Veliz-Cuba Boris Aguilar Seda Arat Reinhard C. Laubenbacher Modeling stochasticity and variability in gene regulatory networks. 5 2012 2012 EURASIP J. Bioinform. Syst. Biol. https://doi.org/10.1186/1687-4153-2012-5 https://www.wikidata.org/entity/Q42126515 db/journals/ejbsb/ejbsb2012.html#MurrugarraVAAL12

Chris J. Kuhlman Henning S. Mortveit David Murrugarra V. S. Anil Kumar 0001 Bifurcations in Boolean Networks. 29-46 2011 Automata http://dmtcs.episciences.org/2975 conf/automata/2011 db/conf/automata/automata2011.html#KuhlmanMMK11

Franziska Hinkelmann David Murrugarra Abdul Salam Jarrah Reinhard C. Laubenbacher A Mathematical Framework for Agent Based Models of Complex Biological Networks http://arxiv.org/abs/1006.0408 2010 CoRR abs/1006.0408 db/journals/corr/corr1006.html#abs-1006-0408

John O. Adeyeye Boris Aguilar Réka Albert Seda Arat Karthik Chandrasekhar Elena S. Dimitrova Anna Dongari-Bagtzoglou Luis Sanchez Giraldo Franziska Hinkelmann Abdul Salam Jarrah Claus Kadelka Chris J. Kuhlman Reinhard C. Laubenbacher Yuan Li Henning S. Mortveit Duc Nguyen Clarissa J. Nobile Austin M. Perry Logan Rose Brandilyn Stigler Alan Veliz-Cuba Anil VullikantiV. S. Anil Kumar 0001 Matthew Wheeler David J. Wooten Jorge G. T. ZañudoJorge Gómez Tejeda Zañudo