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A n^2 RNA Secondary Structure Prediction Algorithm
Markus E. Nebel and Anika Scheid, 3rd International Conference on Bioinformatics, Models, Methods and Algorithms (BIOINFORMATICS), 2012.
A Unified Approach to the Analysis of Horton-Strahler Parameters of Binary Tree Structures
Markus E. Nebel, Random Structures & Algorithms 21, 2002, 252-277. (preprint of the article published in Random Structures & Algorithms (c) Wiley 2002)
Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications
Markus E. Nebel and Frank Weinberg, Journal of Computational Biology (2012) 19(10): 1134-1150
Analysis of Branch Misses in Quicksort
Conrado Martínez, Markus E. Nebel and Sebastian Wild,
ACM-SIAM Meeting on Analytic Algorithmics and Combinatorics 2015 (ANALCO15)
Analysis of Pivot Sampling in Dual-Pivot Quicksort
Analysis of Pivot Sampling in Dual-Pivot Quicksort,
Markus E. Nebel, Sebastian Wild and Conrado Martínez,
submitted
Analysis of Quickselect under Yaroslavskiy's Dual-Pivoting Algorithm
Sebastian Wild, Markus E. Nebel, Hosam Mahmoud, submitted
Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model
Markus E. Nebel, and Anika Scheid, IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, vol. 8 no. 6, 1468-1482
Applying Length-Dependent Stochastic Context-Free Grammars to RNA Secondary Structure Prediction
Frank Weinberg and Markus E. Nebel, Algorithms Vol. 4, No. 4 (2011), 223-238
Average Case Analysis of Java 7's Dual Pivot Quicksort
Sebastian Wild and Markus E. Nebel, in L. Epstein and P. Ferragina (Eds.): ESA 2012, LNCS 7501, Springer, 2012, 825-836.
Average Case and Distributional Analysis of Dual-Pivot Quicksort
Sebastian Wild, Markus E. Nebel, Ralph Neininger, ACM Transactions on Algorithms, to appear.
Combinatorial Properties of RNA Secondary Structures
Markus E. Nebel, Journal of Computational Biology 9/3, 2002, 541 - 574
Combinatorics of RNA secondary structures with base triples
Robert Müller and Markus E. Nebel, Journal of Computational Biology, to appear.
Digital Search Trees with Keys of Variable Length
Markus E. Nebel, R.A.I.R.O. Theoretical Informatics and Applications 30 (6), 1996, 507 - 520
Engineering Java 7's Dual Pivot Quicksort Using MaLiJAn
Sebastian Wild, Markus E. Nebel, Raphael Reitzig and Ulrich Laube,
ACM-SIAM Meeting on Algorithm Engineering & Experiments 2013 (ALENEX13)
Evaluating Algorithms according to their Energy Consumption
Hannah Bayer and Markus E. Nebel, CiE (Computability in Europe) 2009
Evaluating the Effect of Disturbed Ensemble Distributions on SCFG Based Statistical Sampling of RNA Secondary Structures
Anika Scheid and Markus Nebel, BMC Bioinformatics 2012, 13:159 doi:10.1186/1471-2105-13-159
Evaluation of a Sophisticated SCFG Design for RNA Secondary Structure Prediction
Markus E. Nebel and Anika Scheid, Theory in Biosciences (2011) 130: 313-336
Fast String Matching by Using Probabilities: On an Optimal Mismatch Variant of Horspool's Algorithm
Markus E. Nebel, Theoretical Computer Science 359, 2006, 329-343
Generation of RNA pseudoknot structures with genus filtration
Fenix W.D. Huang, Markus E. Nebel and Christian M. Reidys, Mathematical Biosciences (2013), 245(2), 216-225.
Identifying Good Predictions of RNA Secondary Structure
Markus E. Nebel, Proceedings of the Pacific Symposium on Biocomputing 2004, 423-434
Investigation of the Bernoulli-Model of RNA Secondary Structures
Markus E. Nebel, Bulletinof Mathematical Biology 66, 2004, 925 - 964
JAguc -- a software package for environmental diversity analyses
M. E. Nebel, S. Wild, M. Holzhauser, L. Hüttenberger, R. Reitzig, M. Sperber, T. Stoeck, Journal of Bioinformatics and Computational Biology (2011) 9 (6): 749-773
Loops in canonical RNA pseudoknot structures
Markus E. Nebel, Christian M. Reidys and Rita R. Wang, Journal of Computational Biology, December 2011, 18(12): 1793-1806
Maximum Likelihood Analysis of Algorithms and Data Structures
Ulrich Laube and Markus E. Nebel, Theoretical Computer Science, Vol. 411, No. 1 (2010), 188-212
Maximum Likelihood Analysis of Heap Sort
U. Laube and Markus E. Nebel, SIAM Workshop on Analytic Algorithmics and Combinatorics (ANALCO9)
Maximum Likelihood Analysis of the Ford-Fulkerson Method on Special Graphs
Ulrich Laube and Markus E. Nebel, to appear in Algorithmica (2015). DOI: 10.1007/s00453-015-9998-5
New Knowledge on AVL-Trees
Markus E. Nebel, Technical Report 5/99, Fachbereich Informatik, Johann Wolfgang Goethe-Universität Frankfurt, 1999
New Results on the Stack Ramification of Binary Trees
Markus E. Nebel, Journal of Automata, Languages and Combinatorics 2 (3), 1997, 161 - 175
Non Uniform Generation of Combinatorial Objects
Frank Weinberg and Markus E. Nebel, Technical Report University of Kaiserslautern, 2010
On a Statistical Filter for RNA Secondary Structures
Markus E. Nebel, Frankfurter Informatik-Berichte 5/02 (technical report)
On Quantitative Effects of RNA Shape Abstraction
Markus E. Nebel and Anika Scheid, Theory in Biosciences 128, 2009, 211-225
On the Average Complexity of the Membership Problem for a Generalized Dyck Language
Markus E. Nebel, Lecture Notes in Computer Science (FCT 1997) 1279, 1997, 352 - 363
On the Horton-Strahler Number for Combinatorial Tries
Markus E. Nebel, R.A.I.R.O. Theoretical Informatics and Applications 34, 2000, 279 - 296
On the Lexicographical Generation of Compressed Codes
Markus E. Nebel, Information Processing Letters 104, 2007, 95-100
On the Power of Subroutines for Finite State Machines
Markus E. Nebel, Journal of Automata, Languages and Combinatorics 6 (1), 2001, 51 - 74
On the Stack-Size of General Tries
J. Bourdon, M. E. Nebel and B. Vallée, R.A.I.R.O Theoretical Informatics and Applications 35, 2001, 163 - 185
Pivot Sampling in Dual-Pivot Quicksort
Markus E. Nebel, Sebastian Wild, AofA 2014
Predicting RNA Secondary Structures with Pseudoknots by MCMC Sampling
Dirk Metzler and Markus E. Nebel, Journal of Mathematical Biology 56, 2008, 161-181
Random Generation of RNA Secondary Structures According to Native Distributions
Markus E. Nebel and Anika Scheid; a revised version has been publihed at Algorithms for Molecular Biology 2011, 6:24
Random induced subgraphs of Cayley graphs induced by transpositions
Emma Yu Jin and Christian M. Reidys, Discrete Mathematics, to appear
RNA Secondary Structures in a Polymer-Zeta Model -- How Foldings Should be Shaped for Sparsification to Establish a Linear Speedup
Emma Yu Jin and Markus E. Nebel, Journal of Mathematical Biology, to appear.
Statistical RNA Secondary Structure Sampling Based on a Length-Dependent SCFG Model
Anika Scheid and Markus E. Nebel, submitted.
The Expected Order of Saturated RNA Secondary Structures
Emma Yu Jin and Markus E. Nebel, SIAM ANALCO 2012
The scientific works of Rainer Kemp (1949-2004)
P. Flajolet, M.Nebel and H.Prodinger, Theoretical Computer Science 355, 2006, 371-381
The Stack-Size of Combinatorial Tries Revisited
Markus E. Nebel, Discrete Mathematics and Theoretical Computer Science 5, 2002, 1 - 16
The Stack-Size of Tries: A Combinatorial Study
Markus E. Nebel, Theoretical Computer Science 270, 2002, 441 - 461
Topology and prediction of RNA pseudoknots
C .M. Reidys, F. W. D. Huang, J. E. Andersen, R. C. Penner, P. F. Stadler, and M. E. Nebel, Bioinformatics (2011) 27 (8): 1076-1085