Search Results - "NEBEL, MARKUS"

GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach by Müller, Robert, Nebel, Markus E

“…Massive genomic data sets from high-throughput sequencing allow for new insights into complex biological systems such as microbial communities. Analyses of…”
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Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water by STOECK, THORSTEN, BASS, DAVID, NEBEL, MARKUS, CHRISTEN, RICHARD, JONES, MEREDITH D. M., BREINER, HANS-WERNER, RICHARDS, THOMAS A.

“…Sequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology…”
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On the use of sequence-quality information in OTU clustering by Müller, Robert, Nebel, Markus

“…High-throughput sequencing has become an essential technology in life science research. Despite continuous improvements in technology, the produced sequences…”
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Combinatorics of RNA Secondary Structures with Base Triples by Müller, Robert, Nebel, Markus E

“…The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in…”
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Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures by Scheid, Anika, Nebel, Markus E

“…Over the past years, statistical and Bayesian approaches have become increasingly appreciated to address the long-standing problem of computational RNA…”
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RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup by Jin, Emma Yu, Nebel, Markus E.

“…Various tools used to predict the secondary structure for a given RNA sequence are based on dynamic programming used to compute a conformation of minimum free…”
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Analysis of Pivot Sampling in Dual-Pivot Quicksort: A Holistic Analysis of Yaroslavskiy’s Partitioning Scheme by Nebel, Markus E., Wild, Sebastian, Martínez, Conrado

“…The new dual-pivot Quicksort by Vladimir Yaroslavskiy—used in Oracle’s Java runtime library since version 7—features intriguing asymmetries. They make a basic…”
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Topology and prediction of RNA pseudoknots by REIDYS, Christian M, HUANG, Fenix W. D, ANDERSEN, Jørgen E, PENNER, Robert C, STADLER, Peter F, NEBEL, MarkusE

“…Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the…”
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Algebraic and combinatorial properties of common RNA pseudoknot classes with applications by Nebel, Markus E, Weinberg, Frank

“…Predicting RNA structures with pseudoknots in general is an NP-complete problem. Accordingly, several authors have suggested subclasses that provide polynomial…”
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Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences by Nebel, Markus, Pfabel, Cornelia, Stock, Alexandra, Dunthorn, Micah, Stoeck, Thorsten

“…Summary Delineating operational taxonomic units (OTUs) is a central element in any culture‐independent analysis of environmental microbial eukaryotic…”
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Predicting RNA secondary structures with pseudoknots by MCMC sampling by Metzler, Dirk, Nebel, Markus E.

“…The most probable secondary structure of an RNA molecule, given the nucleotide sequence, can be computed efficiently if a stochastic context-free grammar…”
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Random generation of RNA secondary structures according to native distributions by Nebel, Markus E, Scheid, Anika, Weinberg, Frank

“…Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from…”
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Generation of RNA pseudoknot structures with topological genus filtration by Huang, Fenix W.D., Nebel, Markus E., Reidys, Christian M.

“…•RNA structures is filtered by fixed topological genus.•Uniform sampling algorithm for RNA structures of genus g>0.•RNA structures of genus g is weighted by a…”
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Fast string matching by using probabilities : On an optimal mismatch variant of Horspool's algorithm by NEBEL, Markus E

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JAGUC--a software package for environmental diversity analyses by Nebel, Markus E, Wild, Sebastian, Holzhauser, Michael, Hüttenberger, Lars, Reitzig, Raphael, Sperber, Matthias, Stoeck, Thorsten

“…The study of microbial diversity and community structures heavily relies on the analyses of sequence data, predominantly taxonomic marker genes like the small…”
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Evaluation of a sophisticated SCFG design for RNA secondary structure prediction by Nebel, Markus E., Scheid, Anika

“…Predicting secondary structures of RNA molecules is one of the fundamental problems of and thus a challenging task in computational structural biology. Over…”
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Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model by Nebel, Markus E., Scheid, A.

“…There are two custom ways for predicting RNA secondary structures: minimizing the free energy of a conformation according to a thermodynamic model and…”
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Maximum likelihood analysis of algorithms and data structures by Laube, Ulrich, Nebel, Markus E.

“…We present a new approach for an average-case analysis of algorithms and data structures that supports a non-uniform distribution of the inputs and is based on…”
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Loops in canonical RNA pseudoknot structures by Nebel, Markus E, Reidys, Christian M, Wang, Rita R

“…In this article, we compute the limit distributions of the numbers of hairpin-loops, interior-loops and bulges in k-noncrossing RNA structures. The latter are…”
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Applying Length-Dependent Stochastic Context-Free Grammars to RNA Secondary Structure Prediction by Weinberg, Frank, Nebel, Markus E.

“…In order to be able to capture effects from co-transcriptional folding, we extend stochastic context-free grammars such that the probability of applying a rule…”
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