An Analysis of Structural Influences on Selection in RNA Genes (2009)
Mimouni, Naila K., Lyngsø, Rune B., Griffiths-Jones, Sam, Hein, Jotun
Noncoding RNAs (ncRNAs) are transcripts that do not code for protein but rather function as RNA in catalytic, regulatory, or structural roles in the cell. ncRNAs are involved in universally conserved...
We study folding algorithms in the two dimensional Hydrophobic-Hydrophilic model for protein structure formation. We consider three generalizations of the best known approximation algorithm. We show...
Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo
Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in...
Jan Gorodkin, Rune B. Lyngsø, Gary D. Stormo
When a set of coregulated genes share a common structural RNA motif, e.g. a hairpin, most motif search approaches fail to locate the covarying but structurally conserved motif. There do exist methods...
We study folding algorithms in the two dimensional Hydrophobic-Hydrophilic model for protein structure formation. We consider three generalizations of the best known approximation algorithm. We show...
We study folding algorithms in the two dimensional Hydrophobic-Hydrophilic model for protein structure formation. We consider three generalizations of the best known approximation algorithm. We show...
Minimum Recombination Histories by Branch and Bound (2005)
Abstract. Recombination plays an important role in creating genetic diversity within species, and inferring past recombination events is central to many problems in genetics. Given a set M of sampled...
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search (2005)
Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently...
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% (2005)
Havgaard, Jakob Hull, Lyngsø, Rune B., Stormo, Gary D., Gorodkin, Jan
Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in...
Complexity of pseudoknot prediction in simple models (2004)
Abstract. Efficient exact algorithms for finding optimal secondary structures of RNA sequences have been known for a quarter of a century. However, these algorithms are restricted to structures...
Solving the string statistics problem in time O(n log n) (2002)
Gerth Stølting Brodal, Rune B. Lyngsø, Anna Östlin
The string statistics problem consists of preprocessing a string of length n such that given a query pattern of length m, the maximum number of non-overlapping occurrences of the query pattern in the...
Solving the String Statistics Problem in Time O(n log n) (2002)
Gerth Stølting Brodal, Rune B. Lyngsø, Anna Östlin, Ny Munkegade
The string statistics problem consists of preprocessing a string of length n such that given a query pattern of length m, the maximum number of non-overlapping occurrences of the query pattern in the...
Solving the String Statistics Problem in Time O(n log n) (2002)
Gerth Stølting Brodal, Rune B. Lyngsø, Anna Östlin
The string statistics problem consists of preprocessing a string of length n such that given a query pattern of length m, the maximum number of non-overlapping occurrences of the query pattern in the...
Complexity of Comparing Hidden Markov Models (2001)
The basic theory of hidden Markov models was developed and applied to problems in speech recognition in the late 1960's, and has since then been applied to numerous problems, e.g. biological...
This document in subdirectoryDS/00/5/ Computational Biology (2001)
Rune B. Lyngsø, Copyright C, Rune B. Lyngsø, Rune Bang Lyngsø
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...
RNA Pseudoknot Prediction in Energy Based Models (2000)
RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is...
Pseudoknots in RNA Secondary Structures (2000)
RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is...
Pseudoknots in RNA Secondary Structures (2000)
RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is...
Pseudoknots in RNA Secondary Structures (1999)
RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is...
Protein folding in the 2D HP model (1999)
We study folding algorithms in the two dimensional Hydrophobic-Hydrophilic model for protein structure formation. We consider three generalizations of the best known approximation algorithm. We show...
Finding Maximal Pairs with Bounded Gap (1999)
Gerth Stølting Brodal, Rune B. Lyngsø, Jens Stoye
A pair in a string is the occurrence of the same substring twice. A pair is maximal if the two occurrences of the substring cannot be extended to the left and right without making them different. The...
An improved algorithm for RNA secondary structure prediction (1999)
Copyright C, Rune B. Lyngsø, Rune B. Lyngsø, Michael Zuker, Michael Zuker, ...
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...
The Polygamic Marriage Problem (1997)
Peer Berg, Bernt Guldbrandtsen, Rune B. Lyngsø
this paper we consider matchings of a certain kind, namely matchings where each male is paired with at least m and at most n females and each female is paired with at most one male. Denote these...
The foldalign web server for pairwise structural RNA alignment and mutual motif search
Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently...
The foldalign web server for pairwise structural RNA alignment and mutual motif search
Havgaard, Jakob H., Lyngsø, Rune B., Gorodkin, Jan
Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently...
This document in subdirectoryRS/99/12/
Gerth Stølting Brodal, Rune B. Lyngsø, Jens Stoye, Copyright C, Gerth Stølting Brodal, ...
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...
This document in subdirectoryRS/98/3/ Comparison of coding DNA
Rune B. Lyngsø, Jotun Hein, Lyngsø Jotun Hein
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...
This document in subdirectoryRS/99/6/ Measures on hidden Markov models
Rune B. Lyngsø, Henrik Nielsen, Henrik Nielsen
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...
This document in subdirectoryRS/99/16/
Rune B. Lyngsø, Copyright C, Rune B. Lyngsø
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...