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ALMOB
2006
113views more  ALMOB 2006»
9 years 12 months ago
Inverse bifurcation analysis: application to simple gene systems
Background: Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional for...
James Lu, Heinz W. Engl, Peter Schuster
ALMOB
2006
106views more  ALMOB 2006»
9 years 12 months ago
Multiple sequence alignment with user-defined anchor points
Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the qua...
Burkhard Morgenstern, Sonja J. Prohaska, Dirk P&ou...
ALMOB
2006
62views more  ALMOB 2006»
9 years 12 months ago
EXMOTIF: efficient structured motif extraction
Yongqiang Zhang, Mohammed J. Zaki
ALMOB
2006
56views more  ALMOB 2006»
9 years 12 months ago
SMOTIF: efficient structured pattern and profile motif search
Yongqiang Zhang, Mohammed J. Zaki
ALMOB
2006
80views more  ALMOB 2006»
9 years 12 months ago
Pattern statistics on Markov chains and sensitivity to parameter estimation
Background: In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter mu...
Grégory Nuel
ALMOB
2006
110views more  ALMOB 2006»
9 years 12 months ago
New journal: Algorithms for Molecular Biology
This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic ...
Burkhard Morgenstern, Peter F. Stadler
ALMOB
2006
81views more  ALMOB 2006»
9 years 12 months ago
Fast calculation of the quartet distance between trees of arbitrary degrees
Chris Christiansen, Thomas Mailund, Christian N. S...
ALMOB
2006
135views more  ALMOB 2006»
9 years 12 months ago
P-value based visualization of codon usage data
Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both ...
Peter Meinicke, Thomas Brodag, Wolfgang Florian Fr...
ALMOB
2006
86views more  ALMOB 2006»
9 years 12 months ago
Analysis of computational approaches for motif discovery
Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational ...
Nan Li, Martin Tompa
ALMOB
2006
155views more  ALMOB 2006»
9 years 12 months ago
Refining motifs by improving information content scores using neighborhood profile search
The main goal of the motif finding problem is to detect novel, over-represented unknown signals in a set of sequences (e.g. transcription factor binding sites in a genome). The mo...
Chandan K. Reddy, Yao-Chung Weng, Hsiao-Dong Chian...
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