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Volume 3;  2008
Research
Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability
Gang Wu, Ming-Yang Kao, Guohui Lin, and Jia-Huai You
Algorithms Mol Biol. 2008; 3: 1. Published online 2008 January 24. doi: 10.1186/1748-7188-3-1.
PMCID: PMC2267719
Learning from positive examples when the negative class is undetermined- microRNA gene identification
Malik Yousef, Segun Jung, Louise C Showe, and Michael K Showe
Algorithms Mol Biol. 2008; 3: 2. Published online 2008 January 28. doi: 10.1186/1748-7188-3-2.
PMCID: PMC2248178
A scoring matrix approach to detecting miRNA target sites
Simon Moxon, Vincent Moulton, and Jan T Kim
Algorithms Mol Biol. 2008; 3: 3. Published online 2008 March 31. doi: 10.1186/1748-7188-3-3.
PMCID: PMC2365947
Protein sequence and structure alignments within one framework
Gundolf Schenk, Thomas Margraf, and Andrew E Torda
Algorithms Mol Biol. 2008; 3: 4. Published online 2008 April 1. doi: 10.1186/1748-7188-3-4.
PMCID: PMC2390564
On the optimality of the neighbor-joining algorithm
Kord Eickmeyer, Peter Huggins, Lior Pachter, and Ruriko Yoshida
Algorithms Mol Biol. 2008; 3: 5. Published online 2008 April 30. doi: 10.1186/1748-7188-3-5.
PMCID: PMC2430562
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
Amarendran R Subramanian, Michael Kaufmann, and Burkhard Morgenstern
Algorithms Mol Biol. 2008; 3: 6. Published online 2008 May 27. doi: 10.1186/1748-7188-3-6.
PMCID: PMC2430965
A weighted average difference method for detecting differentially expressed genes from microarray data
Koji Kadota, Yuji Nakai, and Kentaro Shimizu
Algorithms Mol Biol. 2008; 3: 8. Published online 2008 June 26. doi: 10.1186/1748-7188-3-8.
PMCID: PMC2464587
Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps
Peter Meinicke, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Petr Karlovsky, and Burkhard Morgenstern
Algorithms Mol Biol. 2008; 3: 9. Published online 2008 June 26. doi: 10.1186/1748-7188-3-9.
PMCID: PMC2464586
A stitch in time: Efficient computation of genomic DNA melting bubbles
Eivind Tøstesen
Algorithms Mol Biol. 2008; 3: 10. Published online 2008 July 17. doi: 10.1186/1748-7188-3-10.
PMCID: PMC2553405
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
Hans Binder, Knut Krohn, and Stephan Preibisch
Algorithms Mol Biol. 2008; 3: 11. Published online 2008 August 29. doi: 10.1186/1748-7188-3-11.
PMCID: PMC2543012
"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
Hans Binder and Stephan Preibisch
Algorithms Mol Biol. 2008; 3: 12. Published online 2008 August 29. doi: 10.1186/1748-7188-3-12.
PMCID: PMC2546411
Fast algorithms for computing sequence distances by exhaustive substring composition
Alberto Apostolico and Olgert Denas
Algorithms Mol Biol. 2008; 3: 13. Published online 2008 October 28. doi: 10.1186/1748-7188-3-13.
PMCID: PMC2615014
HuMiTar: A sequence-based method for prediction of human microRNA targets
Jishou Ruan, Hanzhe Chen, Lukasz Kurgan, Ke Chen, Chunsheng Kang, and Peiyu Pu
Algorithms Mol Biol. 2008; 3: 16. Published online 2008 December 22. doi: 10.1186/1748-7188-3-16.
PMCID: PMC2631598
Software Articles
Noisy: Identification of problematic columns in multiple sequence alignments
Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J Prohaska, and Peter F Stadler
Algorithms Mol Biol. 2008; 3: 7. Published online 2008 June 24. doi: 10.1186/1748-7188-3-7.
PMCID: PMC2464588
Syntenator: Multiple gene order alignments with a gene-specific scoring function
Christian Rödelsperger and Christoph Dieterich
Algorithms Mol Biol. 2008; 3: 14. Published online 2008 November 6. doi: 10.1186/1748-7188-3-14.
PMCID: PMC2590594
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