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Volume 4;  2009
Book Report
Review of “Bioinformatics: A Computing Perspective” edited by Shuba Gopal, Anne Haake, Rhys Price Jones and Paul Tymann
Dae-Won Kim and Hong-Seog Park
Algorithms Mol Biol. 2009; 4: 9. Published online 2009 June 24. doi: 10.1186/1748-7188-4-9.
PMCID: PMC2705354
Research
Lossless filter for multiple repeats with bounded edit distance
Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti, and Marie-France Sagot
Algorithms Mol Biol. 2009; 4: 3. Published online 2009 January 30. doi: 10.1186/1748-7188-4-3.
PMCID: PMC2661881
An image processing approach to computing distances between RNA secondary structures dot plots
Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro, and Danny Barash
Algorithms Mol Biol. 2009; 4: 4. Published online 2009 February 9. doi: 10.1186/1748-7188-4-4.
PMCID: PMC2677394
A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data
Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R Chandra, and I Saira Mian
Algorithms Mol Biol. 2009; 4: 5. Published online 2009 February 24. doi: 10.1186/1748-7188-4-5.
PMCID: PMC2654898
Evolving DNA motifs to predict GeneChip probe performance
WB Langdon and AP Harrison
Algorithms Mol Biol. 2009; 4: 6. Published online 2009 March 19. doi: 10.1186/1748-7188-4-6.
PMCID: PMC2679018
Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
Koji Kadota, Yuji Nakai, and Kentaro Shimizu
Algorithms Mol Biol. 2009; 4: 7. Published online 2009 April 22. doi: 10.1186/1748-7188-4-7.
PMCID: PMC2679019
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series
Sara C Madeira and Arlindo L Oliveira
Algorithms Mol Biol. 2009; 4: 8. Published online 2009 June 4. doi: 10.1186/1748-7188-4-8.
PMCID: PMC2709627
Tracking cells in Life Cell Imaging videos using topological alignments
Axel Mosig, Stefan Jäger, Chaofeng Wang, Sumit Nath, Ilker Ersoy, Kannap-pan Palaniappan, and Su-Shing Chen
Algorithms Mol Biol. 2009; 4: 10. Published online 2009 July 16. doi: 10.1186/1748-7188-4-10.
PMCID: PMC2722650
Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data
Sheron Wen, Chenguang Wang, Arthur Berg, Yao Li, Myron M Chang, Roger B Fillingim, Margaret R Wallace, Roland Staud, Lee Kaplan, and Rongling Wu
Algorithms Mol Biol. 2009; 4: 11. Published online 2009 August 11. doi: 10.1186/1748-7188-4-11.
PMCID: PMC2739217
Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods
László A Zahoránszky, Gyula Y Katona, Péter Hári, András Málnási-Csizmadia, Katharina A Zweig, and Gergely Zahoránszky-Köhalmi
Algorithms Mol Biol. 2009; 4: 12. Published online 2009 October 19. doi: 10.1186/1748-7188-4-12.
PMCID: PMC2774311
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, and Rita Casadio
Algorithms Mol Biol. 2009; 4: 13. Published online 2009 October 22. doi: 10.1186/1748-7188-4-13.
PMCID: PMC2776008
iTriplet, a rule-based nucleic acid sequence motif finder
Eric S Ho, Christopher D Jakubowski, and Samuel I Gunderson
Algorithms Mol Biol. 2009; 4: 14. Published online 2009 October 29. doi: 10.1186/1748-7188-4-14.
PMCID: PMC2784457
Software Article
CHSMiner: a GUI tool to identify chromosomal homologous segments
Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, and Yixue Li
Algorithms Mol Biol. 2009; 4: 2. Published online 2009 January 15. doi: 10.1186/1748-7188-4-2.
PMCID: PMC2647922
Software article
Linear model for fast background subtraction in oligonucleotide microarrays
K Myriam Kroll, Gerard T Barkema, and Enrico Carlon
Algorithms Mol Biol. 2009; 4: 15. Published online 2009 November 16. doi: 10.1186/1748-7188-4-15.
PMCID: PMC2785812
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