Algorithms Mol Biol Volume 6; 2011

Volume 6; 2011

Research

Speeding up the Consensus Clustering methodology for microarray data analysis

Raffaele Giancarlo, Filippo Utro

Algorithms Mol Biol. 2011; 6: 1. Published online 2011 January 14. doi: 10.1186/1748-7188-6-1

PMCID:: PMC3035181

Abstract Full Text PDF–628K

RNA Accessibility in cubic time

Stephan H Bernhart, Ullrike Mückstein, Ivo L Hofacker

Algorithms Mol Biol. 2011; 6: 3. Published online 2011 March 9. doi: 10.1186/1748-7188-6-3

PMCID:: PMC3063221

Abstract Full Text PDF–370K

Efficient algorithms for the discovery of gapped factors

Alberto Apostolico, Cinzia Pizzi, Esko Ukkonen

Algorithms Mol Biol. 2011; 6: 5. Published online 2011 March 23. doi: 10.1186/1748-7188-6-5

PMCID:: PMC3080308

Abstract Full Text PDF–499K

WildSpan: mining structured motifs from protein sequences

Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu

Algorithms Mol Biol. 2011; 6: 6. Published online 2011 March 31. doi: 10.1186/1748-7188-6-6

PMCID:: PMC3082213

Abstract Full Text PDF–4.1M Supplementary Material

An experimental study of Quartets MaxCut and other supertree methods

M Shel Swenson, Rahul Suri, C Randal Linder, Tandy Warnow

Algorithms Mol Biol. 2011; 6: 7. Published online 2011 April 19. doi: 10.1186/1748-7188-6-7

PMCID:: PMC3101644

Abstract Full Text PDF–585K Supplementary Material

An FPT haplotyping algorithm on pedigrees with a small number of sites

Duong D Doan, Patricia A Evans

Algorithms Mol Biol. 2011; 6: 8. Published online 2011 April 19. doi: 10.1186/1748-7188-6-8

PMCID:: PMC3108306

Abstract Full Text PDF–390K

Estimation of alternative splicing isoform frequencies from RNA-Seq data

Marius Nicolae, Serghei Mangul, Ion I Măndoiu, Alex Zelikovsky

Algorithms Mol Biol. 2011; 6: 9. Published online 2011 April 19. doi: 10.1186/1748-7188-6-9

PMCID:: PMC3107792

Abstract Full Text PDF–853K

Haplotypes versus genotypes on pedigrees

Bonnie B Kirkpatrick

Algorithms Mol Biol. 2011; 6: 10. Published online 2011 April 19. doi: 10.1186/1748-7188-6-10

PMCID:: PMC3102622

Abstract Full Text PDF–611K

Listing all sorting reversals in quadratic time

Krister M Swenson, Ghada Badr, David Sankoff

Algorithms Mol Biol. 2011; 6: 11. Published online 2011 April 19. doi: 10.1186/1748-7188-6-11

PMCID:: PMC3110122

Abstract Full Text PDF–326K

Sparse estimation for structural variability

Raghavendra Hosur, Rohit Singh, Bonnie Berger

Algorithms Mol Biol. 2011; 6: 12. Published online 2011 April 19. doi: 10.1186/1748-7188-6-12

PMCID:: PMC3101643

Abstract Full Text PDF–749K

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge

Alexandra M Carvalho, Arlindo L Oliveira

Algorithms Mol Biol. 2011; 6: 13. Published online 2011 April 22. doi: 10.1186/1748-7188-6-13

PMCID:: PMC3112114

Abstract Full Text PDF–724K Supplementary Material

A robust approach based on Weibull distribution for clustering gene expression data

Huakun Wang, Zhenzhen Wang, Xia Li, Binsheng Gong, Lixin Feng, Ying Zhou

Algorithms Mol Biol. 2011; 6: 14. Published online 2011 May 31. doi: 10.1186/1748-7188-6-14

PMCID:: PMC3118357

Abstract Full Text PDF–1011K Supplementary Material

A sub-cubic time algorithm for computing the quartet distance between two general trees

Jesper Nielsen, Anders K Kristensen, Thomas Mailund, Christian NS Pedersen

Algorithms Mol Biol. 2011; 6: 15. Published online 2011 June 3. doi: 10.1186/1748-7188-6-15

PMCID:: PMC3141660

Abstract Full Text PDF–388K Supplementary Material

Efficient unfolding pattern recognition in single molecule force spectroscopy data

Bill Andreopoulos, Dirk Labudde

Algorithms Mol Biol. 2011; 6: 16. Published online 2011 June 6. doi: 10.1186/1748-7188-6-16

PMCID:: PMC3126767

Abstract Full Text PDF–2.1M

A new, fast algorithm for detecting protein coevolution using maximum compatible cliques

Alex Rodionov, Alexandr Bezginov, Jonathan Rose, Elisabeth RM Tillier

Algorithms Mol Biol. 2011; 6: 17. Published online 2011 June 14. doi: 10.1186/1748-7188-6-17

PMCID:: PMC3130660

Abstract Full Text PDF–672K Supplementary Material

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach

Akdes Serin, Martin Vingron

Algorithms Mol Biol. 2011; 6: 18. Published online 2011 June 23. doi: 10.1186/1748-7188-6-18

PMCID:: PMC3152888

Abstract Full Text PDF–4.9M Supplementary Material

Prediction of plant promoters based on hexamers and random triplet pair analysis

A K M Azad, Saima Shahid, Nasimul Noman, Hyunju Lee

Algorithms Mol Biol. 2011; 6: 19. Published online 2011 June 28. doi: 10.1186/1748-7188-6-19

PMCID:: PMC3160368

Abstract Full Text PDF–776K Supplementary Material

Exploiting bounded signal flow for graph orientation based on cause-effect pairs

Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier, Johannes Uhlmann

Algorithms Mol Biol. 2011; 6: 21. Published online 2011 August 25. doi: 10.1186/1748-7188-6-21

PMCID:: PMC3189099

Abstract Full Text PDF–425K

Multi-membership gene regulation in pathway based microarray analysis

Stelios P Pavlidis, Annette M Payne, Stephen M Swift

Algorithms Mol Biol. 2011; 6: 22. Published online 2011 September 22. doi: 10.1186/1748-7188-6-22

PMCID:: PMC3189100

Abstract Full Text PDF–506K

ReCoil - an algorithm for compression of extremely large datasets of dna data

Vladimir Yanovsky

Algorithms Mol Biol. 2011; 6: 23. Published online 2011 October 11. doi: 10.1186/1748-7188-6-23

PMCID:: PMC3219593

Abstract Full Text PDF–311K

Random generation of RNA secondary structures according to native distributions

Markus E Nebel, Anika Scheid, Frank Weinberg

Algorithms Mol Biol. 2011; 6: 24. Published online 2011 October 12. doi: 10.1186/1748-7188-6-24

PMCID:: PMC3354341

Abstract Full Text PDF–1.3M

Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences

Valery O Polyanovsky, Mikhail A Roytberg, Vladimir G Tumanyan

Algorithms Mol Biol. 2011; 6: 25. Published online 2011 October 27. doi: 10.1186/1748-7188-6-25

PMCID:: PMC3223492

Abstract Full Text PDF–467K Supplementary Material

A Partial Least Squares based algorithm for parsimonious variable selection

Tahir Mehmood, Harald Martens, Solve Sæbø, Jonas Warringer, Lars Snipen

Algorithms Mol Biol. 2011; 6: 27. Published online 2011 December 5. doi: 10.1186/1748-7188-6-27

PMCID:: PMC3287970

Abstract Full Text PDF–483K

Software Articles

WordCluster: detecting clusters of DNA words and genomic elements

Michael Hackenberg, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Ángel M Alganza, José L Oliver

Algorithms Mol Biol. 2011; 6: 2. Published online 2011 January 24. doi: 10.1186/1748-7188-6-2

PMCID:: PMC3037320

Abstract Full Text PDF–344K

Fast local fragment chaining using sum-of-pair gap costs

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F Stadler

Algorithms Mol Biol. 2011; 6: 4. Published online 2011 March 18. doi: 10.1186/1748-7188-6-4

PMCID:: PMC3072320

Abstract Full Text PDF–422K Supplementary Material

ViennaRNA Package 2.0

Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker

Algorithms Mol Biol. 2011; 6: 26. Published online 2011 November 24. doi: 10.1186/1748-7188-6-26

PMCID:: PMC3319429

Abstract Full Text PDF–421K Supplementary Material

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