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Jane: A new tool for the cophylogeny reconstruction problem
Chris Conow, Daniel Fielder, Yaniv Ovadia, Ran Libeskind-Hadas
Algorithms for Molecular Biology 2010, 5:16 (3 February 2010)
[Abstract] [Provisional PDF]
Research
Exact distribution of a pattern in a set of random sequences
generated by a Markov source: applications to biological data
Gregory Nuel, Leslie Regad, Juliette Martin, Anne-Claude Camproux
Algorithms for Molecular Biology 2010, 5:15 (26 January 2010)
[Abstract] [Provisional PDF]
Research
ANMM4CBR: a case-based reasoning method for gene expression
data classification
Bangpeng Yao, Shao Li
Algorithms for Molecular Biology 2010, 5:14 (6 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
A simple, practical and complete O(n^3/log(n))-time Algorithm for
RNA folding using the Four-Russians Speedup
Yelena Frid, Dan Gusfield
Algorithms for Molecular Biology 2010, 5:13 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
FlexSnap: Flexible Non-sequential Protein Structure Alignment.
Saeed Salem, Mohammed J. Zaki, Chris Bystroff
Algorithms for Molecular Biology 2010, 5:12 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Efficient algorithms for analyzing segmental duplications
with deletions and inversions in genomes
Crystal L Kahn, Shay Mozes, Benjamin J Raphael
Algorithms for Molecular Biology 2010, 5:11 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
A markov classification model for metabolic pathways
Timothy Hancock, Hiroshi Mamitsuka
Algorithms for Molecular Biology 2010, 5:10 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
A tree-based method for the rapid screening of chemical fingerprints
Thomas G Kristensen, Jesper Nielsen, Christian NS Pedersen
Algorithms for Molecular Biology 2010, 5:9 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
A simulation study comparing supertree and combined analysis methods using SMIDGen
M. SHEL Swenson, Francois Barbancon, Tandy Warnow, C RANDAL Linder
Algorithms for Molecular Biology 2010, 5:8 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Linear-time protein 3-D structure searching with insertions
and deletions
Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
Algorithms for Molecular Biology 2010, 5:7 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Back-translation for discovering distant protein homologies in the presence of frameshift mutations
Marta Girdea, Laurent Noe, Gregory Kucherov
Algorithms for Molecular Biology 2010, 5:6 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Fast prediction of RNA-RNA interaction
Raheleh Salari, Rolf Backofen, S Cenk Sahinalp
Algorithms for Molecular Biology 2010, 5:5 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli
Algorithms for Molecular Biology 2010, 5:4 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Phylogenetic comparative assembly
Peter Husemann, Jens Stoye
Algorithms for Molecular Biology 2010, 5:3 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Constructing majority-rule supertrees
Jianrong Dong, David Fernandez-Baca, F.r. McMorris
Algorithms for Molecular Biology 2010, 5:2 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
Refining transcriptional regulatory networks using network evolutionary models and gene histories
Xiuwei Zhang, Bernard M.E. Moret
Algorithms for Molecular Biology 2010, 5:1 (4 January 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research
An asymmetric approach to preserve common intervals while sorting by reversals
Marília DV Braga, Christian Gautier, Marie-France Sagot
Algorithms for Molecular Biology 2009, 4:16 (30 December 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Software article
Linear model for fast background subtraction in oligonucleotide microarrays
K Myriam Kroll, Gerard T Barkema, Enrico Carlon
Algorithms for Molecular Biology 2009, 4:15 (16 November 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Research
iTriplet, a rule-based nucleic acid sequence motif finder
Eric S Ho, Christopher D Jakubowski, Samuel I Gunderson
Algorithms for Molecular Biology 2009, 4:14 (29 October 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Research
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
Algorithms for Molecular Biology 2009, 4:13 (22 October 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
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