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Algorithms for Molecular Biology, Volume 4

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Volume 4, 2009

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Raazesh Sainudiin, Thomas L. York:
Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces.
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  - journals/almob/WangDYLL09
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Zhen Wang, Guohui Ding, Zhong-Hao Yu, Lei Liu, Yixue Li:
CHSMiner: a GUI tool to identify chromosomal homologous segments.
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  - journals/almob/PeterlongoSLPS09
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Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti, Marie-France Sagot:
Lossless filter for multiple repeats with bounded edit distance.
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  - journals/almob/IvryMASB09
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Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro, Danny Barash:
An image processing approach to computing distances between RNA secondary structures dot plots.
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  - journals/almob/BhadraBCM09
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Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R. Chandra, I. Saira Mian:
A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data.
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  - journals/almob/LangdonH09
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William B. Langdon, Andrew P. Harrison:
Evolving DNA motifs to predict GeneChip probe performance.
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  - journals/almob/KadotaNS09
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Koji Kadota, Yuji Nakai, Kentaro Shimizu:
Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity.
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  - journals/almob/MadeiraO09
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Sara C. Madeira, Arlindo L. Oliveira:
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series.
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  - journals/almob/KimP09
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Dae-Won Kim, Hong-Seog Park:
Review of "Bioinformatics: A Computing Perspective" edited by Shuba Gopal, Anne Haake, Rhys Price Jones and Paul Tymann.
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  - journals/almob/MosigJWNEPC09
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Axel Mosig, Stefan Jäger, Chaofeng Wang, Sumit Kumar Nath, Ilker Ersoy, Kannappan Palaniappan, Su-Shing Chen:
Tracking cells in Life Cell Imaging videos using topological alignments.
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  - journals/almob/WenWBLCFWSKW09
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Sheron Wen, Chenguang Wang, Arthur Berg, Yao Li, Myron M. Chang, Roger B. Filligim, Margaret R. Wallace, Roland Staud, Lee Kaplan, Rongling Wu:
Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data.
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  - journals/almob/ZahoranszkyKHMZZ09
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László A. Zahoránszky, Gyula Y. Katona, Péter Hári, András Málnási-Csizmadia, Katharina Anna Zweig, Gergely Zahoránszky-Köhalmi:
Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods. 12
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  - journals/almob/FariselliSMC09
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Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio:
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. 13
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Eric S. Ho, Christopher D. Jakubowski, Samuel I. Gunderson:
iTriplet, a rule-based nucleic acid sequence motif finder. 14
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  - journals/almob/KrollBC09
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K. Myriam Kroll, Gerard T. Barkema, Enrico Carlon:
Linear model for fast background subtraction in oligonucleotide microarrays. 15
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Marília D. V. Braga, Christian Gautier, Marie-France Sagot:
An asymmetric approach to preserve common intervals while sorting by reversals. 16

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