Algorithms in bioinformatics : 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013 : proceedings / Aaron Darling, Jens Stoye (eds.).

By: (13th : WABI (Workshop) (13th : 2013 : Sophia Antipolis, France)
Contributor(s): Darling, Aaron [editor.] | Stoye, Jens [editor.]
Material type: TextTextSeries: SerienbezeichnungLecture notes in computer science: 8126.; Lecture notes in computer science: Publisher: Heidelberg : Springer, [2013]Copyright date: ©2013Description: 1 online resource (xiv, 378 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9783642404535; 3642404537; 3642404529; 9783642404528Subject(s): Computer algorithms -- Congresses | Bioinformatics -- Mathematics -- Congresses | Mathematics | Computing Methodologies | Phenomena and Processes | Biological Science Disciplines | Information Science | Natural Science Disciplines | Disciplines and Occupations | Biology | Mathematical Concepts | Algorithms | Computational Biology | Computer algorithmsGenre/Form: Congress. | Electronic books. | Ebook. | Conference papers and proceedings. Additional physical formats: Printed edition:: No titleDDC classification: 005.1 LOC classification: QA76.9.A43 | W33 2013Other classification: SS 4800 | 004 | BIO 110f | DAT 899f | DAT 530f Online resources: Click here to access online
Contents:
Extending the Reach of Phylogenetic Inference / Bernard M.E. Moret -- Protein (Multi- )Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework / Ramanuja Simha, Hagit Shatkay -- Towards Reliable Automatic Protein Structure Alignment / Xuefeng Cui [and others] -- A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions / Arnon Mazza [and others] -- Faster Mass Decomposition / Kai Dührkop [and others] -- On NP-Hardness of the Paired de Bruijn Sound Cycle Problem / Evgeny Kapun, Fedor Tsarev -- Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing / Denisa Duma [and others] -- A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths / Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi -- A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data / Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot.
Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures / Rolf Backofen [and others] -- Faster Algorithms for RNA-Folding Using the Four-Russians Method / Balaji Venkatachalam, Dan Gusfield, Yelena Frid -- Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree / Jesper Jansson, Chuanqi Shen, Wing-Kin Sung -- The Generalized Robinson-Foulds Metric / Sebastian Böcker, Stefan Canzar, Gunnar W. Klau -- Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time / Constantinos Tsirogiannis, Brody Sandel -- Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs / Sudheer Vakati, David Fernández-Baca -- Unifying Parsimonious Tree Reconciliation / Nicolas Wieseke, Matthias Bernt, Martin Middendorf -- Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes / Ilya Minkin, Anand Patel, Mikhail Kolmogorov -- On the Matrix Median Problem / João Paulo Pereira Zanetti, Priscila Biller, João Meidanis.
A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications / Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz -- MSARC: Multiple Sequence Alignment by Residue Clustering / Michał Modzelewski, Norbert Dojer -- Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs / Limor Leibovich, Zohar Yakhini -- Probabilistic Approaches to Alignment with Tandem Repeats / Michal Nánási, Tomáš Vinař, Broňa Brejová -- Multiscale Identification of Topological Domains in Chromatin / Darya Filippova [and others] -- Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data / Charalampos E. Tsourakakis -- Phylogenetic Analysis of Cell Types Using Histone Modifications / Nishanth Ulhas Nair, Yu Lin, Philipp Bucher -- Detecting Superbubbles in Assembly Graphs / Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya -- Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads / Viraj Deshpande [and others] -- Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs / Kamil Salikhov, Gustavo Sacomoto, Gregory Kucherov.
Summary: This book constitutes the refereed proceedings of the 13th International Workshop on Algorithms in Bioinformatics, WABI 2013, held in Sophia Antipolis, France, in September 2013. WABI 2013 is one of seven workshops which, along with the European Symposium on Algorithms (ESA), constitute the ALGO annual meeting and highlights research in algorithmic work for bioinformatics, computational biology and systems biology. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. The 27 full papers presented were carefully reviewed and selected from 61 submissions. The papers cover all aspects of algorithms in bioinformatics, computational biology and systems biology.
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Extending the Reach of Phylogenetic Inference / Bernard M.E. Moret -- Protein (Multi- )Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework / Ramanuja Simha, Hagit Shatkay -- Towards Reliable Automatic Protein Structure Alignment / Xuefeng Cui [and others] -- A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions / Arnon Mazza [and others] -- Faster Mass Decomposition / Kai Dührkop [and others] -- On NP-Hardness of the Paired de Bruijn Sound Cycle Problem / Evgeny Kapun, Fedor Tsarev -- Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing / Denisa Duma [and others] -- A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths / Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi -- A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data / Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot.

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures / Rolf Backofen [and others] -- Faster Algorithms for RNA-Folding Using the Four-Russians Method / Balaji Venkatachalam, Dan Gusfield, Yelena Frid -- Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree / Jesper Jansson, Chuanqi Shen, Wing-Kin Sung -- The Generalized Robinson-Foulds Metric / Sebastian Böcker, Stefan Canzar, Gunnar W. Klau -- Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time / Constantinos Tsirogiannis, Brody Sandel -- Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs / Sudheer Vakati, David Fernández-Baca -- Unifying Parsimonious Tree Reconciliation / Nicolas Wieseke, Matthias Bernt, Martin Middendorf -- Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes / Ilya Minkin, Anand Patel, Mikhail Kolmogorov -- On the Matrix Median Problem / João Paulo Pereira Zanetti, Priscila Biller, João Meidanis.

A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications / Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz -- MSARC: Multiple Sequence Alignment by Residue Clustering / Michał Modzelewski, Norbert Dojer -- Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs / Limor Leibovich, Zohar Yakhini -- Probabilistic Approaches to Alignment with Tandem Repeats / Michal Nánási, Tomáš Vinař, Broňa Brejová -- Multiscale Identification of Topological Domains in Chromatin / Darya Filippova [and others] -- Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data / Charalampos E. Tsourakakis -- Phylogenetic Analysis of Cell Types Using Histone Modifications / Nishanth Ulhas Nair, Yu Lin, Philipp Bucher -- Detecting Superbubbles in Assembly Graphs / Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya -- Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads / Viraj Deshpande [and others] -- Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs / Kamil Salikhov, Gustavo Sacomoto, Gregory Kucherov.

Includes bibliographical references and index.

Online resource; title from PDF title page (SpringerLink, viewed September 30, 2013).

This book constitutes the refereed proceedings of the 13th International Workshop on Algorithms in Bioinformatics, WABI 2013, held in Sophia Antipolis, France, in September 2013. WABI 2013 is one of seven workshops which, along with the European Symposium on Algorithms (ESA), constitute the ALGO annual meeting and highlights research in algorithmic work for bioinformatics, computational biology and systems biology. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. The 27 full papers presented were carefully reviewed and selected from 61 submissions. The papers cover all aspects of algorithms in bioinformatics, computational biology and systems biology.

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