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The Resource Algorithms for Computational Biology : First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings

Algorithms for Computational Biology : First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings

Label
Algorithms for Computational Biology : First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings
Title
Algorithms for Computational Biology
Title remainder
First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings
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Language
eng
Member of
Cataloging source
MiAaPQ
Literary form
non fiction
Nature of contents
dictionaries
Series statement
Lecture Notes in Computer Science / Lecture Notes in Bioinformatics
Series volume
v.8542
Algorithms for Computational Biology : First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings
Label
Algorithms for Computational Biology : First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedings
Link
http://libproxy.rpi.edu/login?url=https://ebookcentral.proquest.com/lib/rpi/detail.action?docID=3093402
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Copyright
Related Contributor
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Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
  • Preface -- Organization -- Table of Contents -- Invited Talks -- Comparative Genomics Approaches to Identifying Functionally Related Genes* -- 1 Introduction -- 2 What Is the Gene "Function"? -- 3 Homology-Based Functional Assignments -- 3.1 Annotation by Similarity -- 3.2 Family/Superfamily Annotation -- 4 Using Genome Comparisons for Predicting Protein Functions -- 4.1 Phylogenetic Profiling -- 4.2 Genomic Neighborhood -- 4.3 Gene Coexpression -- 4.4 Protein Domain Fusions -- 4.5 Protein-Protein Interactions -- 5 Combining Disparate Data into a Single Annotation -- 6 Conclusions -- References -- Regular Papers -- A Greedy Algorithm for Hierarchical Complete Linkage Clustering -- 1 Introduction -- 2 Algorithm and Its Implementation -- 2.1 The Basic Idea -- 2.2 Some Details -- 3 Sketch of Our Main Application -- 4 Experiments -- 5 Conclusion -- References -- Vester's Sensitivity Model for Genetic Networks with Time-Discrete Dynamics -- 1 Introduction -- 2 TheMethod -- 2.1 Linear Programming -- 2.2 Vester's Sensitivity Model -- 3 Data -- 3.1 Data Analysis -- 4 Computational Results -- 5 Conclusions and Future Work -- References -- Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem -- 1 Introduction -- 2 Formal Description of the Problems -- 3 Computational Complexity -- 4 Inapproximability Results for -- 5 A Polynomial-Time Approximation Algorithm for -- 6 Conclusion -- References -- Heuristics for the Sorting by Length-Weighted Inversions Problem on Signed Permutations -- 1 Introduction -- 2 Definitions -- 3 TheMeta-heuristic -- 3.1 Neighborhood -- 3.2 Local Search -- 3.3 Building Solutions -- 4 Experimental Results -- 5 Conclusions -- References -- On Low Treewidth Graphs and Supertrees -- 1 Introduction -- 2 Preliminaries -- 3 MainResults -- 4 Beyond Treewidth 2 -- 5 Conclusion -- References
  • On Optimal Read Trimming in Next Generation Sequencing and Its Complexity -- 1 Introduction -- 2 Problems and Notation -- 3 Complexity -- 4 Polynomial-Time Algorithms for Relaxations of the Problems -- 5 Case Studies -- 6 Applications -- 7 Conclusions -- References -- On the Implementation of Quantitative Model Refinement -- 1 Introduction -- 2 The Heat Shock Response (HSR) -- 3 Quantitative Model Refinement -- 3.1 QuantitativeModel Refinement -- 3.2 Adding the Acetylation Details to the HSR Model through Data Refinement -- 4 Quantitative Refinement in Rule-Based Models -- 4.1 A RuleBender Implementation of the Basic HSR Model -- 4.2 A RuleBender Implementation of the Acetylation-Refined HSR Model -- 5 Quantitative Refinement in Petri Net Models -- 5.1 A Petri Net for the Basic HSR Model -- 5.2 Petri Nets for the Acetylation-Refined HSR Model -- 6 Quantitative Refinement in PRISM Models -- 6.1 A PRISM Implementation of the Basic HSR Model -- 6.2 A PRISM Implementation of the Acetylation-Refined HSR Model -- 6.3 Model Checking of the HSR Models -- 7 Discussion -- References -- HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads -- 1 Introduction -- 2 Methods -- 2.1 Modeling -- 2.2 Parameter Estimation -- 2.3 Variant Calling and Haplotype Inference -- 3 Results -- 3.1 Simulation Analysis -- 3.2 Real Data Analysis -- 3.3 Required Computational Resource -- 4 Conclusions -- References -- Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads -- 1 Introduction -- 2 Inversion Pattern in the de Bruijn Graph -- 2.1 Preliminaries -- 2.2 Inversion Pattern -- 3 Algorithm for Inversion Pattern Detection -- 3.1 Main Algorithm -- 3.2 Canonical Representation of Occurrences -- 3.3 Presence of Small Inverted Repeats at the Breakpoints
  • 3.4 Distinguishing Inversions from Approximate Repeats -- 4 Results -- 4.1 Results on a Bacterial Genome -- 4.2 Results on More Complex Genomes -- 4.3 Time and Memory Performances -- 5 Discussion and Conclusion -- References -- Modeling the Geometry of the Endoplasmic Reticulum Network -- 1 Problem -- 2 Model -- 3 Problem Formulation and Resolution -- 3.1 Binary Linear Programming Resolution -- 3.2 Linear Programming Formulation -- 4 Tests -- 4.1 Runtimes for the Solution of the Basic Problem -- 4.2 Runtimes of Real-Life Testcases with the Full Model -- 4.3 Real-Life Testcase Results and a Comparison with Actual Topologies -- 5 Discussion -- References -- On Sorting of Signed Permutations by Prefix and Suffix Reversals and Transpositions -- 1 Introduction -- 2 Basic Definitions -- 3 Sorting by Signed Prefix Reversals -- 4 Sorting by Signed Prefix Reversals and Signed Suffix Reversals -- 5 Sorting by Signed Prefix Reversals and Prefix Transpositions -- 6 Sorting by Signed Prefix Reversals, Prefix Transpositions, Signed Suffix Reversals and Suffix Transpositions -- 7 Results -- References -- On the Diameter of Rearrangement Problems -- 1 Introduction -- 2 Definitions -- 3 Families -- 4 Bounds -- 5 Conclusion and Future Work -- References -- Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network -- 1 Introduction -- 2 Methods -- 2.1 Problem Definition and Observations -- 2.2 Anchor Vertices -- 2.3 Efficient Enumeration of Spokes -- 2.4 Efficient Enumeration of All Connected Subgraphs -- 2.5 Correctness -- 3 Experimental Results -- 4 Conclusion -- References -- On Algorithmic Complexity of Biomolecular Sequence Assembly Problem -- 1 Introduction -- 2 The Dovetail-Path Framework -- 3 Shortest Superstring Problem ( -- 4 Graph-Theoretic Formulation -- 4.1 Strings, Overlaps and Overlap Graph -- 4.2 String Graph
  • 4.3 De Bruijn Graph -- 5 Discussion -- References -- A Closed-Form Solution for Transcription Factor Activity Estimation Using Network Component Analysis -- 1 Introduction -- 2 CFNINCA: NINCA with Closed Form Solutions -- 2.1 Estimating Connectivity Matrix -- 2.2 Estimating the TFA Matrix -- 3 Simulation Results -- 3.1 Synthetic and Hemoglobin Test Data -- 3.2 Results S.Cerevisiae Cell Cycle Data -- 3.3 Robustness to Errors in Prior Information -- 3.4 Run Time Comparison -- 4 Conclusions -- References -- SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints -- 1 Introduction -- 2 Methods -- 2.1 Preprocessing -- 2.2 Modeling for Paired-End Reads -- 2.3 Parameter Estimation by the EM Algorithm -- 3 Results -- 3.1 Simulation Data Analysis -- 3.2 Real Data Analysis -- 3.3 Computational Resources -- 4 Discussion -- References -- Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures -- 1 Introduction -- 1.1 Constrained Elements in Eukaryote Genomes -- 1.2 Analyzing Sequence Composition through a Combination of -- 2 Methods -- 2.1 Datasets Retrieval -- 2.2 Treatment of Sequences and Extraction of Surrogate Sequences -- 2.3 From Sequences to the N-Gram Graph Similarity Vector Space -- 3 Results and Discussion -- 3.1 Inter-Species Comparisons of Background Sequences -- 3.2 Classification Experiments of Constrained DNA Sequences -- 3.3 Genomic Signatures Perform Better in Classifying Genomic Segments of Functional Importance and Different Origin -- 4 Conclusions -- References -- Inference of Boolean Networks from Gene Interaction Graphs Using a SAT Solver -- 1 Introduction -- 2 Boolean Networks via Propositional Logic -- 2.1 Boolean Networks and Interaction Graphs -- 2.2 Representation of Boolean Networks -- 3 Experiments -- 3.1 The -- 4 Concluding Remarks -- References
  • RRCA: Ultra-Fast Multiple In-species Genome Alignments -- 1 Introduction -- 2 Preliminaries -- 3 Computing an Alignment with Referential Compression -- 3.1 Computing an Initial Alignment -- 3.2 Completing an Alignment with Recursive Referential Compression -- 4 Discussion -- 5 Conclusion -- References -- Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric -- 1 Introduction -- 2 The Maximum Contact Map Overlap Metric -- 3 Nearest Neighbor Classification of Protein Structures -- 3.1 Finding Family Representatives -- 3.2 Dominance between Target Protein Structures -- 3.3 Classification Algorithm -- 4 Validation Setup -- 5 Computational Results -- 5.1 Characterizing the Distance Measure -- 5.2 Results for the SCOPCath Benchmark -- 5.3 Results for the Extended SCOPCath Benchmark -- 6 Conclusion -- References -- Author Index
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1 online resource (285 pages)
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online
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9783319079530
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computer
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rdamedia
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remote

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