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algorithms bioinformatics, wabi 2021, 12th workshop [pdf]

Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia by Ben Raphael, Jijun Tang

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About this book :-
Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia written by Ben Raphael, Jijun Tang edited by S. Istrail, P. Pevzner, and M. Waterman .
This book constitutes the refereed proceedings of the 12th International Workshop on Algorithms in Bioinformatics, WABI 2012, held in Ljubljana, Slovenia, in September 2012. WABI 2012 is one of six workshops which, along with the European Symposium on Algorithms (ESA), constitute the ALGO annual meeting and focuses on algorithmic advances in bioinformatics, computational biology, and systems biology with a particular emphasis on discrete algorithms and machine-learning methods that address important problems in molecular biology. The 35 full papers presented were carefully reviewed and selected from 92 submissions. The papers include algorithms for a variety of biological problems including phylogeny, DNA and RNA sequencing and analysis, protein structure, and others.

Book Detail :-
Title: Algorithms in Bioinformatics: 12th International Workshop, WABI 2012
Edition:
Author(s): Ben Raphael, Jijun Tang, edit by S. Istrail, P. Pevzner, and M. Waterman
Publisher: Springer-Verlag Berlin Heidelberg
Series:
Year: 2012
Pages: 465
Type: PDF
Language: English
ISBN: 9783642331220,364233122X,9783642331213,3642331211
Country: US
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About Author :- Ben Raphael is from Brown University, Department of Computer Science, P.O. Box 1910, Providence, RI 02912, USA, E-mail: braphael@cs.brown.edu. His research focuses on the design of combinatorial and statistical algorithms for the interpretation of biological data. Recent areas of emphasis include cancer evolution, network/pathway analysis of genetic variants, and structural variation in human and cancer genomes. His group’s algorithms have been used in multiple projects from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Jijun Tang is from University of South Carolina, Department of Computer Science and Engineering, 301 Main Street, Columbia, SC 29208, USA, E-mail: jtang@cse.sc.edu. Tang's research interests include computational biology and bioinformatics, machine learning and big data analysis, algorithm development and high performance computing, as well as computer gaming and scientific simulation.

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Book Contents :-
Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia written by Ben Raphael, Jijun Tang edited by S. Istrail, P. Pevzner, and M. Waterman . cover the following topics.
1. Preserving Inversion Phylogeny Reconstruction
2. Fast Phylogenetic Tree Reconstruction Using Locality-Sensitive Hashing
3. Efficient Computation of Popular Phylogenetic Tree Measures
4. SibJoin: A Fast Heuristic for Half-Sibling Reconstruction
5. Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models
6. Estimating Population Size via Line Graph Reconstruction
7. Extracting Conflict-Free Information from Multi-labeled Trees
8. Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs
9. An Optimal Reconciliation Algorithm for Gene Trees with Polytomies
10. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference
11. Anne-Muriel Arigon Chifolleau, Vincent Ranwez, and Vincent Berry RNA Tree Comparisons via Unrooted Unordered Alignments
12. Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots (Extended Abstract)
13. d-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data
14. CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population
15. Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters
16. Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches
17. Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes
18. Succinct de Bruijn Graphs
19. Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter
20. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly
21. MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing
22. How Accurately Can We Model Protein Structures with Dihedral Angles?
23. Resolving Spatial Inconsistencies in Chromosome Conformation Data
24. MS-DPR: An Algorithm for Computing Statistical Significance of Spectral Identifications of Non-linear Peptides
25. FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation
26. Lightweight LCP Construction for Next-Generation Sequencing Datasets
27. Sign Assignment Problems on Protein Networks
28. Sparse Learning Based Linear Coherent Bi-clustering
29. A Simplified View of DCJ-Indel Distance
30. DCJ-indel Distance with Distinct Operation Costs
31. Hidden Breakpoints in Genome Alignments
32. A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads
33. Tandem Halving Problems by DCJ
34. A Practical Approximation Algorithm for Solving Massive Instances of Hybridization Number
35. Distributed String Mining for High-Throughput Sequencing Data



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