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1st INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY

AlCoB 2014

Tarragona, Spain

July 1-3, 2014

http://grammars.grlmc.com/alcob2014/

PROGRAM

Tuesday, July 1:

9:15 - 10:15 Registration

10:15 - 10:25 Opening

10:25 - 11:15 Michael Galperin: Comparative Genomics Approaches to Identifying Functionally Related Genes – Invited Lecture

11:15 - 11:45 Coffee Break

11:45 - 13:00 Liana Amaya Moreno, Ozlem Defterli, Armin Fügenschuh, Gerhard-Wilhelm Weber: Vester's Sensitivity Model for Genetic Networks with Time-Discrete Dynamics

Sebastian Wandelt, Ulf Leser: RRCA: Ultra-fast Multiple In-Species Genome Alignments

David A. Rosenblueth, Stalin Muñoz, Miguel Carrillo, Eugenio Azpeitia: Inference of Boolean Networks from Gene Interaction Graphs using a SAT Solver

13:00 - 14:30 Lunch

14:30 - 15:45 Laurent Lemarchand, Reinhardt Euler, Congping Lin, Imogen Sparkes: Modeling the Geometry of the Endoplasmic Reticulum Network

Sean Maxwell, Mark R. Chance, Mehmet Koyutürk: Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network

Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi, Ion Petre: On the Implementation of Quantitative Model Refinement

15:45 - 16:00 Break

16:00 - 16:50 Jason Papin: Network Analysis of Microbial Pathogens – Invited Lecture

Wednesday, July 2:

9:00 - 9:50 Uwe Ohler: Decoding Non-coding Regulatory Regions in DNA and RNA (I) – Invited Tutorial

9:50 - 10:00 Break

10:00 - 11:15 Dimitris Polychronopoulos, Anastasia Krithara, Christoforos Nikolaou, Giorgos Paliouras, Yannis Almirantis, George Giannakopoulos: Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures

Inken Wohlers, Mathilde Le Boudic-Jamin, Hristo Djidjev, Gunnar W. Klau, Rumen Andonov: Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric

Tomohiko Ohtsuki, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Testuo Shibuya, Masao Nagasaki: SVEM: A Structural Variant Estimation Method using Multi-Mapped Reads on Breakpoints

11:15 - 11:45 Coffee Break

11:45 - 13:00 Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo: Mapping-free and Assembly-free Discovery of Inversion Breakpoints from Raw NGS Reads

Giuseppe Narzisi, Bud Mishra, Michael C. Schatz: On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

Ivo Hedtke, Ioana Lemnian, Matthias Müller-Hannemann, Ivo Grosse: On Optimal Read Trimming in Next Generation Sequencing and Its Complexity

13:00 - 14:30 Lunch

14:30 - 15:20 Annie Chateau, Rodolphe Giroudeau: Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem

Ernst Althaus, Andreas Hildebrandt, Anna Katharina Hildebrandt: A Greedy Algorithm for Hierarchical Complete Linkage Clustering

15:30 Visit of the City

Thursday, July 3:

9:00 - 9:50 Uwe Ohler: Decoding Non-coding Regulatory Regions in DNA and RNA (II) – Invited Tutorial

9:50 - 10:00 Break

10:00 - 11:15 Carla Negri Lintzmayer, Zanoni Dias: On Sorting of Signed Permutations by Prefix and Suffix Reversals and Transpositions

Thiago da Silva Arruda, Ulisses Dias, Zanoni Dias: Heuristics for the Sorting by Length-Weighted Inversions Problem on Signed Permutations

Alexander Grigoriev, Steven Kelk, Nela Lekić: On Low Treewidth Graphs and Supertrees

11:15 - 11:45 Coffee Break

11:45 - 13:00 Carla Negri Lintzmayer, Zanoni Dias: On the Diameter of Rearrangement Problems

Amina Noor, Aitzaz Ahmad, Bilal Wajid, Erchin Serpedin, Mohamed Nounou, Hazem Nounou: A Closed-Form Solution for Transcription Factor Activity Estimation using Network Component Analysis

Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata, Yukuto Sato, Yosuke Kawai, Masao Nagasaki: HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Informative Reads

13:00 Closing