Ebook: 7th International Conference on Practical Applications of Computational Biology & Bioinformatics

The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.

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The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.

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The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.

Content:
Front Matter....Pages 1-10
Gene Functional Prediction Using Clustering Methods for the Analysis of Tomato Microarray Data....Pages 1-6
Analysis of Word Symmetries in Human Genomes Using Next-Generation Sequencing Data....Pages 7-13
A Clustering Framework Applied to DNA Microarray Data....Pages 15-22
Segmentation of DNA into Coding and Noncoding Regions Based on Inter-STOP Symbols Distances....Pages 23-28
Assignment of Novel Functions to Helicobacter pylori 26695’s Genome....Pages 29-36
Analysing Quality Measures of Phasing Algorithms in Genome-Wide Haplotyping....Pages 37-44
Search Functional Annotations Genetic Relationships of Coffee through Bio2RDF....Pages 45-51
A Cellular Automaton Model of the Effects of Maspin on Cell Migration....Pages 53-60
Quantitative Characterization of Protein Networks of the Oral Cavity....Pages 61-68
Analysing Relevant Diseases from Iberian Tweets....Pages 69-76
Optimized Workflow for the Healthcare Logistic: Case of the Pediatric Emergency Department....Pages 77-84
Boosting the Detection of Transposable Elements Using Machine Learning....Pages 85-91
On an Individual-Based Model for Infectious Disease Outbreaks....Pages 93-100
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools....Pages 101-109
HaptreeBuilder: Web Generation and Visualization of Risk Haplotype Trees....Pages 111-117
Speeding Up Phylogenetic Model Checking....Pages 119-126
Comp2ROC....Pages 127-135
Network Visualization Tools to Enhance Metabolic Engineering Platforms....Pages 137-144
A Workflow for the Application of Biclustering to Mass Spectrometry Data....Pages 145-153
Back Matter....Pages 155-156

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The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.

Content:
Front Matter....Pages 1-10
Gene Functional Prediction Using Clustering Methods for the Analysis of Tomato Microarray Data....Pages 1-6
Analysis of Word Symmetries in Human Genomes Using Next-Generation Sequencing Data....Pages 7-13
A Clustering Framework Applied to DNA Microarray Data....Pages 15-22
Segmentation of DNA into Coding and Noncoding Regions Based on Inter-STOP Symbols Distances....Pages 23-28
Assignment of Novel Functions to Helicobacter pylori 26695’s Genome....Pages 29-36
Analysing Quality Measures of Phasing Algorithms in Genome-Wide Haplotyping....Pages 37-44
Search Functional Annotations Genetic Relationships of Coffee through Bio2RDF....Pages 45-51
A Cellular Automaton Model of the Effects of Maspin on Cell Migration....Pages 53-60
Quantitative Characterization of Protein Networks of the Oral Cavity....Pages 61-68
Analysing Relevant Diseases from Iberian Tweets....Pages 69-76
Optimized Workflow for the Healthcare Logistic: Case of the Pediatric Emergency Department....Pages 77-84
Boosting the Detection of Transposable Elements Using Machine Learning....Pages 85-91
On an Individual-Based Model for Infectious Disease Outbreaks....Pages 93-100
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools....Pages 101-109
HaptreeBuilder: Web Generation and Visualization of Risk Haplotype Trees....Pages 111-117
Speeding Up Phylogenetic Model Checking....Pages 119-126
Comp2ROC....Pages 127-135
Network Visualization Tools to Enhance Metabolic Engineering Platforms....Pages 137-144
A Workflow for the Application of Biclustering to Mass Spectrometry Data....Pages 145-153
Back Matter....Pages 155-156
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