Advances in Intelligent Systems and Computing

Volume 803

Series editor

Janusz Kacprzyk, Polish Academy of Sciences, Warsaw, Polande-mail: kacprzyk@ibspan.waw.pl

The series “Advances in Intelligent Systems and Computing” contains publications on theory,applications, and design methods of Intelligent Systems and Intelligent Computing. Virtually alldisciplines such as engineering, natural sciences, computer and information science, ICT, economics,business, e-commerce, environment, healthcare, life science are covered. The list of topics spans all theareas of modern intelligent systems and computing such as: computational intelligence, soft computingincluding neural networks, fuzzy systems, evolutionary computing and the fusion of these paradigms,social intelligence, ambient intelligence, computational neuroscience, artificial life, virtual worlds andsociety, cognitive science and systems, Perception and Vision, DNA and immune based systems,self-organizing and adaptive systems, e-Learning and teaching, human-centered and human-centriccomputing, recommender systems, intelligent control, robotics and mechatronics includinghuman-machine teaming, knowledge-based paradigms, learning paradigms, machine ethics, intelligentdata analysis, knowledge management, intelligent agents, intelligent decision making and support,intelligent network security, trustmanagement, interactive entertainment,Web intelligence andmultimedia.

The publications within “Advances in Intelligent Systems and Computing” are primarily proceedingsof important conferences, symposia and congresses. They cover significant recent developments in thefield, both of a foundational and applicable character. An important characteristic feature of the series isthe short publication time and world-wide distribution. This permits a rapid and broad dissemination ofresearch results.

Advisory Board

Chairman

Nikhil R. Pal, Indian Statistical Institute, Kolkata, Indiae-mail: nikhil@isical.ac.in

Members

Rafael Bello Perez, Universidad Central “Marta Abreu” de Las Villas, Santa Clara, Cubae-mail: rbellop@uclv.edu.cu

Emilio S. Corchado, University of Salamanca, Salamanca, Spaine-mail: escorchado@usal.es

Hani Hagras, University of Essex, Colchester, UKe-mail: hani@essex.ac.uk

László T. Kóczy, Széchenyi István University, Győr, Hungarye-mail: koczy@sze.hu

Vladik Kreinovich, University of Texas at El Paso, El Paso, USAe-mail: vladik@utep.edu

Chin-Teng Lin, National Chiao Tung University, Hsinchu, Taiwane-mail: ctlin@mail.nctu.edu.tw

Jie Lu, University of Technology, Sydney, Australiae-mail: Jie.Lu@uts.edu.au

Patricia Melin, Tijuana Institute of Technology, Tijuana, Mexicoe-mail: epmelin@hafsamx.org

Nadia Nedjah, State University of Rio de Janeiro, Rio de Janeiro, Brazile-mail: nadia@eng.uerj.br

Ngoc Thanh Nguyen, Wroclaw University of Technology, Wroclaw, Polande-mail: Ngoc-Thanh.Nguyen@pwr.edu.pl

Jun Wang, The Chinese University of Hong Kong, Shatin, Hong Konge-mail: jwang@mae.cuhk.edu.hk

More information about this series at http://www.springer.com/series/11156

Florentino Fdez-RiverolaMohd Saberi Mohamad • Miguel RochaJuan F. De Paz • Pascual GonzálezEditors

Practical Applicationsof Computational Biologyand Bioinformatics,12th International Conference

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EditorsFlorentino Fdez-RiverolaEscuela Superior de Ingeniería InformáticaUniversidad de VigoOurense, Spain

Mohd Saberi MohamadFaculty of Computing, Departmentof Software Engineering

Universiti Teknologi MalaysiaJohor, Malaysia

Miguel RochaDepartment de InformáticaUniversidade do MinhoBraga, Portugal

Juan F. De PazDepartamento de Informática y Automática,Facultad de Ciencias

Universidad de SalamancaSalamanca, Spain

Pascual GonzálezDepartamento de Sistemas InformáticosUniversidad de Castilla-La ManchaAlbacete, AlbaceteSpain

ISSN 2194-5357 ISSN 2194-5365 (electronic)Advances in Intelligent Systems and ComputingISBN 978-3-319-98701-9 ISBN 978-3-319-98702-6 (eBook)https://doi.org/10.1007/978-3-319-98702-6

Library of Congress Control Number: 2018954643

© Springer Nature Switzerland AG 2019This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or partof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations,recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmissionor information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodology now known or hereafter developed.The use of general descriptive names, registered names, trademarks, service marks, etc. in thispublication does not imply, even in the absence of a specific statement, that such names are exempt fromthe relevant protective laws and regulations and therefore free for general use.The publisher, the authors, and the editors are safe to assume that the advice and information in thisbook are believed to be true and accurate at the date of publication. Neither the publisher nor theauthors or the editors give a warranty, express or implied, with respect to the material contained herein orfor any errors or omissions that may have been made. The publisher remains neutral with regard tojurisdictional claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature Switzerland AGThe registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

Next generation sequencing technologies, together with other emerging and quitediverse experimental techniques are evolving rapidly, creating numerous types ofomics data. These are creating new challenges for the expanding fields ofBioinformatics and Computational Biology, which seek to analyse, process,integrate and extract meaningful knowledge from these data. This calls for newalgorithms and approaches from fields such as Databases, Statistics, Data Mining,Machine Learning, Optimization, Computer Science, Machine Learning andArtificial Intelligence. Clearly, Biology is increasingly becoming a science ofinformation, requiring tools from the computational sciences. To address thesechallenges, we have seen the surge of a new generation of interdisciplinary sci-entists with a strong background in the biological and computational sciences.

The International Conference on Practical Applications of ComputationalBiology & Bioinformatics (PACBB) is an annual international meeting dedicated toemerging and challenging applied research in Bioinformatics and ComputationalBiology. Building on the success of previous events, the 12th edition of PACBBConference will be held on 20–22 June 2018 in the University of Castilla-LaMancha, Toledo (Spain). In this occasion, special issues will be published by theInterdisciplinary Sciences-Computational Life Sciences, Journal of IntegrativeBioinformatics, Neurocomputing, Knowledge and Information Systems: AnInternational Journal covering extended versions of selected articles.

This volume gathers the accepted contributions for the 12th edition of the PACBBConference after being reviewed by different reviewers, from an internationalcommittee from 13 countries. PACBB’18 technical program includes 26 papersspanning many different sub-fields in Bioinformatics and Computational Biology.

Therefore, this event will strongly promote the interaction of researchers fromdiverse fields and distinct international research groups. The scientific content willbe challenging and will promote the improvement of the valuable work that is beingcarried out by the participants. In addition, it will promote the education of youngscientists, in a post-graduate level, in an interdisciplinary field.

v

We would like to thank all the contributing authors and sponsors, as well as themembers of the Program Committee and the Organizing Committee for their hardand highly valuable work and support. Their effort has helped to contribute to thesuccess of the PACBB’18 event. PACBB’18 wouldn’t exist without yourassistance.

Mohd Saberi MohamadPACBB’18 Programme Co-chairs

Miguel P. RochaPACBB’18 Programme Co-chairs

Juan F. De PazPACBB’18 Programme Co-chairs

Florentino Fdez-RiverolaPACBB’18 Organizing Co-chairs

Pascual GonzálezPACBB’18 Organizing Co-chairs

vi Preface

Organization

General Co-chairs

Mohd Saberi Mohamad Universiti Malaysia Kelantan, MalaysiaMiguel Rocha University of Minho, PortugalJuan F. De Paz University of Salamanca, SpainFlorentino Fdez-Riverola University of Vigo, SpainPascual González University of Castilla-La Mancha, Spain

Program Committee

Alberto López University of Salamanca, SpainAlejandro F. Villaverde IIM-CSIC, SpainAlexandre Perera Lluna Universitat Politècnica de Catalunya, SpainAlfonso Rodriguez-Paton Universidad Politecnica de Madrid, SpainAlfredo Vellido Alcacena UPC, SpainAlicia Troncoso University Pablo de Olavide, SpainÁlvaro Lozano University of Salamanca, SpainAmin Shoukry Egypt-Japan University of Science

and Technology, EgyptAmparo Alonso University of A Coruña, SpainAna Cristina Braga University of Minho, PortugalAna Margarida Sousa University of Minho, PortugalAnália Lourenço University of Vigo, SpainAndré Sales University of Salamanca, SpainArmando Pinho Universty of Aveiro, PortugalBoris Brimkov Rice University, USACarlos A. C. Bastos University of Aveiro, PortugalCarole Bernon IRIT/UPS, France

vii

Carolyn Talcott Stanford University, USADaniel Glez-Peña University of Vigo, SpainDaniel Hernández University of Salamanca, SpainDavid Hoksza Charles University in Prague, Czech RepublicDavid Rodríguez Penas IIM-CSIC, SpainDiego M. Jiménez University of Salamanca, SpainEduardo Valente IPCB, SpainEva Lorenzo Iglesias University of Vigo, SpainFernanda Brito Correia University of Aveiro, PortugalFernando Diaz-Gómez University of Valladolid, SpainFilipe Liu University of Minho, PortugalFrancisco Couto University of Lisboa, PortugalGabriel Villarrubia University of Salamanca, SpainGael Pérez Rodríguez University of Vigo, SpainGiovani Librelotto Federal University of Santa Maria, BrasilGustavo Isaza University of Caldas, ColombiaGustavo Santos-García University of Salamanca, SpainHugo López-Fernández University of Vigo, SpainIsabel C. Rocha University of Minho, PortugalJavier Bajo Technical University of Madrid, SpainJavier Caridad University of Salamanca, SpainJavier De Las Rivas CSIC, SpainJavier Pérez University of Salamanca, SpainJoão Ferreira University of Lisboa, PortugalJoel P. Arrais DEI/CISUC University of Coimbra, PortugalJorge Vieira IBMC, Porto, PortugalJosé Antonio Castellanos

GarzónUniversity of Salamanca, Spain

José Luis Oliveira Universty of Aveiro, PortugalJosep Gómez Universitat Rovira i Virgili, SpainJuan Ramos University of Salamanca, SpainJulio R. Banga IIM-CSIC, SpainLoris Nanni University of Bologna, ItalyLourdes Borrajo Diz University of Vigo, SpainLucía Martín University of Salamanca, SpainLuis F. Castillo University of Caldas, ColombiaLuis M. Rocha Indiana University, USAMª Araceli Sanchís de Miguel University of Carlos III, SpainManuel Álvarez Díaz University of A Coruña, SpainMarcelo Maraschin Federal University of Santa Catarina,

Florianopolis, BrazilMarcos Martinez-Romero Stanford University, UKMaría Navarro University of Salamanca, SpainMaria Olivia Pereira IBB - CEB Centre of Biological Engineering,

Portugal

viii Organization

Martin Krallinger CNIO, SpainMartín Pérez-Pérez University of Vigo, SpainMasoud Daneshtalab University of Turku, FinlandMiguel Reboiro University of Vigo, SpainMohd Firdaus Raih National University of Malaysia, MalaysiaNarmer Galeano Cenicafé, ColombiaNuno F. Azevedo University of Porto, PortugalNuno Fonseca CRACS/INESC, Porto, PortugalOscar Dias CEB/IBB, Universidade do Minho, PortugalPatricia González University of A Coruña, Computer Architecture

Group (GAC), SpainPaula Jorge IBB - CEB Centre of Biological Engineering,

PortugalPedro G. Ferreira Ipatimup - Institute of Molecular Pathology

and Immunology of the University of Porto,Portugal

Pierpaolo Vittorini University of L’Aquila, ItalyRamón Doallo University of A Coruña, SpainRené Alquezar Mancho UPC, SpainRita Ascenso Polytecnic Institute of Leiria, PortugalRita Margarida Teixeira

AscensoESTG – IPL, Portugal

Rosalía Laza University of Vigo, SpainRui Camacho Universty of Porto, PortugalRuben Martín University of Salamanca, SpainSara C. Madeira IST/INESC ID, Lisbon, PortugalSérgio Deusdado Polytecnic Institute of Bragança, PortugalSergio Matos DETI/IEETA, PortugalThierry Lecroq Univeristy of Rouen, FranceTurki Turki King Abdulaziz University, Saudi ArabiaValentin Brimkov SUNY Buffalo State College, USAVera Afreixo University of Aveiro, PortugalYeray Mezquita University of Salamanca, SpainYingbo Cui National University of Defense Technology,

China

Organization ix

PACBB 2018 Sponsors

x Organization

Contents

A Hybrid of Simple Constrained Artificial Bee Colony Algorithmand Flux Balance Analysis for Enhancing Lactate and Succinatein Escherichia Coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Mei Kie Hon, Mohd Saberi Mohamad, Abdul Hakim Mohamed Salleh,Yee Wen Choon, Muhammad Akmal Remli, Mohd Arfian Ismail,Sigeru Omatu, and Juan Manuel Corchado

Parameter Estimation of Essential Amino Acids in Arabidopsisthaliana Using Hybrid of Bees Algorithm and Harmony Search . . . . . . 9Mei Yee Aw, Mohd Saberi Mohamad, Chuii Khim Chong, Safaai Deris,Muhammad Akmal Remli, Mohd Arfian Ismail, Juan Manuel Corchado,and Sigeru Omatu

In Silico Modeling and Simulation Approach for ApoptosisCaspase Pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Pedro Pablo González-Pérez and Maura Cárdenas-García

Molecular Dynamic Simulations Suggest that P152R MutationWithin MeCP2 Can Lead to Higher DNA Binding Affinityand Loss of Selective Binding to Methylated DNA . . . . . . . . . . . . . . . . . 27Dino Franklin

Impact of Genealogical Features in Transthyretin FamilialAmyloid Polyneuropathy Age of Onset Prediction . . . . . . . . . . . . . . . . . 35Maria Pedroto, Alípio Jorge, João Mendes-Moreira, and Teresa Coelho

Feature Selection and Polydispersity Characterizationfor QSPR Modelling: Predicting a Tensile Property . . . . . . . . . . . . . . . . 43Fiorella Cravero, Santiago Schustik, María Jimena Martínez,Carlos D. Barranco, Mónica F. Díaz, and Ignacio Ponzoni

xi

Methods of Creating Knowledge Graph by Linking BiologicalDatabases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Nazar Zaki, Chandana Tennakoon, Hany Al Ashwal,Alanoud Al Jaberi, and Amel Al Ameri

QSAR Modelling for Drug Discovery: Predicting the Activityof LRRK2 Inhibitors for Parkinson’s Disease UsingCheminformatics Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63Víctor Sebastián-Pérez, María J. Martínez, Carmen Gil,Nuria E. Campillo, Ana Martínez, and Ignacio Ponzoni

Improving the Use of Deep Convolutional Neural Networksfor the Prediction of Molecular Properties . . . . . . . . . . . . . . . . . . . . . . . 71Niclas Ståhl, Göran Falkman, Alexander Karlsson, Gunnar Mathiason,and Jonas Boström

An Analysis of Symmetric Words in Human DNA:Adjacent vs Non-adjacent Word Distances . . . . . . . . . . . . . . . . . . . . . . . 80Carlos A. C. Bastos, Vera Afreixo, João M. O. S. Rodrigues,and Armando J. Pinho

A Bioinformatics Protocol for Quickly Creating Large-ScalePhylogenetic Trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88Hugo López-Fernández, Pedro Duque, Sílvia Henriques, Noé Vázquez,Florentino Fdez-Riverola, Cristina P. Vieira, Miguel Reboiro-Jato,and Jorge Vieira

Deep Learning Analysis of Binding Behavior of Virus DisplayedPeptides to AuNPs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97Haebom Lee, Jun Jo, Yong Oh Lee, Korkmaz Zirpel Nuriye,and Leon Abelmann

Compression of Amino Acid Sequences . . . . . . . . . . . . . . . . . . . . . . . . . 105Diogo Pratas, Morteza Hosseini, and Armando J. Pinho

NET-ASAR: A Tool for DNA Sequence Search Basedon Data Compression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114Manuel Gaspar, Diogo Pratas, and Armando J. Pinho

Can an Integrative SNP Approach Substitute StandardIdentification in Comprehensive Case/Control Analyses? . . . . . . . . . . . . 123Anna Papiez, Marcin Skrzypski, Amelia Szymanowska-Narloch,Ewa Jassem, Agnieszka Maciejewska, Ryszard Pawlowski,Rafal Dziadziuszko, Jacek Jassem, Witold Rzyman, and Joanna Polanska

Simple Pattern-only Heuristics Lead to Fast Subgraph MatchingStrategies on Very Large Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131Antonino Aparo, Vincenzo Bonnici, Giovanni Micale, Alfredo Ferro,Dennis Shasha, Alfredo Pulvirenti, and Rosalba Giugno

xii Contents

In Silico Predictions for Fucoxanthin Production by the DiatomPhaeodactylum Tricornutum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139Claudia M. Bauer, Paulo Vilaça, Fernanda Ramlov,Eva Regina de Oliveira, Débora Q. Cabral, Caroline Schmitz,Rafaela Gordo Corrêa, Miguel Rocha, and Marcelo Maraschin

EvoPPI: A Web Application to Compare Protein-Protein Interactions(PPIs) from Different Databases and Species . . . . . . . . . . . . . . . . . . . . . 149Noé Vázquez, Sara Rocha, Hugo López-Fernández, André Torres,Rui Camacho, Florentino Fdez-Riverola, Jorge Vieira, Cristina P. Vieira,and Miguel Reboiro-Jato

A Review on Metabolomics Data Analysis for Cancer Applications . . . . 157Sara Cardoso, Delora Baptista, Rebeca Santos, and Miguel Rocha

A Framework for the Automatic Combination and Evaluationof Gene Selection Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166Bastien Grasnick, Cindy Perscheid, and Matthias Uflacker

Parallel Cellular Automaton Tumor Growth Model . . . . . . . . . . . . . . . . 175Alberto G. Salguero, Manuel I. Capel, and Antonio J. Tomeu

MOSCA: An Automated Pipeline for Integrated Metagenomicsand Metatranscriptomics Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 183João Carlos Sequeira, Miguel Rocha, Maria Madalena Alves,and Andreia Ferreira Salvador

Metabolite Integration Pipeline for the Improvement of HumanMetabolic Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192Vítor Vieira, Jorge Ferreira, Ruben Rodrigues, and Miguel Rocha

A Genetic Programming Approach Applied to Feature Selectionfrom Medical Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200José A. Castellanos-Garzón, Juan Ramos, Yeray Mezquita Martín,Juan F. de Paz, and Ernesto Costa

A DNA Sequence Corpus for Compression Benchmark . . . . . . . . . . . . . 208Diogo Pratas and Armando J. Pinho

17a-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulvalactuca (Chlorophyta) by 1H-NMR Spectroscopyand Bioinformatics Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216Debora Cabral, Sara Cardoso, Silvana Rocco, Maurício Sforça,Simone Fanan Hengeltraub, Cláudia Bauer, Miguel Rocha,and Marcelo Maraschin

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

Contents xiii