Bioinformatics and Biomedical Engineering: Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015, Proceedings, Part I

710 Pages·2015·43.107 MB·English

by  Francisco Ortuño, Ignacio Rojas (eds.)

Francisco Ortuño
Ignacio Rojas (Eds.)
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Bioinformatics and
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Third International Conference, IWBBIO 2015
Granada, Spain, April 15–17, 2015
Proceedings, Part I
123
Lecture Notes in Bioinformatics 9043
Subseries of Lecture Notes in Computer Science
LNBISeriesEditors
SorinIstrail
BrownUniversity,Providence,RI,USA
PavelPevzner
UniversityofCalifornia,SanDiego,CA,USA
MichaelWaterman
UniversityofSouthernCalifornia,LosAngeles,CA,USA
LNBIEditorialBoard
AlbertoApostolico
GeorgiaInstituteofTechnology,Atlanta,GA,USA
SørenBrunak
TechnicalUniversityofDenmarkKongensLyngby,Denmark
MikhailS.Gelfand
IITP,ResearchandTrainingCenteronBioinformatics,Moscow,Russia
ThomasLengauer
MaxPlanckInstituteforInformatics,Saarbrücken,Germany
SatoruMiyano
UniversityofTokyo,Japan
EugeneMyers
MaxPlanckInstituteofMolecularCellBiologyandGenetics
Dresden,Germany
Marie-FranceSagot
UniversitéLyon1,Villeurbanne,France
DavidSankoff
UniversityofOttawa,Canada
RonShamir
TelAvivUniversity,RamatAviv,TelAviv,Israel
TerrySpeed
WalterandElizaHallInstituteofMedicalResearch
Melbourne,VIC,Australia
MartinVingron
MaxPlanckInstituteforMolecularGenetics,Berlin,Germany
W.EricWong
UniversityofTexasatDallas,Richardson,TX,USA
Francisco Ortuño Ignacio Rojas (Eds.)
Bioinformatics and
Biomedical Engineering
Third International Conference, IWBBIO 2015
Granada, Spain, April 15-17, 2015
Proceedings, Part I
1 3
VolumeEditors
FranciscoOrtuño
IgnacioRojas
UniversidaddeGranada
Dpto.deArquitecturayTecnologíadeComputadores(ATC)
E.T.S.deIngenieríasenInformáticayTelecomunicación,CITIC-UGR
Granada,Spain
E-mail:{fortuno,irojas}@ugr.es
ISSN0302-9743 e-ISSN1611-3349
ISBN978-3-319-16482-3 e-ISBN978-3-319-16483-0
DOI10.1007/978-3-319-16483-0
SpringerChamHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2015934926
LNCSSublibrary:SL8–Bioinformatics
©SpringerInternationalPublishingSwitzerland2015
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Preface
Weareproudtopresentthesetoffinalacceptedfull papersforthethirdedition
of the IWBBIO conference “International Work-Conference on Bioinformatics
andBiomedicalEngineering”heldinGranada(Spain)duringApril15–17,2015.
The IWBBIO 2015 (International Work-Conference on Bioinformatics and
Biomedical Engineering) seeks to provide a discussion forum for scientists, en-
gineers, educators, and students about the latest ideas and realizations in the
foundations, theory, models, andapplications for interdisciplinaryandmultidis-
ciplinary research encompassing disciplines of computer science, mathematics,
statistics, biology, bioinformatics, and biomedicine.
The aims of IWBBIO 2015 is to create a friendly environment that could
lead to the establishment or strengthening of scientific collaborations and ex-
changes among attendees, and therefore, IWBBIO 2015 solicited high-quality
original research papers (including significant work-in-progress) on any aspect
of Bioinformatics, Biomedicine, and Biomedical Engineering.
New computational techniques and methods in machine learning; data min-
ing;textanalysis;patternrecognition;dataintegration;genomicsandevolution;
next generation sequencing data; protein and RNA structure; protein function
and proteomics; medical informatics and translational bioinformatics; compu-
tational systems biology; modeling and simulation and their application in life
sciencedomain,biomedicine,andbiomedicalengineeringwereespeciallyencour-
aged.ThelistoftopicsinthesuccessiveCallforPapershasalsoevolved,resulting
in the following list for the present edition:
1. Computationalproteomics.Analysisofprotein–proteininteractions.Pro-
tein structure modeling. Analysis of proteinfunctionality. Quantitative pro-
teomicsandPTMs.Clinicalproteomics.Proteinannotation.Dataminingin
proteomics.
2. Next generation sequencing and sequence analysis.Denovosequenc-
ing, re-sequencing, and assembly. Expression estimation. Alternative splic-
ing discovery. Pathway Analysis. Chip-seq and RNA-Seq analysis. Metage-
nomics. SNPs prediction.
3. HighperformanceinBioinformatics.Parallelizationforbiomedicalanal-
ysis. Biomedical and biological databases. Data mining and biological text
processing. Large-scale biomedical data integration. Biological and medi-
cal ontologies. Novel architecture and technologies (GPU, P2P, Grid,...) for
Bioinformatics.
4. Biomedicine.BiomedicalComputing.Personalizedmedicine.Nanomedicine.
Medical education. Collaborative medicine. Biomedical signal analysis.
Biomedicine in industry and society. Electrotherapyand radiotherapy.
5. Biomedical Engineering. Computer-assisted surgery. Therapeutic
engineering. Interactive 3D modeling. Clinical engineering. Telemedicine.
VI Preface
Biosensors and data acquisition. Intelligent instrumentation. Patient Moni-
toring. Biomedical robotics. Bio-nanotechnology.Genetic engineering.
6. Computational systems for modeling biological processes.Inference
ofbiologicalnetworks.MachinelearninginBioinformatics.Classificationfor
biomedical data. MicroarrayData Analysis. Simulation and visualization of
biological systems. Molecular evolution and phylogenetic modeling.
7. Healthcare and diseases. Computational support for clinical decisions.
Image visualization and signal analysis. Disease control and diagnosis.
Genome-phenome analysis. Biomarker identification. Drug design. Compu-
tational immunology.
8. E-Health.E-Healthtechnologyanddevices. E-Healthinformationprocess-
ing.Telemedicine/E-Healthapplicationandservices.MedicalImageProcess-
ing. Video techniques for medical images. Integration of classical medicine
and E-Health.
After acarefulpeerreviewandevaluationprocess(268submissionweresub-
mitted and each submission was reviewed by at least 2, and on the average
2.7, Program Committee members or Additional Reviewer), 134 papers were
accepted to be included in LNBI proceedings.
During IWBBIO 2015 several Special Sessions will be carried out. Special
Sessions will be a very useful tool to complement the regular program with
new and emerging topics of particular interest for the participating community.
Special Sessions that emphasizeon multidisciplinaryand transversalaspects, as
well as cutting-edge topics are especially encouraged and welcome, and in this
edition of IWBBIO 2015 are the following:
1. SS1:ExpandingConceptofChaperoneTherapyforInheritedBrain
Diseases
Chaperonetherapyisanewconceptofmoleculartherapeuticapproach,first
developed for lysosomal diseases, utilizing small molecular competitive in-
hibitors of lysosomal enzymes. This concept has been gradually targeted to
manydiseasesofothercategories,utilizingvariouscompounds notnecessar-
ily competitive inhibitorsbut alsonon-competitiveinhibitorsorendogenous
protein chaperones (heat-shock proteins).
Inthissession,wediscusscurrenttrendsofchaperonetherapytargetingvar-
ioustypes ofneurologicalandnon-neurologicaldiseasescausedbymisfolded
mutant proteins. This molecular approachwill opena new therapeutic view
for a wide variety of diseases, genetic and non-genetic, and neurologicaland
non-neurological,in the near future.
Organizer: Dr. Prof. Yaping Tian, Department of Clinical Bio-
chemistry, Chinese PLA General Hospital, Beijing (China).
2. SS2:Quantitative and SystemsPharmacology:Thinkinginawider
”systems-level”context accelerates drug discovery and enlightens
our understanding of drug action
“Quantitative and Systems Pharmacology (QSP) is an emerging discipline
focused on identifying and validating drug targets, understanding existing
Preface VII
therapeuticsanddiscoveringnewones.ThegoalofQSPistounderstand,in
a precise,predictivemanner,how drugsmodulatecellularnetworksin space
andtimeandhowtheyimpacthumanpathophysiology.”(QSPWhitePaper
- October, 2011)
Over the past three decades, the predominant paradigm in drug discovery
was designing selective ligands for a specific target to avoid unwanted side
effects. However, in the current postgenomic era, the aim is to design drugs
that perturb biological networks rather than individual targets. The chal-
lenge is to be able to consider the complexity of physiological responses to
treatmentsatveryearlystagesofthedrugdevelopment.Inthisway,current
effort has been put into combining 0 chemogenomics with network biology
to implementnew network-pharmacologyapproachestodrugdiscovery;i.e.,
polypharmacology approaches combined with systems biology information,
which advance further in both improving efficacy and predicting unwanted
off-target effects. Furthermore, the use of network biology to understand
drug action outputs treasured information, i.e., for pharmaceutical compa-
nies, such as alternative therapeutic indications for approved drugs, asso-
ciations between proteins and drug side effects, drug–drug interactions, or
pathways, and gene associations which provide leads for new drug targets
that may drive drug development.
Following the line of QSP Workshops I and II (2008, 2010), the QSP White
Paper (2011), or QSP Pittsburgh Workshop (2013), the goal of this sym-
posium is to bring together interdisciplinary experts to help advance the
understanding of how drugs act, with regard to their beneficial and toxic
effects, by sharing new integrative, systems-basedcomputational, or experi-
mental approaches/tools/ideas which allow to increase the probability that
the newly discovered drugs will prove therapeutically beneficial, together
with a reduction in the risk of serious adverse events.
Organizer: Violeta I. Perez-Nueno, Ph.D., Senior Scientist, Har-
monic Pharma, Nancy (France).
3. SS3: Hidden Markov Model (HMM) for Biological Sequence Mod-
eling Sequence Modeling is one of the most important problems in bioin-
formatics. In the sequential data modeling, Hidden MarkovModels(HMMs)
have been widely used to find similarity between sequences. Some of the
most important topics in this session are:
(a) Modeling of biological sequences in bioinformatics;
(b) The application of Hidden Markov Models(HMM);
(c) HMM in modeling of sequential data;
(d) The advantages of HMM in biological sequence modeling compared to
other algorithms;
(e) The new algorithms of training HMM;
(f) Gene sequence modeling with HMM;
Organizer:MohammadSoruri,DepartmentofElectricaland Com-
puter Engineering, University of Birjand, Birjand (Iran).
VIII Preface
4. SS4: Advances in Computational Intelligence for Bioinformatics
and Biomedicine Biomedicine and, particularly, Bioinformatics are in-
creasingly and rapidly becoming data-based sciences, an evolution driven
by technological advances in image and signal non-invasive data acquisition
(exemplified by the 2014 Nobel Prize in Chemistry for the development of
super-resolved fluorescence microscopy). In the Biomedical field, the large
amount of data generated from a wide range of devices and patients is cre-
ating challenging scenarios for researchers, related to storing, processing,
and even just transferring information in its electronic form, all these com-
poundedbyprivacyandanonymitylegalissues.Thiscanequallybeextended
to Bioinformatics, with the burgeoning of the .omics sciences.
New data requirements require new approaches to data analysis, some of
the most interesting ones are currently stemming from the fields of Com-
putational Intelligence (CI) and Machine Learning (ML). This session is
particularly interested in the proposal of novel CI and ML approaches to
problems in the biomedical and bioinformatics domains.
Topics that are of interest in this session include (but are not necessarily
limited to):
(a) Novel applications of existing CI and ML methods to biomedicine and
bioinformatics.
(b) Novel CI and ML techniques for biomedicine and bioinformatics.
(c) CI andML-basedmethods toimprovemodelinterpretabilityinbiomed-
ical problems, including data/model visualization techniques.
(d) NovelCI andML techniques fordealing withnonstructuredandhetero-
geneous data formats.
More information at
http://www.cs.upc.edu/ avellido/research/conferences/
IWBBIO15-CI-BioInfMed.html
Main Organizer: Alfredo Vellido, PhD, Department of Computer
Science, Universitat Polit´ecnica de Catalunya, BarcelonaTECH
(UPC), Barcelona (Spain).
Co-organizers: Jesus Giraldo, PhD, Institut de Neuroci`encies and
Unitat de Bioestad´ıstica, Universitat Auto`noma de Barcelona
(UAB), Cerdanyola del Vall`es, Barcelona (Spain).
Ren´e Alqu´ezar, PhD, Department of Computer Science, Universi-
tat Polit´ecnica de Catalunya, BarcelonaTECH (UPC), Barcelona
(Spain).
5. SS5: Tools for Next Generation Sequencing data analysisNextGen-
eration Sequencing (NGS) is the main term used to describe a number of
different modern sequencing technologies such as Illumina, Roche 454 Se-
quencing, Ion torrent, SOLiD sequencing, and Pacific Biosciences. These
technologies allow us to sequence DNA and RNA more quickly and cheaply
thanSangersequencingandhaveopenednewwaysforthestudyofgenomics,
transcriptomics, and molecular biology, among others.
Preface IX
Thecontinuousimprovementsonthosetechnologies(longerreadlength,bet-
terreadquality,greaterthroughput,etc.),andthebroadapplicationofNGS
in several research fields, have produced (and still produce) a huge amount
of software tools for the analysis of NGS genomic/transcriptomicdata.
We invite authors to submit original research, pipelines, and review articles
on topics related to software tools for NGS data analysis such as (but not
limited to):
(a) Tools for data preprocessing (quality control and filtering).
(b) Tools for sequence alignment.
(c) Tools for de novo assembly.
(d) Tools for the analysis of genomic data: identification and annotation of
genomic variants (variant calling, variant annotation).
(e) Tools for functional annotationto describe domains, orthologs,genomic
variants, controlled vocabulary (GO, KEGG, InterPro...).
(f) Toolsfortheanalysisoftranscriptomicdata:RNA-Seqdata(quantifica-
tion,normalization,filtering,differentialexpression)andtranscriptsand
isoforms finding.
(g) Tools for Chip-Seq data.
(h) Tools for“big-data”analysis of reads and assembled reads.
Organizers: Javier Perez Florido, PhD, Genomics and Bioinfor-
matics Platform of Andalusia (GBPA), Seville, (Spain).
Antonio Rueda Martin, Genomics and Bioinformatics Platform of
Andalusia (GBPA), Seville, (Spain).
M. Gonzalo Claros Diaz, PhD, Department of Molecular Biology
and Biochemistry, University of Malaga (Spain).
6. SS6: Dynamics Networks in System Medicine
Over the past two decades, It Is Increasingly Recognized that a biological
function can only rarely be attributed to an individual molecule. Instead,
most biological functions arise from signaling and regulatory pathways con-
necting many constituents, such as proteins and small molecules, allowing
them to adapt to environmental changes.“Following on from this principle,
a diseasephenotype is rarelyaconsequenceof anabnormalityina single ef-
fectorgeneproduct,butreflectsvariousprocessesthatinteractinacomplex
network.”Offering a unifying language to describe relations within such a
complex system has made network science a central component of systems
biologyandrecentlysystemmedicine.Despite the knowledgethatbiological
networks can change with time and environment, much of the efforts have
takenastaticview.Time-varyingnetworkssupportricherdynamicsandmay
better reflectunderlying biologicalchangesin abnormalstate versusnormal
state and this provides a powerful motivation and application domain for
computational modeling. We introduce this session on the Dynamics Net-
works in System Medicine to encourage and support the development of
computational methods that elucidate the Dynamics Networks and its ap-
plicationinmedicine.Wewilldiscusscurrenttrendsandpotentialbiological
andclinicalapplicationsofnetwork-basedapproachesto humandisease.We
X Preface
aim to bring together experts in different fields in order to promote cross
fertilization between different communities.
Organizer:NarsisAftabKiani,PhD,ComputationalMedicineUnit,
Department of Medicine, Karolinska Institute (Sweden).
7. SS7: Interdisciplinary puzzles of measurements in biological
systems
Natural sciences demand measurements of the subject of interest as a nec-
essarypartof the experimental process.Thus, for the proper understanding
of the obtained datasets, it is the necessity to take into question all math-
ematical, biological, chemical, or technical conditions affecting the process
of the measurement itself. While assumptions and recommendations within
the field itself are usually concerned, some issues, especially discretization,
quantization,experimenttime, self-organization,andconsequentanomalous
statistics might cause puzzling behavior.
Inthisspecialsectionwedescribeparticularexamplesacrossdisciplineswith
joint systems theory-based approach, including noise and baseline filtration
inmassspectrometry,imageprocessingandanalysis,anddistributedknowl-
edge database. The aim of this section is to present a general overview of
the systemic approach.
Organizer: Jan Urban, PhD, Laboratory of Signal and Image
Processing, Institute of Complex Systems, Faculty of Fisheries
and protection of Waters, University of South Bohemia. (Czech
republic).
8. SS8: Biological Networks: Insight from interactions
The complete sequencing of the human genome has shown us a new era of
SystemsBiology(SB)referredtoasomics.Fromgenomicstoproteomicsand
furthermore,“Omics”-es existing nowadays integrate many areas of biology.
This resulted in an essential ascent from Bioinformatics to Systems Biology
leaving room for identifying the number of interactions in a cell. Tools have
been developed to utilize evolutionary relationships toward understanding
uncharacterized proteins, while there is a need to generate and understand
functional interaction networks. A systematic understanding of genes and
proteins in a regulatory network has resulted in the birth of Systems Biol-
ogy (SB), there-by raising several unanswered questions. Through this con-
ference,wewillraisesomequestionsonwhyandhowinteractions,especially
protein–protein interactions (PPI), are useful while discussing methods to
removefalsepositivesbyvalidatingthedata.Theconferenceisaimedatthe
following two focal themes:
(a) Bioinformaticsandsystemsbiologyfordecipheringtheknown–unknown
regions.
(b) Systems Biology of regulatory networks and machine learning.
Organizers:Prof. AlfredoBenso,PhD, Department of Controland
Computer Engineering, Politecnico di Torino (Italy).
Dr. Prashanth Suravajhala, PhD, Founder of Bioclues.org and Di-
rector of Bioinformatics.org