Table Of ContentIgnacio Rojas · Olga Valenzuela ·
Fernando Rojas · Luis Javier Herrera ·
Francisco Ortuño (Eds.)
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3 Bioinformatics and
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B Biomedical Engineering
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9th International Work-Conference, IWBBIO 2022
Maspalomas, Gran Canaria, Spain, June 27–30, 2022
Proceedings, Part I
123
Lecture Notes in Bioinformatics 13346
Subseries of Lecture Notes in Computer Science
SeriesEditors
SorinIstrail
BrownUniversity,Providence,RI,USA
PavelPevzner
UniversityofCalifornia,SanDiego,CA,USA
MichaelWaterman
UniversityofSouthernCalifornia,LosAngeles,CA,USA
EditorialBoardMembers
SørenBrunak
TechnicalUniversityofDenmark,KongensLyngby,Denmark
MikhailS.Gelfand
IITP,ResearchandTrainingCenteronBioinformatics,Moscow,Russia
ThomasLengauer
MaxPlanckInstituteforInformatics,Saarbrücken,Germany
SatoruMiyano
UniversityofTokyo,Tokyo,Japan
EugeneMyers
MaxPlanckInstituteofMolecularCellBiologyandGenetics,Dresden,Germany
Marie-FranceSagot
UniversitéLyon1,Villeurbanne,France
DavidSankoff
UniversityofOttawa,Ottawa,Canada
RonShamir
TelAvivUniversity,RamatAviv,TelAviv,Israel
TerrySpeed
WalterandElizaHallInstituteofMedicalResearch,Melbourne,VIC,Australia
MartinVingron
MaxPlanckInstituteforMolecularGenetics,Berlin,Germany
W.EricWong
UniversityofTexasatDallas,Richardson,TX,USA
Moreinformationaboutthissubseriesathttps://link.springer.com/bookseries/5381
· ·
Ignacio Rojas Olga Valenzuela
· ·
Fernando Rojas Luis Javier Herrera
Francisco Ortuño (Eds.)
Bioinformatics and
Biomedical Engineering
9th International Work-Conference, IWBBIO 2022
Maspalomas, Gran Canaria, Spain, June 27–30, 2022
Proceedings, Part I
Editors
IgnacioRojas OlgaValenzuela
UniversityofGranada FacultyofSciences
Granada,Spain UniversityofGranada
Granada,Spain
FernandoRojas
ETSIIT.CITIC-UGR LuisJavierHerrera
UniversityofGranada ETSIIT
Granada,Spain UniversityofGranada
Granada,Spain
FranciscoOrtuño
UniversityofGranada
Granada,Spain
ISSN 0302-9743 ISSN 1611-3349 (electronic)
LectureNotesinBioinformatics
ISBN 978-3-031-07703-6 ISBN 978-3-031-07704-3 (eBook)
https://doi.org/10.1007/978-3-031-07704-3
LNCSSublibrary:SL8–Bioinformatics
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Preface
We are proud to present the final set of accepted full papers for the 9th International
Work-ConferenceonBioinformaticsandBiomedicalEngineering(IWBBIO2022)held
inGranCanaria,Spain,duringJune27–30,2022.
IWBBIO seeks to provide a discussion forum for scientists, engineers, educators,
andstudentsaboutthelatestideasandrealizationsinthefoundations,theory,models,
and applications for interdisciplinary and multidisciplinary research encompassing
disciplines of computer science, mathematics, statistics, biology, bioinformatics, and
biomedicine.
TheaimofIWBBIO2022wastocreateafriendlyenvironmentthatcouldleadto
the establishment or strengthening of scientific collaborations and exchanges among
attendees,andthereforeIWBBIO2022solicitedhigh-qualityoriginalresearchpapers
(includingsignificantworkinprogress)onanyaspectofbioinformatics,biomedicine,
andbiomedicalengineering.
Submissions relating to new computational techniques and methods in machine
learning;datamining;textanalysis;patternrecognition;dataintegration;genomicsand
evolution;nextgenerationsequencingdata;proteinandRNAstructure;proteinfunction
and proteomics; medical informatics and translational bioinformatics; computational
systems biology; modeling and simulation; and their application in the life science
domain,biomedicine,andbiomedicalengineeringwereespeciallyencouraged.Thelist
of topics in the call for papers has also evolved, resulting in the following list for the
presentedition:
1. Computational proteomics. Analysis of protein-protein interactions. Protein
structuremodeling. Analysis ofprotein functionality. Quantitative proteomics and
PTMs.Clinicalproteomics.Proteinannotation.Datamininginproteomics.
2. Next generation sequencing and sequence analysis. De novo sequencing, re-
sequencing, and assembly. Expression estimation. Alternative splicing discovery.
Pathwayanalysis.Chip-seqandRNA-Seqanalysis.Metagenomics.SNPsprediction.
3. High performance in bioinformatics. Parallelization for biomedical analysis.
Biomedical and biological databases. Data mining and biological text processing.
Largescalebiomedicaldataintegration.Biologicalandmedicalontologies.Novel
architectureandtechnologies(GPU,P2P,Grid,etc)forbioinformatics.
4. Biomedicine.Biomedicalcomputing.Personalizedmedicine.Nanomedicine.Med-
icaleducation.Collaborativemedicine.Biomedicalsignalanalysis.Biomedicinein
industryandsociety.Electrotherapyandradiotherapy.
5. Biomedical engineering. E-computer-assisted surgery. Therapeutic engineering.
Interactive3Dmodelling.Clinicalengineering.Telemedicine.Biosensorsanddata
acquisition. Intelligent instrumentation. Patient monitoring. Biomedical robotics.
Bio-nanotechnology.Geneticengineering.
6. Computational systems for modelling biological processes. Inference of
biological networks. Machine learning in bioinformatics. Classification for
vi Preface
biomedicaldata.Microarraydataanalysis.Simulationandvisualizationofbiological
systems.Molecularevolutionandphylogeneticmodeling.
7. Healthcare and diseases. Computational support for clinical decisions. Image
visualizationandsignalanalysis.Diseasecontrolanddiagnosis.Genome-phenome
analysis.Biomarkeridentification.Drugdesign.Computationalimmunology.
8. E-health. E-health technology and devices. E-health information processing.
Telemedicine/E-health application and services. Medical image processing. Video
techniquesformedicalimages.IntegrationofclassicalmedicineandE-health.
9. COVID-19.Aspecialsessionanalyzingdifferentaspects,fieldsofapplication,and
technologiesthathavebeenappliedagainstCOVID-19.
Afteracarefulpeerreviewandevaluationprocess(eachsubmissionwasreviewedby
atleast2,andonaverage3.1,ProgramCommitteemembersoradditionalreviewers),75
paperswereaccepted,accordingtotherecommendationsofreviewersandtheauthors’
preferences,tobeincludedintheLNBIproceedings.
IWBBIO2022featuredseveralSpecialSessions,whichareaveryusefultoolinorder
tocomplementtheregularprogramwithnewandemergingtopicsofparticularinterest
for the participating community. Special Sessions that emphasized multidisciplinary
andtransversalaspects,aswellascutting-edgetopicswereespeciallyencouragedand
welcomed,andinthiseditionofIWBBIO2022thefollowingwerereceived:
– SS1. High-throughput Genomics: Bioinformatic Tools and Medical
Applications.
Genomicsisconcernedwiththesequencingandanalysisofanorganism’sgenome.It
isinvolvedintheunderstandingofhoweverysinglegenecanaffecttheentiregenome.
This goal is mainly afforded using the current, cost-effective, high-throughput
sequencing technologies. These technologies produce a huge amount of data that
usually require high-performance computing solutions and open new ways for the
studyofgenomics,aswellastranscriptomics,geneexpression,andsystemsbiology,
amongothers.Thecontinuousimprovementsandbroaderapplicationsofsequencing
technologiesareproducingacontinuousnewdemandforimprovedhigh-throughput
bioinformaticstools.
In this context, the generation, integration, and interpretation of genetic and
genomic data is driving a new era of healthcare and patient management. Medical
genomics (or genomic medicine) is an emerging discipline that involves the use of
genomic information about a patient as part of the clinical care with diagnostic or
therapeuticpurposestoimprovethehealthoutcomes.Moreover,itcanbeconsidered
a subset of precision medicine that has an impact in the fields of oncology, phar-
macology, rare and undiagnosed diseases, and infectious diseases. The aim of this
SpecialSessionwastobringtogetherresearchersinmedicine,genomics,andbioin-
formatics to translate medical genomics research into new diagnostic, therapeutic,
andpreventivemedicalapproaches.Therefore,weinvitedauthorstosubmitoriginal
research, new tools or pipelines, and update and review articles on relevant topics,
suchas(butnotlimitedto):
Preface vii
(cid:129) Toolsfordatapre-processing(qualitycontrolandfiltering)
(cid:129) Toolsforsequencemapping
(cid:129) Toolsforthecomparisonoftworeadlibrarieswithoutanexternalreference
(cid:129) Toolsforgenomicvariants(suchasvariantcallingorvariantannotation)
(cid:129) Tools for functional annotation: identification of domains, orthologues, genetic
markers,andcontrolledvocabulary(GO,KEGG,InterPro,etc.)
(cid:129) ToolsforgeneexpressionstudiesandtoolsforChip-Seqdata
(cid:129) Integrativeworkflowsandpipelines
Organizers:M.GonzaloClaros,DepartmentofMolecularBiologyandBiochemistry,
University of Málaga, Spain; Javier Pérez Florido, Bioinformatics Research Area,
Fundación Progreso y Salud, Seville, Spain; and Francisco M. Ortuño, Department
ofComputerArchitectureandTechnology,UniversityofGranada,Spain.
– SS2. Feature Selection, Extraction, and Data Mining in Bioinformatics:
Approaches,Methods,andAdaptations.
Variousapplicationsofbioinformatics,systembiology,andbiophysicsmeasurement
dataminingrequireproper,accurate,andprecisepreprocessingordatatransformation
beforetheanalysisitself.Here,themostimportantissuesarecoveredbythefeature
selection and extraction techniques to translate the raw data into the inputs for the
machinelearningandmultivariatestatisticalgorithms.Evenifthisisacomplextask,it
reducestheproblemdimensionality,byremovingredundantorirrelevantdata,without
affecting significantly the principal information. The methods and approaches are
oftenconditionedbythephysicalpropertiesofthemeasurementprocess,mathemat-
icallycongruentdescriptionandparameterization,andbiologicalaspectsofspecific
tasks.Withtheincreasingadoptionofartificialintelligencemethodstosolvebioinfor-
maticsproblems,itisnecessarytounderstandtheconditionalityofsuchalgorithms,
to choose and use the correct approach and avoid misinterpretations, artefacts, and
aliasingeffects.Theadoptionoftenusesexistingknowledgefromdifferentfields,and
directapplicationmightunderestimatetherequiredconditionsandcorrupttheanalysis
results.ThisSpecialSessionprovidedaforumtodicussthemultidisciplinaryover-
laps, development, implementation, and adoption of feature and selection methods
fordatasetswithabiologicalorigininordertosetupthepipelinefrommeasurement
design through signal processing to obtaining the results. The topic should cover
theoreticalquestions,practicalexamples,andresultsverifications.
Organizer: Jan Urban, Laboratory of Signal and Image Processing, Institute of
ComplexSystems,SouthBohemianResearchCenterofAquacultureandBiodiversity
ofHydrocenoses,FacultyofFisheriesandProtectionofWaters,UniversityofSouth
Bohemia,CzechRepublic.
– SS3.SmartHealthcareSolutionsforHandlingCOVID-19.
Smart healthcare plays an important role towards providing robust solutions,
especiallyforCOVID-19relatedproblems,bothlocallyandglobally.Collectionand
interpretation of data worldwide and systematic research helps in identifying the
potentialsolutionsaswellaspredictingthefutureissues.ThisSpecialSessionwas
viii Preface
organizedtoemphasizethepotentialproblemsandtherelatedsolutions,focusingon
thefollowingtopics:
(cid:129) Smartwearablehealthcare
(cid:129) Microbiologicalanalysis
(cid:129) Minimalinvasivesensors
(cid:129) Biomedicalwastemanagement
(cid:129) Drug-inducedtherapy
(cid:129) Earlypredictionanddiagnosis
(cid:129) Biostatisticaldrivensolution
(cid:129) ExplainableAIanddeeplearningdrivensolutions
Organizer: N.Sriraam, Department of Medical Electronics, M.S. Ramaiah Institute
ofTechnology,India.
– SS4.ComputationalSystemsforModelingofMedicalMicroSensors.
Medicalsensorsaremicrodevicescontainingseveralpartsmainlyincludingmicro-
tubes,micro-valves,biological/bodyfluids(blood,plasma,saliva,etc.),andchemical
materials(reagentsandothermaterials).Microfluidicsisaninterdisciplinaryfieldthat
involvesthescienceandtechnologyoffluidflowthroughsystemswithmicroscales.
Computationalsystemsandengineeringsimulationareessentialfromthestarttothe
endofthemedicalsensordesignanddevelopmentprocess.Themainadvantagesof
computational systems (AI, CFD, etc.) in medical sensors design and development
areasfollows:
(cid:129) Improvementandoptimizationofdesign
(cid:129) Accelerationinmedicaldeviceinnovation
(cid:129) Reductionofcostandfailurerisk
(cid:129) Reductionofproductiontimesandregulatoryapprovalprocesses
ThemainobjectivesofthisSpecialSessionwereasfollows:
(cid:129) Todeterminetheroleofcomputationalsystems(AI,CFD,etc.)inmedicalsensors
designanddevelopment
(cid:129) Todeterminetheroleofsimulationinoptimingtheanalysisprocessanddesignof
medicalmicro-sensors
(cid:129) To discuss the use of computational fluid dynamics (CFD) in analyzing medical
microsensors
(cid:129) To discuss the use of computational systems to combine engineering, biology,
chemical,andothercriteria
Organizers: Patrizia Piro and Behrouz Pirouz, Department of Civil Engineering,
UniversityofCalabria,Italy.
Itisimportanttonotethatforthesakeofconsistencyandreadabilitytheaccepted
papersareorganizaedinto15chaptersovertwovolumes,essentiallyfollowingthetopics
Preface ix
listincludedinthecallforpapers.Thefirstvolume(LNBI13346),entitled“Bioinfor-
maticsandBiomedicalEngineering.PartI”isdividedintoeightmainpartsandincludes
thecontributionson
1. BiomedicalComputing
2. BiomedicalEngineering
3. BiomedicalSignalAnalysis
4. Biomedicine.NewAdvancesandApplications
5. BiosensorsandDataAcquisition
6. ImageVisualizationandSignalAnalysisinBiomedicalApplications
7. ComputationalSupportforClinicalDecisions
8. COVID-19.BioinformaticsandBiomedicine
The second volume (LNBI 13347), entitled “Bioinformatics and Biomedical
Engineering. Part II” is divided into seven main parts and includes the contributions
on:
1. Chip-seqandRNA-SeqAnalysis
2. BioinformaticsandBiomarkerIdentication
3. ComputationalProteomics
4. ComputationalSystemsforModellingBiologicalProcesses
5. Feature Selection, Extraction, and Data Mining in Bioinformatics: Approaches,
Methods,andAdaptations
6. MachineLearninginBioinformatics
7. NextGenerationSequencingandSequenceAnalysis
This9theditionofIWBBIOwasorganizedbytheUniversityofGranada.Wewish
to thank our main sponsor as well as the Department of Computer Architecture and
Computer Technology at the University of Granada (CITIC-UGR) and International
SocietyforComputationalBiology(ISCB)fortheirsupportandgrants.Wealsowish
to thank the editors in charge of different international journals for their interest in
publishingspecialissuesofaselectionofthebestpapersofIWBBIO2022.Inthisedition
ofIWBBIOthereweretwoawards(bestcontributionawardandbestcontributionfrom
studentparticipant)sponsoredbytheEditorialOfficeofGenes,aMDPIjournal.
We would also like to express our gratitude to the members of the different
committees for their support, collaboration, and good work. We especially thank the
ProgramCommittee,thereviewers,andtheSpecialSessionorganizers.Wealsowantto
expressourgratitudetotheEasyChairplatform.Finally,wewishtothankSpringerfor
theircontinuoussupportandcooperation.
April2022 IgnacioRojas
OlgaValenzuela
FernandoRojas
LuisJavierHerrera
FranciscoOrtuño
