Translational Bioinformatics in Healthcare and Medicine (Volume 13) (Advances in ubiquitous sensing applications for healthcare, Volume 13) PDF
Preview Translational Bioinformatics in Healthcare and Medicine (Volume 13) (Advances in ubiquitous sensing applications for healthcare, Volume 13)
ADVANCES IN UBIQUITOUS SENSING APPLICATIONS FOR HEALTHCARE 13 Translational Bioinformatics in Healthcare and Medicine Volume 13 Edited by Khalid Raza Assistant Professor, Department of Computer Science, Jamia Millia Islamia (Central University), India Nilanjan Dey Associate Professor, JIS University, Kolkata, India Series Editors Nilanjan Dey Amira S. Ashour Simon James Fong Academic PressisanimprintofElsevier 125London Wall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,Langford Lane,Kidlington,OxfordOX5 1GB,UnitedKingdom Copyright©2021ElsevierInc.Allrightsreserved. Nopart ofthispublicationmay bereproduced ortransmitted inanyform orbyanymeans, electronicor mechanical,including photocopying, recording,oranyinformation storageandretrieval system,withoutpermission inwritingfromthePublisher. Details onhowtoseek permission, furtherinformation aboutthePublisher’spermissions policiesandourarrangements with organizations suchastheCopyrightClearanceCenterandtheCopyrightLicensing Agency,canbefoundatourwebsite: www.elsevier.com/permissions. Thisbookandtheindividual contributionscontainedinitareprotected undercopyrightbythePublisher (otherthanasmay benotedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging. As newresearchandexperiencebroadenourunderstanding, changesinresearch methods,professional practices,ormedical treatmentmay becomenecessary. Practitionersandresearchers mustalwaysrelyontheir ownexperience andknowledgeinevaluatingandusingany information,methods,compounds,orexperiments describedherein. Inusingsuchinformation ormethodsthey shouldbe mindfuloftheirown safetyandthesafetyofothers,including partiesforwhom theyhaveaprofessional responsibility. Tothefullestextentofthelaw,neither thePublisher,northeauthors, contributors, oreditors,assume anyliabilityforany injuryand/ordamagetopersonsorpropertyasamatterofproductsliability,negligence orotherwise,or fromanyuseor operation ofanymethods,products, instructions,or ideascontainedinthematerialherein. LibraryofCongressCataloging-in-Publication Data Acatalogrecord forthisbook isavailablefromtheLibrary ofCongress BritishLibraryCataloguing-in-Publication Data Acataloguerecord forthisbook isavailablefromtheBritishLibrary ISBN:978-0-323-89824-9 Forinformation onallAcademic Presspublications visitourwebsite at https://www.elsevier.com/books-and-journals Publisher:StacyMasucci SeniorAcquisitions Editor: RafaelE.Teixeira SeniorEditorialProjectManager: SusanIkeda ProductionProjectManager:Niranjan Bhaskaran CoverDesigner: MatthewLimbert TypesetbyTNQTechnologies JamiaMilliaIslamia(CentralUniversity),NewDelhi(India),completed100yearsonOctober29,2020.Ontheoccasion of the centenary celebration, this volume is dedicated to all the founders, forefathers, teachers, researchers, students, staff, and other stakeholders of Jamia Millia Islamia for their selfless and valuable contributions. Contributors Kayode I. Adenuga, Faculty of Enterprise, Creative and Jaypee University of Information Technology, Wakna- Professional Studies, Farnborough College of Tech- ghat, Himachal Pradesh, India nology, Hampshire, United Kingdom E.J. Garba, Computer Science Department, Modibbo Nadia Ahmad, Department of Biotechnology and Bio- Adama University of Technology, Yola, Adamawa informatics, Jaypee University of Information Tech- State, Nigeria nology, Waknaghat, Himachal Pradesh, India A.B. Garko, Computer Science Department Federal Uni- Salim Ahmad, Department of Computer Science, Jamia versity Dutse, Jigawa State, Nigeria Millia Islamia, New Delhi, Delhi, India RajeshKumarGazara,LaboratóriodeQuímicaeFunção Naeem Ahmad, Department of Computer Applications, de Proteínas e Peptídeos, Centro de Biociências e Bio- Madanapalle Institute of Technology and Science, tecnologia,UniversidadeEstadualdoNorteFluminense Madanapalle, Andhra Pradesh, India DarcyRibeiro,CamposdosGoytacazes,RiodeJaneiro, Brazil Shaban Ahmad, Department of Computer Science, Jamia Millia Islamia, New Delhi, Delhi, India Arabinda Ghosh, Department of Botany, Guwahati Uni- versity, Assam, Guwahati, India Sarra Akermi, Annotations Analytics Pvt Ltd., Gurgaon, Haryana, India Yuzo Iano, School of Electrical Engineering and Com- puting (FEEC), State University of Campinas (UNI- Afroj Alam, Department of Computer Application, Inte- CAMP), Campinas, São Paulo, Brazil gral University, Lucknow, Uttar Pradesh, India Md Tauseef Alam, Department of Computer Science, Nor Syahidatul Nadiah Ismail, Faculty of Computing, Universiti Malaysia Pahang, Pekan, Pahang, Malaysia Jamia Millia Islamia, New Delhi, Delhi, India Rangel Arthur, Faculty of Technology (FT), State Uni- Sunil Jayant, Annotations Analytics Pvt Ltd., Gurgaon, Haryana, India versity of Campinas (UNICAMP), Limeira, São Paulo, Brazil Surabhi Johari, School of Biosciences Institute of Man- agementStudiesGhaziabad(UniversityCourses),Uttar Rejaul Karim Barbhuiya, National Council of Educa- Pradesh, India tional Research and Training, New Delhi, Delhi, India AnamBeg,DepartmentofComputerScience,JamiaMillia G.R. Karpagam, PSG College of Technology, Coimba- tore, Tamil Nadu, India Islamia, New Delhi, Delhi, India Rubina Chongtham, Department of Botany, Deshbandhu Fatima Nazish Khan, Department of Computer Science, Jamia Millia Islamia, New Delhi, Delhi, India College, University of Delhi, New Delhi, Delhi, India MohinikantiDas,DepartmentofBotany,CollegeofBasic Laxman Kumar, Department of Botany, Jamia Hamdard, New Delhi, Delhi, India Science&Humanities,OrissaUniversityofAgriculture and Technology, Bhubaneswar, Odisha, India Narendra Kumar, Department of Biotechnology and Bioinformatics, Jaypee University of Information Rutumbara Dash, School of Life Sciences, Sambalpur Technology, Waknaghat, Himachal Pradesh, India University, Burla, Odisha, India Reinaldo Padilha França, School of Electrical Engineer- Meet Kumari, Department of Electronics and Communi- cationEngineering,PunjabiUniversity,Patiala,Punjab, ing and Computing (FEEC), State University of Cam- India pinas (UNICAMP), Campinas, São Paulo, Brazil Ekta Gandotra, Department of Computer Science & Aina Umairah Mazlan, Faculty of Computing, Universiti Malaysia Pahang, Pekan, Pahang, Malaysia Engineering and Information Technology (CSE & IT), xi xii Contributors Piyus Mohanty, Department of Biotechnology and NoorAzidaSahabudin,FacultyofComputing,Universiti Bioinformatics, Jaypee University of Information Malaysia Pahang, Pekan, Pahang, Malaysia Technology, Waknaghat, Himachal Pradesh, India Abhishek Sahu, School of Life Sciences, Sambalpur Ana Carolina Borges Monteiro, School of Electrical University, Burla, Odisha, India Engineering and Computing (FEEC), State University Reecha Sharma, Department of Electronics and Commu- of Campinas (UNICAMP), Campinas, São Paulo, nication Engineering, Punjabi University, Patiala, Pun- Brazil jab, India L.J. Muhammad, Mathematics and Computer Science Ashwani Sharma, Computational Centre, Rennes, France Department, Federal University of Kashere, Gombe State, Nigeria Anu Sheetal, Department of Electronics and Communi- cation Engineering, Guru Nanak Dev University, Gur- N.D. Oye, Computer Science Department, Modibbo daspur, Punjab, India Adama University of Technology, Yola, Adamawa State, Nigeria Yengkhom Disco Singh, Department of Post Harvest Technology, College of Horticulture and Forestry, Manasa Kumar Panda, School of Life Sciences, Central Agricultural University, Pasighat, Arunachal Sambalpur University, Burla, Odisha, India; Environ- Pradesh, India ment & Sustainability Department, CSIR- IMMT, Bhubaneswar, Odisha, India Subrata Sinha, Centre for Biotechnology and Bio- informatics Dibrugarh University, Assam, Dibrugarh, Rafat Parveen, Department of Computer Science, Jamia India Millia Islamia, New Delhi, Delhi, India P. Sivakumar, PSG College of Technology, Coimbatore, Sahar Qazi, Department of Computer Science, Jamia Tamil Nadu, India Millia Islamia, New Delhi, Delhi, India S. Sridevi, PSG College of Technology, Coimbatore, Ayyagari Ramlal, Department of Botany, University of Tamil Nadu, India Delhi, New Delhi, Delhi, India Sandhya Verma, Shri Vaishnav Institute of Science, Shri Ismail Rashid, Computer Science Faculty, Bakhtar Uni- Vaishnav Vidyapeeth Vishwavidyalaya, Indore, Mad- versity, Kabul, Afghanistan hya Pradesh, India Khalid Raza, Department of Computer Science, Jamia B. Vinoth Kumar, PSG College of Technology, Coim- Millia Islamia, New Delhi, Delhi, India batore, Tamil Nadu, India Muhammad Akmal Remli, Institute for Artificial Intelli- S. Vishnuvardhan, PSG College of Technology, Coim- genceandBigData,UniversitiMalaysiaKelantan,Kota batore, Tamil Nadu, India Bharu, Kelantan, Malaysia; Data Science Department, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, G.M. Wajiga, Computer Science Department, Modibbo Adama University of Technology, Yola, Adamawa Malaysia State, Nigeria About the Editors KhalidRazaisanassistantprofessorattheDepartmentofComputerScience,JamiaMillia Islamia (Central University), New Delhi. Dr. Raza has been honored with “ICCR Chair Visiting Professor” by the Indian Council for Cultural Relation (ICCR), Ministry of For- eignAffairs,GovernmentofIndia,anddeputedatthefacultyofComputerandInformation Sciences, Ain Shams University, Cairo, Egypt. He has over 10years of teaching and research experience in the field of translational bioinformatics and computational intelli- gence applications in healthcare. He has contributed over 70 research articles in reputed journals and edited books. He has authored and edited books with reputed publishers. He has reviewed over 150 research articles for reputed journals and conferences in the last 5years. Dr. Raza has delivered several keynote addresses, invited talks, public lectures, and seminars in national and international conferences, workshops, and chaired technical sessionsatvariousconferences.Hehasservedasthetechnicalprogramcommitteemember of several international conferences and workshops. He has also executed two Indian government-fundedresearchprojects.Dr.Razaisamemberofseveralprofessionalbodies. His research interests include translational bioinformatics, computational intelligence methods, and applications in bioinformatics and health-informatics. Nilanjan Dey is an associate professor, Department of Computer Science and Engineer- ing, JIS University, Kolkata, India. He is a visiting fellow of the University of Reading, UK. He was an honorary visiting scientist at Global Biomedical Technologies, Inc., CA, USA (2012e15). He was awarded his PhD from Jadavpur University in 2015. He has authored and edited more than 70 books with Elsevier, Wiley, CRC Press, and Springer, andpublishedmorethan300papers.HeistheeditorinchiefoftheInternationalJournalof Ambient Computing and Intelligence, IGI Global, associated editor of IEEE Access, and International Journal of Information Technology, Springer. He is the series co-editor of Springer Tracts in Nature-Inspired Computing, Springer, series co-editor of Advances in Ubiquitous Sensing Applications for Healthcare, Elsevier, and series editor of Computa- tional Intelligence in Engineering Problem Solving and Intelligent Signal Processing and Data Analysis, CRC. His main research interests include medical imaging, machine learning, computer-aided diagnosis, data mining, etc. He is the Indian ambassador of the International Federation for Information Processing, Young ICT Group, and senior member of IEEE. xiii Preface Modernbiologicexperiments,includinghigh-throughputmeasurementtechniquessuchasnext-generationsequencingand microarraytechnologies,havegeneratedmassiveamountsofbiologicdata,givingrisetovariousbiologicdatabases.These databases are valuable resources and tools for various stakeholders including but not limited to biologists, clinicians, bioinformaticians, and healthcare professionals. Translational bioinformatics is an emerging field of studies that involves thedevelopmentofstorage,analytics,andsophisticatedcomputationalmethodstotransformvoluminousbiomedicaldata into proactive, predictive, preventative, and participatory healthcare. The final product of translation bioinformatics is newlydiscoveredknowledgethatcanbedisseminatedtoavarietyoffieldsincludinghealthcareandmedicine.Further,in theeraofinterdisciplinaryandmultidisciplinarysciences,suchasbio-informatics,chemo-informatics,health-informatics, viro-informatics,drug-informatics,andsoon,itisdifficultforthetargetaudiencetofindasingleresourcecoveringvarious aspects of informatics related to healthcare and medicine. Translational Bioinformatics in Healthcare and Medicine, part of the Advances in Ubiquitous Sensing Application for Healthcare series, offers a detailed overview of translational bioinformatics, translational medicine in healthcare, precision medicine and personalized treatment, IoT and blockchain applications in healthcare, clinical applications of biologic databases and electronic health records, translational bioinformatics in drug discovery, drug repurposing and cancerresearch,viro-informaticsandviraldiseasedatabases,machinelearningapplicationsintranslationalbioinformatics, and real-case applications of translational bioinformatics in healthcare and medicine. Thiseditedvolumecontains18chaptersthatbringtogethervariousaspectsoftranslationalbioinformaticsinhealthcare andmedicineandbundlethemasauniqueresourceofknowledge.Eachchapterisreviewedbytheeditorialboardforits originality,correctness,technicalstrength,presentationquality,interesttoreaders,andrelevancetothethemeofthebook. Itisnotonlyavaluableresourceforhealtheducators,clinicians,andhealthcareprofessionalsbutalsograduatestudentsof biology, biostatistics, biomedical sciences, bioinformatics, and interdisciplinary sciences. Khalid Raza Nilanjan Dey (Editors) xv Acknowledgments The editors and contributors are very thankful to all the anonymous reviewers for their valuable expert comments and suggestionson the chapters. Special thanks goto theserieseditors, editorial project manager,publication and production manager, and other editorial staff members of Elsevier for their necessary support despite the ongoing COVID-19 pandemic. xvii Chapter 1 Translational bioinformatics in healthcare: past, present, and future Sahar Qazi and Khalid Raza* DepartmentofComputerScience,JamiaMilliaIslamia,NewDelhi,Delhi,India *Correspondingauthor:E-mail:[email protected] Chapter outline 1. Introduction 1 5. Theroadahead:futureprospects 7 2. Originoftranslationalbioinformatics:abigleap 2 6. Conclusions 9 3. Scopeandapplications 4 Listofabbreviation 10 3.1. Pharmacogenomics 4 Acknowledgments 10 3.2. Omics-basedfields 5 References 10 4. Limitationswithbiologicdata:ethicalchallenges 7 1. Introduction Bioinformaticsisamultidisciplinaryfieldofsciencethatencapsulatesbiology,chemistry,physics,statistics,andcomputer science as base domains to solve complex biologic phenomenon. Bioinformatics is one of the magnanimously growing scientific fields that are very flexible. Thus, Nancy Lorenzi has defined bioinformatics as an “amoeba e without any definite shape or size.” The main purpose of bioinformatics is to store, analyze, and retrieve essential information about organisms that can in turn help understand the dynamics of such organisms. The term “bioinformatics” was coined by Paulien Hogeweg and Ben Hesper in 1970 (Hogeweg, 1978). Howbeit, the study of bioinformatics was initiated in the early1950sbytheleadingpioneerandfounderofbioinformaticsasasubject,MargaretOakleyDayhoff,alsoknownasthe “mother and father of bioinformatics.” Dayhoff worked in the application of mathematics and computational methods to the fields and applied them to biochemistry-based problems. She dexterously worked toward developing databases that stored vital information about the proteins and nucleic acids and also developed various tools for analysis (Hunt, 1983). Point/Percent Accepted Mutations (PAM) is one such substitution matrix devised by her to identify single (point) amino aciddisplacementintheprimarystructureorproteinsequencesacceptedbythenaturalselectionprocess.Thismatrixwas meanttoreducethesizeofthedatafilesdescribingtheaminoacidsequences(Pevsner,2009).Bioinformaticshaschanged its definition since the 1950s to the 1970s through 2000s. Today, bioinformatics is much more than a simple analysis of proteins and nucleic acid sequences. The basis of bioinformatics lies in the data provided and generated. The human body is made up of cells whose processing unit is DNA (deoxyribonucleic acid), which provides essential information about organisms and also aids in predictingtheriskofdiseasesinthefuture.Previously,biologicsequencedatawasretrievedbydoingtraditionalmethods ofsequencing,namelySanger’ssequencing,developedinthe1950swhereFredrickSangerfirstsequencedinsulinprotein. However, since it was a tedious process to compare multiple sequences manually, Dayhoff developed the first protein sequence database and published her books about the same (Eck and Dayhoff, 1966). Current sequencing technologies, includingNextGenerationSequencing(NGS)(RazaandAhmad,2019)andNanoporeSequencing(RazaandQazi,2019), have generated a large amount of data. Another pioneer in bioinformatics origin was Elvin A. Kabat, who executed 1 TranslationalBioinformaticsinHealthcareandMedicine.https://doi.org/10.1016/B978-0-323-89824-9.00001-X Copyright©2021ElsevierInc.Allrightsreserved.
The list of books you might like
