Table Of ContentADVANCES 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
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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
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