Translational bioinformatics in healthcare: past, present, and future

Abstract Back in 2003, chemists, biologists, statisticians, and computational scientists came together on one platform and brought out the entire human genome, known as The Human Genome Project. The completion of the project not only provided genomic data but also led to the formation of many new branches. Bioinformatics is like an ameba: it does not have any specific shape or size. It has grown from simple genomic analysis and expanded itself to omics-based analysis, drug designing and discovery, network biology, expression analysis, epigenetics, immunology, cheminformatics, and so on. This chapter highlights the trend change from the germination of bioinformatics to its growth in various domains of biologic, chemical, physical, and computational sciences, making it translational bioinformatics. The purpose of this chapter is to systematically introduce fundamental concepts of translational bioinformatics, its scope, and applications in healthcare, ethical issues related to the use of personal genome in healthcare, and its future perspectives for better healthcare management.

[1]  W. Bush,et al.  Bridging the Gaps in Personalized Medicine Value Assessment: A Review of the Need for Outcome Metrics across Stakeholders and Scientific Disciplines , 2019, Public Health Genomics.

[2]  Khalid Raza,et al.  Smart biosensors for an efficient point of care (PoC) health management , 2020 .

[3]  Sahar Qazi,et al.  In silico library design, screening and MD simulation of COX-2 inhibitors for anticancer activity , 2020 .

[4]  R. Altman Translational Bioinformatics: Linking the Molecular World to the Clinical World , 2012, Clinical pharmacology and therapeutics.

[5]  Khalid Raza,et al.  Clustering analysis of cancerous microarray data , 2014 .

[6]  Lucila Ohno-Machado,et al.  Translational bioinformatics: linking knowledge across biological and clinical realms , 2011, J. Am. Medical Informatics Assoc..

[7]  J. Overhage,et al.  Advancing the Science for Active Surveillance: Rationale and Design for the Observational Medical Outcomes Partnership , 2010, Annals of Internal Medicine.

[8]  Sahar Qazi,et al.  COVID-19: Hard Road to Find Integrated Computational Drug and Repurposing Pipeline , 2020, Studies in Computational Intelligence.

[9]  Sanjay Kumar,et al.  Mathematical model for plant-insect interaction with dynamic response to PAD4-BIK1 interaction and effect of BIK1 inhibition , 2019, Biosyst..

[10]  Johan Wagemans,et al.  A New Perceptual Bias Reveals Suboptimal Population Decoding of Sensory Responses , 2012, PLoS Comput. Biol..

[11]  Heng Zhu,et al.  Overview of Protein Microarrays , 2013, Current protocols in protein science.

[12]  Khalid Raza,et al.  Protein features identification for machine learning-based prediction of protein-protein interactions , 2017, bioRxiv.

[13]  D. Berwick,et al.  The triple aim: care, health, and cost. , 2008, Health affairs.

[14]  Philip R. O. Payne,et al.  From Molecules to Patients: The Clinical Applications of Translational Bioinformatics , 2015, Yearbook of Medical Informatics.

[15]  A. Paulus,et al.  The chromosome-centric human proteome project: a call to action. , 2013, Journal of proteome research.

[16]  T. Insel,et al.  Brain disorders? Precisely , 2015, Science.

[17]  Khalid Raza,et al.  Reconstruction of gene regulatory network of colon cancer using information theoretic approach , 2013, ArXiv.

[18]  Riccardo Miotto,et al.  Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams , 2016, Briefings Bioinform..

[19]  Christopher G. Chute,et al.  Some experiences and opportunities for big data in translational research , 2013, Genetics in Medicine.

[20]  Mansaf Alam,et al.  Recurrent neural network based hybrid model for reconstructing gene regulatory network , 2014, Comput. Biol. Chem..

[21]  Philip R. O. Payne Chapter 1: Biomedical Knowledge Integration , 2012, PLoS Comput. Biol..

[22]  Khalid Raza Reconstruction, Topological and Gene Ontology Enrichment Analysis of Cancerous Gene Regulatory Network Modules , 2016 .

[23]  A. Órfão,et al.  Protein microarrays: technological aspects, applications and intellectual property. , 2013, Recent patents on biotechnology.

[24]  Sahar Qazi,et al.  Towards a VIREAL Platform: Virtual Reality in Cognitive and Behavioural Training for Autistic Individuals , 2019 .

[25]  Cui Tao,et al.  OAE: The Ontology of Adverse Events , 2014, J. Biomed. Semant..

[26]  Jessica D. Tenenbaum,et al.  Translational Bioinformatics: Past, Present, and Future , 2016, Genom. Proteom. Bioinform..

[27]  Manuel Fuentes,et al.  Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project. , 2015, Journal of proteome research.

[28]  Sahar Qazi,et al.  In Silico Analysis and Comparative Molecular Docking Study of FDA Approved Drugs with Transforming Growth Factor Beta Receptors in Oral Submucous Fibrosis , 2020, Indian Journal of Otolaryngology and Head & Neck Surgery.

[29]  Khalid Raza,et al.  Recent advancement in next-generation sequencing techniques and its computational analysis , 2016, Int. J. Bioinform. Res. Appl..

[30]  Khalid Raza,et al.  Raw Sequence to Target Gene Prediction: An Integrated Inference Pipeline for ChIP-Seq and RNA-Seq Datasets , 2018, Advances in Intelligent Systems and Computing.

[31]  Khalid Raza,et al.  Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods , 2019, Comput. Biol. Chem..

[32]  Khalid Raza,et al.  Soft Computing Approach for Modeling Genetic Regulatory Networks , 2012, ACITY.

[33]  Melissa Haendel,et al.  A sea of standards for omics data: sink or swim? , 2013, J. Am. Medical Informatics Assoc..

[34]  S. Hanash,et al.  The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome , 2012, Nature Biotechnology.

[35]  Michael Eisenstein GSK collaborates with Apple on ResearchKit , 2015, Nature Biotechnology.

[36]  Pauline Hogeweg,et al.  Simulating the growth of cellular forms , 1978 .

[37]  Khalid Raza,et al.  iMTF-GRN: Integrative Matrix Tri-Factorization for Inference of Gene Regulatory Networks , 2019, IEEE Access.

[38]  M. Sardar,et al.  Ampicillin Silver Nanoformulations against Multidrug resistant bacteria , 2019, Scientific Reports.

[39]  Khalid Raza,et al.  MKL-GRNI: A parallel multiple kernel learning approach for supervised inference of large-scale gene regulatory networks , 2021, PeerJ Comput. Sci..

[40]  Xu Han,et al.  An integrated pharmacokinetics ontology and corpus for text mining , 2013, BMC Bioinformatics.

[41]  George Johnson,et al.  Kabat Database and its applications: 30 years after the first variability plot , 2000, Nucleic Acids Res..

[42]  Atul J. Butte,et al.  Viewpoint Paper: Translational Bioinformatics: Coming of Age , 2008, J. Am. Medical Informatics Assoc..

[43]  Lang Li,et al.  The potential of translational bioinformatics approaches for pharmacology research. , 2015, British journal of clinical pharmacology.

[44]  Khalid Raza,et al.  Analysis of Microarray Data using Artificial Intelligence Based Techniques , 2015, Biotechnology.

[45]  Dana Pascovici,et al.  Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools , 2018, International journal of molecular sciences.

[46]  Nigam H. Shah,et al.  The coming age of data-driven medicine: translational bioinformatics' next frontier , 2012, J. Am. Medical Informatics Assoc..

[47]  Sahar Qazi,et al.  Nanopore sequencing technology and Internet of living things: A big hope for U-healthcare , 2019, Sensors for Health Monitoring.

[48]  L. Lesko Drug Research and Translational Bioinformatics , 2012, Clinical pharmacology and therapeutics.

[49]  Emidio Capriotti,et al.  Bioinformatics for personal genome interpretation , 2012, Briefings Bioinform..

[50]  Khalid Raza,et al.  Fuzzy logic based approaches for gene regulatory network inference , 2018, Artif. Intell. Medicine.

[51]  Joel Dudley,et al.  Translational Bioinformatics Approaches to Drug Development. , 2013, Advances in wound care.

[52]  M. Khoury,et al.  “Drivers” of Translational Cancer Epidemiology in the 21st Century: Needs and Opportunities , 2013, Cancer Epidemiology, Biomarkers & Prevention.

[53]  M. O. Dayhoff,et al.  Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences , 1966, Science.

[54]  Amisha,et al.  Overview of artificial intelligence in medicine , 2019, Journal of family medicine and primary care.

[55]  Bairong Shen,et al.  Translational Biomedical Informatics in the Cloud: Present and Future , 2013, BioMed research international.

[56]  Khalid Raza,et al.  From Telediagnosis to Teletreatment: The Role of Computational Biology and Bioinformatics in Tele-Based Healthcare , 2019 .

[57]  Christos A. Ouzounis,et al.  Rise and Demise of Bioinformatics? Promise and Progress , 2012, PLoS Comput. Biol..

[58]  Khalid Raza,et al.  Filgrastim loading in PLGA and SLN nanoparticulate system: a bioinformatics approach , 2020, Drug development and industrial pharmacy.

[59]  Richard Simon,et al.  Implementing personalized cancer genomics in clinical trials , 2013, Nature Reviews Drug Discovery.