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|a Genomic surveillance and pandemic preparedness /
|c edited by Rajesh Pandey.
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|a London, United Kingdom ;
|a San Diego, CA :
|b Academic Press,
|c 2023.
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|a Front Cover -- Genomic Surveillance and Pandemic Preparedness -- Genomic Surveillance and Pandemic Preparedness -- Copyright -- Contents -- List of contributors -- Preface -- A -- Pathogens and host: genomics perspective -- 1 -- Population-level differences in COVID-19 prevalence, severity, and clinical outcome -- Introduction -- Measuring the burden of disease: prevalence and incidence -- Prevalence -- Incidence -- Types of prevalence -- Factors affecting prevalence -- Seroprevalence: measuring infection status in the population -- Decoding COVID-19 prevalence: a population-based approach -- Spectrum of disease severity -- Populations-based deciphering of COVID-19 severity -- Comorbidities -- Sex -- Age -- Genetic -- Population-based understanding of COVID-19 clinical outcome -- Conclusions -- Future perspectives -- References -- 2 -- Host genetics in disease susceptibility and protection -- Introduction -- Methods and technologies -- Tuberculosis -- HIV-1/AIDS -- Malaria -- Leprosy -- Viral hepatitis -- Inborn errors of immunity -- COVID-19 -- Conclusions and future directions -- References -- 3 -- RNA as modulators of infection outcome: potential usage for genomic surveillance -- Introduction -- Evolution of pathogenic RNA viruses -- Genome surveillance as a strategy to unravel viral pathogenicity and transmission -- Whole genome sequencing in RNA surveillance -- Evolution of WGS in genome surveillance -- Use of metagenomics in RNA surveillance -- Target-based genome sequencing -- Variation in RNA can modulate infection outcomes -- Impact of RNA structure variations on viral infections -- RNA interactions and infectivity -- Global initiatives for pathogen surveillance -- Acknowledgments -- References -- B -- Pathogen diversity -- 4 -- Genomic surveillance of bacterial pathogens: expanding horizons -- Introduction.
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| 505 |
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|a Genomic surveillance of bacterial pathogens -- Salmonella Typhi (S. Typhi) -- Mycobacterium tuberculosis (M.tb) -- Pseudomonas aeruginosa -- Neisseria gonorrhoeae -- Staphylococcus aureus -- Other pathogenic bacteria -- Role of machine learning (ML) and artificial intelligence (AI) in genomics surveillance -- Incorporating ML/AI methodologies in genomic surveillance -- Global surveillance efforts-data resource -- Conclusion -- References -- C -- Cofactors in addition to pathogen -- 5 -- Host immune responses in COVID-19: implication for preexisting chronic systemic inflammation -- Introduction -- SARS-CoV-2 transmission and clinical features -- Immune response in SARS-CoV-2 pathogenesis -- The "cytokine storm" -- Chronic inflammatory disorders and associated cytokine profile -- Rheumatic disorders -- Inflammatory bowel disease -- Chronic obstructive pulmonary disorder (COPD) -- Atherosclerosis -- Diabetes mellitus -- Conclusion -- References -- 6 -- Role of co-infections in modulating disease severities and clinical phenotypes -- Prelude to the chapter -- Preamble to the topic -- Opening pandora's box: explaining co-infections -- What happens when the primary pathogen infects? -- What co-infections have to do with disease severity and outcome? -- Are these co-infections advantageous or deleterious? -- Introducing transcriptionally active microbes (TAMs) -- Human gut microbiome and the SARS-CoV-2 -- Dataset acquire and pre-processing -- Quality control analysis -- From reads to assembly -- From fragments to taxa (binning) -- Statistical analysis -- Probiotics -- Prebiotics -- Postbiotics -- FMT -- References -- Further reading -- 7 -- Wastewater surveillance: a quick guide to check community health -- Introduction -- Wastewater surveillance -- The methodology employed in environmental and wastewater surveillance -- SARS-CoV-2 surveillance.
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|a Polio surveillance in sewage samples -- Surveillance for Cryptosporidium and Giardia -- Surveillance of hepatitis E virus -- Environmental monitoring of Aichi virus, human bocavirus noroviruses, Adenoviruses, Sapoviruses, and Astroviruses -- Wastewater surveillance for typhoid transmission -- Wastewater surveillance for antibiotic-resistome and mobilome -- Multidrug-resistant Pseudomonas aeruginosa outbreaks and antimicrobial-resistant pathogens -- Surveillance of antibiotic-resistant Escherichia coli -- Role of environment surveillance in effective public health management -- Challenges in successful environmental/waste water surveillance -- Conclusion and future perspectives -- References -- D -- Future pandemic preparedness -- 8 -- Experimental repertoire to elucidate the functional landscape of host-pathogen interactome -- Introduction -- Experimental approach to understand host-pathogen interaction -- Molecular, cell biology, model systems -- Immediate detection, diagnostics, surveillance, prognostic markers -- Building and aligning to the theme of "genomic surveillance and pandemic preparedness" -- Pathogen genomics: diagnosis, surveillance, and functional genomics -- Pathogen genomics for diagnosis and surveillance -- Choice of platform: high throughput or high priority? -- Functional genomics: mutations and genome architecture of pathogen -- Population, phylogenetic and, mutation studies -- Identifying and annotating mutations -- Associating mutations to clinical and phenotypic variables -- Statistical analysis -- Comparative genomic and metagenomic analysis -- Detecting or confirming a new microbe or similarity with previously known microbe/s -- Culturing-based detection technique -- Immunological-based detection technique -- Molecular-based detection technique -- Understanding the host response through genomics and transcriptomics.
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|a Multilayered understanding of host genome: genomic and transcriptomic knowledge -- Granularity of data, bulk or single-cell RNA sequencing: which one to use? -- Single-cell RNA sequencing: choice of platform -- Analytical approaches toward RNA-seq and single-cell RNA-seq data -- RNA-seq data repositories: where to find the files -- Counting method -- Differential gene expression methods for RNA-seq -- Analyzing the single-cell data: dos and don'ts -- WGS and array based techniques for detection -- Gene expression profiling -- Genotyping -- Host genetic variants: SNPs and haplotype associated risk factors -- Structural conformation of genome: 3D interaction and gene regulation -- Detection of TADs and interactions within TADs -- Summary -- References -- 9 -- Computational means to understand and elucidate host-pathogen interaction and outcome -- Introduction -- Pathogen classification and invasion -- Elude host defenses and colonize -- Infection eradication -- Prediction algorithms for PHI -- Homology-based methods -- Structure-based methods -- Motif interaction methods -- Machine learning and artificial intelligence to predict PPI/PHI -- Host-pathogen interactions databases -- Discussions and future scopes -- Conclusion -- References -- 10 -- Genomic surveillance system and technologies -- Genomic surveillance system -- Collection of clinical data, imaging data, and biological samples -- Generation of laboratory and sequencing data from biological samples -- Analysis of sequenced data -- Analysis of multimodal data -- Reporting insights -- Genomic surveillance architecture -- High performance compute and storage (HPCS) system -- Information gateway (IG) -- Genomic surveillance technologies -- Data security -- Anonymization -- Artificial intelligence (AI) and federated learning (FL) -- References -- E -- Roadmap ahead.
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|a 11 -- Interactions shaping the interactome: genome surveillance inclusive of host-pathogen -- Introduction -- Understanding interactions in the context of host and pathogen -- Basic concepts of host-pathogen interaction-commensalism, colonization, infection, and disease -- Infectious diseases: high incidences, mortality rate, and population diversity -- An exploration of the host pathogen interactome (HPI) -- HPI: a multifaceted approach to understanding infectious diseases -- Host entry by the pathogen -- Evasion of host defenses by pathogens -- Pathogen replication in the host and host response -- Tools to study HPI -- HPI in infectious diseases -- Concepts of perennial and seasonal infections across viral, bacterial, and fungal infections -- Mycobacterium tuberculosis (mTB) -- Transmission and pathogenesis -- Genomics, HPI and tuberculosis -- Influenza -- Transmission and pathogenesis -- Genomics, HPI and influenza -- COVID-19 -- Genome sequence and origin of the SARS-CoV-2 -- Genomic insights into host-pathogen interaction in COVID-19 -- Dengue -- Transmission and pathogenesis -- Genomics, HPI and dengue -- Tiered analysis of genomic surveillance for pathogen and host interactions -- Genomic surveillance in infectious diseases -- Multiomic technologies and NGS utilities (tools/techniques) to decipher HPI -- Conclusion -- Current advances in host-pathogen interaction studies aiding in clinical outcomes -- Future perspectives of host-pathogen interaction studies -- References -- 12 -- Health informatics and data science for pandemic preparedness -- One Health and data as a public good -- Molecular surveillance and response -- Immune observatories -- Data science and social science -- References -- 13 -- Harsh environmental stressors of high altitude on pathogens susceptibility -- Background -- HA exposure on T and B lymphocytes -- Neurological system.
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| 520 |
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|a Genomic Surveillance and Pandemic Preparedness offers practical, in-depth instruction in where, how, and why genomic surveillance may be applied.Drawing heavily from the learnings during the COVID-19 pandemic, this book covers different aspects of microbes with a focus on viral genome sequencing and analysis, implementation and inference of.
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| 650 |
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|a Pandemics
|x Prevention.
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| 650 |
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|a Genomics.
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| 650 |
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|a COVID-19 (Disease)
|x Genetic aspects.
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| 650 |
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2 |
|a Genomics
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| 650 |
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6 |
|a Génomique.
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| 650 |
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6 |
|a COVID-19
|x Aspect génétique.
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| 650 |
|
7 |
|a Genomics
|2 fast
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| 655 |
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|a Electronic books.
|2 local
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| 700 |
1 |
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|a Pandey, Rajesh,
|d 1971-
|1 https://id.oclc.org/worldcat/entity/E39PCjy6FpXMcFHwyjTf74K36X
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| 710 |
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|a ScienceDirect (Online service)
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| 776 |
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|i ebook version :
|z 9780443187681
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| 776 |
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|c Original
|z 044318769X
|z 9780443187698
|w (OCoLC)1355437806
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| 856 |
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|z Connect to the full text of this electronic book
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|a Elsevier ScienceDirect 2026-2027
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|a Texas A&M University
|b College Station
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|d Available Online
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|e RA652 .G46 2023
|h Library of Congress classification
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| 998 |
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|l Available Online
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