Vaccines of the 21st Century and Vaccinomics: Data-Enabled Science Meets Global Health to Spark Collective Action for Vaccine Innovation

Özdemir, Vural; Pang, Tikki; Knoppers, Bartha Maria; Avard, Denise; Faraj, Samer; Zawati, Ma’n H.; Kolker, Eugene

doi:10.1089/omi.2011.03ed

Cited by 15 publications

(9 citation statements)

References 30 publications

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“…The term ''omics'' in biological sciences widely encompasses genomics, transcriptomics, proteomics, and metabolomics which refers to the study of DNA, mRNA, proteins and metabolites, respectively. While ''omics'' is now indispensable in the search of novel biomarkers for drug and vaccine development (Hu et al, 2011;Ozdemir et al, 2011), its application to microalgae is just beginning to emerge in the last few years. Furthermore, to date, no review attempt has been undertaken to evaluate the successful integration of ''omic'' approaches in algal biofuel research.…”

mentioning

confidence: 99%

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

Misra

Panda²,

Parida³

2013

OMICS: A Journal of Integrative Biology

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Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other ''omic'' approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of ''omics'' in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of ''omic'' approaches in the metabolic pathway studies for microalgal biofuel production.

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mentioning

confidence: 99%

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

Misra

Panda²,

Parida³

2013

OMICS: A Journal of Integrative Biology

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“…The rate of increase in sequencing data requires new, trans‐disciplinary approaches to efficiently translate the influx of new data into ground‐breaking discoveries. Communities like Data‐Enabled Life Sciences Alliance (DELSA Global) stand to promote a collective innovation through interdisciplinary research and transdisciplinary engagement . Grand challenges in modern life sciences can be only solved through concerted effort of scientific collectives like DELSA Global.…”

Section: Resultsmentioning

confidence: 99%

Optimizing high performance computing workflow for protein functional annotation

Stanberry

Rekepalli

Liu

et al. 2014

Concurrency and Computation

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Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

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“…In the Nineties, Rino Rappuoli, Global Head of Vaccines Research at Novartis, Siena, Italy, introduced the concept of reverse vaccinology for the design of a vaccine [8][9][10] first against Neisseria meningitidis and very recently against Streptococcus B group. Since then due to the explosion of OMICS sciences [11,12] and technologies, biomolecular arrays have emerged as an important tool for vaccine development and implementation: research has focused above all on the exploitation of DNA arrays for different purposes, assessing safety and immunogenicity, evaluating the stability of the virus and bacterium strain, identifying sub-types and genotyping the strain responsible of the outbreak. Only recently protein arrays were used to discover new antigenic determinants for vaccine development, such as membrane proteins and other components or virulence factors, especially those expressed at high values, which are expected to better stimulate the lymphocyte reactions.…”

Section: Nappa Technologymentioning

confidence: 99%

NAPPA-Based Vaccines for a New Proteogenomics Approach for Public Health

Bragazzi¹,

Pechkova²,

Nicolini³

2015

NanoWorld J

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Vaccinology was developed for the first time in 1796 when Jenner empirically implemented a vaccine against smallpox using animal-to-human cowpox inoculation. Since then, it has become a very complex science due to the merging of disciplines ranging from structural and functional, cellular and molecular biology and immunology to bioinformatics and nanobiotechnology, as well as systems biology and synthetic biology and engineering. In the frame of evidence-based medicine (EBM), evidence-based vaccinology emerged as an important sub-field: vaccinology has nowadays become more and more predictive and personalized. With the discovery that many patients with cancer develop antibodies against p53 (the so-called oncoantibodies), it was evident that oncoprotein are immunogenic and can be used for immunotherapeutics purposes. In this manuscript, we report Nucleic Acid Programmable Protein Arrays (NAPPA)-based Quartz Crystal Microbalance (QCM) measurement of p53 immunogenicity and kinetics, in the perspective of developing an effective p53 therapy. NAPPA-based QCM_D can be a useful platform for proving the immunogenicity of oncoprotein-based vaccines. Recently, the field of vaccinology has extended from vaccines for infectious diseases to vaccines not only preventive but also therapeutic for chronic-degenerative diseases such as cancer. Peptide-based immunotherapeutics has been proven to be quite effective for cancer treatment and NAPPA-based QCM_D has the promise of providing clinicians with quick, rapid and cheap measurement of oncoprotein kinetics and bindings with immune cells. Moreover, it can be a precious tool for implementing personalized and predictive vaccinology.

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Vaccines of the 21st Century and Vaccinomics: Data-Enabled Science Meets Global Health to Spark Collective Action for Vaccine Innovation

Cited by 15 publications

References 30 publications

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

Optimizing high performance computing workflow for protein functional annotation

NAPPA-Based Vaccines for a New Proteogenomics Approach for Public Health

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