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Data mining of cancer vaccine trials: a bird's-eye view

Xiaohong Cao, Karen B Maloney, Vladimir Brusic
2008 Immunome Research  
Presentation of results is facilitated by visualization tools that summarize the landscape of ongoing and completed cancer vaccine trials.  ...  Summarization and visualization of these data represents a cost-effective means of making informed decisions about future cancer vaccine clinical trials.  ...  Richard Fitzpatrick for insightful discussion. We are grateful to Genzyme Corporation for the use of programming resources.  ... 
doi:10.1186/1745-7580-4-7 pmid:19077266 pmcid:PMC2639543 fatcat:tncov5vtobe45fm4tay4sfvzay

Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development—A Perspective Review

Rahul Chatterjee, Mrinmoy Ghosh, Susrita Sahoo, Santwana Padhi, Namrata Misra, Visakha Raina, Mrutyunjay Suar, Young-Ok Son
2021 Vaccines  
Bioinformatics platforms and various computational tools and databases are also essential for the identification of promising vaccine targets making the best use of genomic resources, for further experimental  ...  The present review focuses on the various stages of the vaccine development process and the vaccines available for COVID-19.  ...  Acknowledgments: We would like to acknowledge Krishn Kumar Verma for his support of the scientific visualization; and the School of Biotechnology, Kalinga Institute of Industrial Technology, and KIIT Technology  ... 
doi:10.3390/vaccines9080812 pmid:34451937 pmcid:PMC8402397 fatcat:urw75khyavfqrozw4kwaryvwo4

CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants

Luis F. Cedeño-Pérez, Laura Gómez-Romero
2022 Viruses  
In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes.  ...  CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/v14030561 pmid:35336968 pmcid:PMC8955889 fatcat:fcep5uurenfbhopm5ttb4rsjki

Landscapes of binding antibody and T-cell responses to pox-protein HIV vaccines in Thais and South Africans

Lue Ping Zhao, Andrew Fiore-Gartland, Lindsay N. Carpp, Kristen W. Cohen, Nadine Rouphael, Llewellyn Fleurs, One Dintwe, Michael Zhao, Zoe Moodie, Youyi Fong, Nigel Garrett, Ying Huang (+18 others)
2020 PLoS ONE  
As additional immune response assays are standardized and validated, we anticipate our framework will be increasingly valuable for multivariate analysis.  ...  Our approach can be used to advance vaccine development objectives, including the characterization and comparison of candidate vaccine multivariate immune responses and improved design of studies to identify  ...  protection analysis results; and E) to guide the selection of assays for future vaccine trials.  ... 
doi:10.1371/journal.pone.0226803 pmid:31999736 pmcid:PMC6992005 fatcat:nemeotjhpvah5hth7m5vtfsabm

Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants [article]

Simone Parn, Gabriel Jabbour, Vincent Nguyenkhoa, Sivanesan Dakshanamurthy
2021 bioRxiv   pre-print
The analysis of CD8 and CD4 T cell epitopes revealed multiple potential vaccine constructs that cover a high percentage of the world population.  ...  The landscape of SARS-CoV-2 T cell epitopes that we identified can help lead SARS-CoV-2 vaccine development as well as epitope-based peptide vaccine research in the future.  ...  Acknowledgements We wish to acknowledge for the support by Lombardi Comprehensive Cancer Center, Georgetown University Medical Center.  ... 
doi:10.1101/2021.09.21.461301 fatcat:rfs2fecqdvap7motexqsmjoa7i

What, Where, When and How of COVID-19 Patents Landscape: A Bibliometrics Review

Kunmeng Liu, Xiaoming Zhang, Yuanjia Hu, Weijie Chen, Xiangjun Kong, Peifen Yao, Jinyu Cong, Huali Zuo, Jian Wang, Xiang Li, Benzheng Wei
2022 Frontiers in Medicine  
Descriptive statistics and social network analysis were used in the patent landscape.  ...  Patents might act as an additional source of information for informing research and policy and anticipating important future technology developments.  ...  ACKNOWLEDGMENTS We gratefully acknowledge Zixuan Gu from the University of Macau for valuable comments that helped in improving this work.  ... 
doi:10.3389/fmed.2022.925369 pmid:35847804 pmcid:PMC9283760 fatcat:jk4ulqjfnvc5pexbb4jkwi6g6a

Big Data Analytics in Immunology: A Knowledge-Based Approach

Guang Lan Zhang, Jing Sun, Lou Chitkushev, Vladimir Brusic
2014 BioMed Research International  
The knowledgebases built using KB-builder will speed up rational vaccine design by providing accurate and well-annotated data coupled with tailored computational analysis tools and workflow.  ...  A set of well-defined workflow types with rich summarization and visualization capacity facilitates the transformation from data to critical information and knowledge.  ...  In TANTIGEN, an interactive visualization tool, mutation map, has been implemented to provide a global view of all mutations reported in a tumor antigen.  ... 
doi:10.1155/2014/437987 pmid:25045677 pmcid:PMC4090507 fatcat:ppn4w3xgsrdkxkxwf5mvxqhbne

Intellectual Structure of Coronavirus Research: A Perspective From an Author Cocitation Analysis

Junyi Mei, Dangzhi Zhao, Andreas Strotmann
2020 Frontiers in Research Metrics and Analytics  
The present study examines the intellectual structure of research on coronavirus, as revealed from an author co-citation analysis using citation data retrieved from the Web of Science Core Collection and  ...  Four major dimensions are identified: I) outbreaks, II) viral structure and function, III) vaccine and therapeutic development, and IV) coronaviruses found in a range of animals.  ...  methods and visualized via network analysis tools.  ... 
doi:10.3389/frma.2020.595370 pmid:33870058 pmcid:PMC8025971 fatcat:erijzn76hrfgfmh2m4caufpp6q

A Structural Landscape of Neutralizing Antibodies Against SARS-CoV-2 Receptor Binding Domain

Ling Niu, Kathryn N Wittrock, Gage C Clabaugh, Vikram Srivastava, Michael W Cho
2021 Frontiers in Immunology  
The global scientific community has responded rapidly to understand immune correlates of protection to develop vaccines and immunotherapeutics against the virus.  ...  The major goal of this mini review is to summarize current understanding of the structural landscape of neutralizing antibodies (nAbs) that target the receptor binding domain (RBD) of viral spike (S) glycoprotein  ...  Better understanding of their potency and how they bind their target epitopes could allow for the design of more effective vaccines and improve immunotherapeutic agents.  ... 
doi:10.3389/fimmu.2021.647934 pmid:33995366 pmcid:PMC8113771 fatcat:lxt4ubqau5chfla4t7suixkmpa

Elimination of cervical cancer: challenges for developing countries

Ann Marie Beddoe
2019 ecancermedicalscience  
Cervical cancer is one of the most preventable cancers today, yet over 500,000 new cases are diagnosed globally each year and every 2 minutes a woman dies from cervical cancer.  ...  The burden of this disease and the highest mortality from cervical cancer occur in developing countries.  ...  What was present in the US at that time were basic screening tools: availability of Pap smears, colposcopy, pathology infrastructure, treatment facilities and organised cancer registration.  ... 
doi:10.3332/ecancer.2019.975 pmid:31921346 pmcid:PMC6946419 fatcat:f637d7khpzbg3ppx5fc3gyo4zq

TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes

Guanglan Zhang, Lou Chitkushev, Lars Rønn Olsen, Derin B. Keskin, Vladimir Brusic
2021 BMC Bioinformatics  
It hosts a set of tailored data analytics tools tightly integrated with the data to form meaningful analysis workflows. It is freely available at  ...  In TANTIGEN 2.0, we significantly expanded coverage in both immune response targets (T cell epitopes and HLA ligands) and tumor antigens.  ...  Acknowledgments Tantigen 2.0 was presented at the 2019 IEEE International Conference on Bioinformatics and Biomedicine.  ... 
doi:10.1186/s12859-021-03962-7 pmid:33849445 fatcat:iqbw7msfsra5vlujkkabrtm2va

Reactive vaccination in the presence of disease hotspots

A. S. Azman, J. Lessler
2014 Proceedings of the Royal Society of London. Biological Sciences  
Reactive vaccination has recently been adopted as an outbreak response tool for cholera and other infectious diseases.  ...  Owing to the global shortage of oral cholera vaccine, health officials must quickly decide who and where to distribute limited vaccine.  ...  The authors thank the Infectious Disease Dynamics group at Johns Hopkins Bloomberg School of Public Health, Helen Matzger (BMGF) and Francisco Luquero (MSF/Epicentre) for the useful discussions.  ... 
doi:10.1098/rspb.2014.1341 pmid:25392464 pmcid:PMC4262159 fatcat:irkvsnkwyvdu5cfc73kg6zecj4

Identification of Tumor Antigens and Design of mRNA Vaccine for Colorectal Cancer Based on the Immune Subtype

Cong Liu, Dimitri Papukashvili, Yu Dong, Xingyun Wang, Xing Hu, Nuo Yang, Jie Cai, Fengfei Xie, Nino Rcheulishvili, Peng George Wang
2022 Frontiers in Cell and Developmental Biology  
Our results revealed a complex immune landscape that may provide directions for mRNA vaccine treatment of CRC and define appropriate vaccination patients.  ...  We herein identified potential antigens for designing an effective mRNA vaccine, further to build an immune landscape for the accurate selection of patients for mRNA vaccine therapy.  ...  The present study aims to predict the potential tumor antigen of CRC for designing an mRNA vaccine.  ... 
doi:10.3389/fcell.2021.783527 pmid:35127707 pmcid:PMC8811447 fatcat:5gkfzrccfzcp3hykymyzozqr3m

Vaccine Design through Machine Learning and Nanotechnology to Terminate COVID-19 Pandemic

Hyunjo Kim, School of Pharmacy, Yonsei University, South Korea, Jae-Hoon Song, Chairman of Asian-Pacific Research Foundation for Infectious and ANSORP, South Korea
2020 Journal of Virology Research & Reports  
Nanotechnology tools can play a pivotal role in advancing COVID-19 treatment and vaccine design.  ...  In the absence of a specific antiviral against SARS- CoV-2, present therapeutics target the multifaceted molecular interactions involved in viral infections and major comprises repurposing already existing  ...  Global COVID-19 Vaccine Landscape COVID-19 is known to be very contagious and has many routes of transmission.  ... 
doi:10.47363/jvrr/2020(1)122 fatcat:a7oba4pxdzeupphl7u4kr62wky

Towards a Chimeric Vaccine against Multiple Isolates of Mycobacteroides - An Integrative Approach [article]

Rohit Satyam, Tulika Bhardwaj, Niraj Kumar Jha
2019 bioRxiv   pre-print
Our final vaccine construct, V6 qualified for all tests such as absence for allergenicity, presence of antigenicity, etc. and contains β defensin adjuvant, linkers, LAMP1 signal peptide, and PADRE (Pan  ...  However, the recent cases of Mycobacteroides developing drug resistance reported along with the improper practice of medicine intrigued us to explore its genomic and proteomic canvas at a global scale.  ...  Acknowledgments: The authors would like to express their sincere gratitude to Noida Institute of Engineering and Technology for providing necessary infrastructure.  ... 
doi:10.1101/2019.12.15.869081 fatcat:ts6bw3emhvd3dlt3r5yg7aniry
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