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Your search keyword '"Melendrez, Melanie C."' showing total 17 results
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17 results on '"Melendrez, Melanie C."'

1. Precision Tracing of Household Dengue Spread Using Inter--and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand

Author

Berry, Irina Maljkovic, Melendrez, Melanie C., Pollett, Simon, Figueroa, Katherine, Buddhari, Darunee, Klungthong, Chonticha, Nisalak, Ananda, Panciera, Michael, Thaisomboonsuk, Butsaya, Li, Tao, Vallard, Tyghe G., Macareo, Louis, Yoon, In-Kyu, Thomas, Stephen J., Endy, Timothy, and Jarman, Richard G.

Subjects
Cladistic analysis -- Usage, Dengue -- Control -- Distribution, Households -- Health aspects, Contact tracing -- Methods -- Technology application, Disease transmission -- Control -- Distribution, Technology application, Company distribution practices, Health
Abstract

Dengue virus (DENV) causes an estimated 390 million infections each year, 96 million of which manifest as clinical disease (2). Dengue is endemic in >100 countries. An estimated 3.9 billion [...]

Published
2021
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2. Dengue diversity across spatial and temporal scales : Local structure and the effect of host population size

Author

Salje, Henrik, Lessler, Justin, Berry, Irina Maljkovic, Melendrez, Melanie C., Endy, Timothy, Kalayanarooj, Siripen, A-Nuegoonpipat, Atchareeya, Chanama, Sumalee, Sangkijporn, Somchai, Klungthong, Chonticha, Thaisomboonsuk, Butsaya, Nisalak, Ananda, Gibbons, Robert V., Iamsirithaworn, Sopon, Macareo, Louis R., Yoon, In-Kyu, Sangarsang, Areerat, Jarman, Richard G., and Cummings, Derek A. T.

Published
2017

3. Salmonella

Author

Lewis, April M., primary, Melendrez, Melanie C., additional, and Fink, Ryan C., additional

Published
2019
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6. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity

Author

Maljkovic Berry, Irina, primary, Melendrez, Melanie C, additional, Bishop-Lilly, Kimberly A, additional, Rutvisuttinunt, Wiriya, additional, Pollett, Simon, additional, Talundzic, Eldin, additional, Morton, Lindsay, additional, and Jarman, Richard G, additional

Published
2019
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7. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity.

Author

Berry, Irina Maljkovic, Melendrez, Melanie C, Bishop-Lilly, Kimberly A, Rutvisuttinunt, Wiriya, Pollett, Simon, Talundzic, Eldin, Morton, Lindsay, Jarman, Richard G, and Maljkovic Berry, Irina

Subjects
*PUBLIC health research, *COMMUNICABLE diseases, *EMERGING infectious diseases, *CAPACITY building, *BIOINFORMATICS, *INFORMATION superhighway, *COMMUNICABLE disease epidemiology, *RESEARCH, *SEQUENCE analysis, *RESEARCH methodology, *PUBLIC health, *LABORATORIES, *EVALUATION research, *MEDICAL cooperation, *COMPARATIVE studies, *GENOMICS, *EPIDEMICS, *GENOMES
Abstract

Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics. [ABSTRACT FROM AUTHOR]

Published
2020
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8. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Author

Kilianski, Andy, Yao, Shijie, Carcel, Patrick, Roth, Pierce, Schulte, Josh, Donarum, Greg B., Fochler, Ed T., Hill, Jessica M., Liem, Alvin T., Wiley, Michael R., Ladner, Jason T., Pfeffer, Bradley P., Elliot, Oliver T., Petrosov, Alexandra, Jima, Dereje D., Vallard, Tyghe G., Melendrez, Melanie C., Skowronski, Evan, Quan, Phenix-Lan, Lipkin, W. Ian, Gibbons, Henry S., Hirschberg, David L., Palacios, Gustavo F., and Rosenzweig, C. Nicole

Subjects
Identification, Pathogenic microorganisms, Medical records--Data processing, Medicine
Abstract

Background The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. Results The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. Conclusions By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.

Published
2015
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9. Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread

Author

Maljkovic Berry, Irina, primary, Melendrez, Melanie C., additional, Li, Tao, additional, Hawksworth, Anthony W., additional, Brice, Gary T., additional, Blair, Patrick J., additional, Halsey, Eric S., additional, Williams, Maya, additional, Fernandez, Stefan, additional, Yoon, In-Kyu, additional, Edwards, Leslie D., additional, Kuschner, Robert, additional, Lin, Xiaoxu, additional, Thomas, Stephen J., additional, and Jarman, Richard G., additional

Published
2016
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10. Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia

Author

Timmermans, Ans, primary, Melendrez, Melanie C., additional, Se, Youry, additional, Chuang, Ilin, additional, Samon, Nou, additional, Uthaimongkol, Nichapat, additional, Klungthong, Chonticha, additional, Manasatienkij, Wudtichai, additional, Thaisomboonsuk, Butsaya, additional, Tyner, Stuart D., additional, Rith, Sareth, additional, Horm, Viseth Srey, additional, Jarman, Richard G., additional, Bethell, Delia, additional, Chanarat, Nitima, additional, Pavlin, Julie, additional, Wongstitwilairoong, Tippa, additional, Saingam, Piyaporn, additional, El, But Sam, additional, Fukuda, Mark M., additional, Touch, Sok, additional, Sovann, Ly, additional, Fernandez, Stefan, additional, Buchy, Philippe, additional, Chanthap, Lon, additional, and Saunders, David, additional

Published
2016
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12. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Author

Kilianski, Andy, primary, Carcel, Patrick, additional, Yao, Shijie, additional, Roth, Pierce, additional, Schulte, Josh, additional, Donarum, Greg B., additional, Fochler, Ed T., additional, Hill, Jessica M., additional, Liem, Alvin T., additional, Wiley, Michael R., additional, Ladner, Jason T., additional, Pfeffer, Bradley P., additional, Elliot, Oliver, additional, Petrosov, Alexandra, additional, Jima, Dereje D., additional, Vallard, Tyghe G., additional, Melendrez, Melanie C., additional, Skowronski, Evan, additional, Quan, Phenix-Lan, additional, Lipkin, W. Ian, additional, Gibbons, Henry S., additional, Hirschberg, David L., additional, Palacios, Gustavo F., additional, and Rosenzweig, C. Nicole, additional

Published
2015
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13. Characterization Based on the 56-Kda Type-Specific Antigen Gene of Orientia tsutsugamushi Genotypes Isolated from Leptotrombidium Mites and the Rodent Host Post-Infection

Author

Takhampunya, Ratree, primary, Monkanna, Taweesak, additional, Leepitakrat, Surachai, additional, Richards, Allen L., additional, Promsathaporn, Sommai, additional, Richardson, Jason H., additional, Paris, Daniel H., additional, Tippayachai, Bousaraporn, additional, Melendrez, Melanie C., additional, and Schuster, Anthony L., additional

Published
2014
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