Melanie C. Melendrez
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View article: Dengue diversity across spatial and temporal scales: Local structure and the effect of host population size
Dengue diversity across spatial and temporal scales: Local structure and the effect of host population size Open
A fundamental mystery for dengue and other infectious pathogens is how observed patterns of cases relate to actual chains of individual transmission events. These pathways are intimately tied to the mechanisms by which strains interact and…
View article: Editorial: Curriculum Applications in Microbiology: Bioinformatics in the Classroom
Editorial: Curriculum Applications in Microbiology: Bioinformatics in the Classroom Open
We would like to thank all of the authors who submitted to this special topic, committed to the furthering of academic creativity, excellence, and rigor in the challenging and virtual instructional world of SARS-CoV-2 (COVID-19). To you an…
View article: Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand
Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand Open
Dengue control approaches are best informed by granular spatial epidemiology of these viruses, yet reconstruction of inter- and intra-household transmissions is limited when analyzing case count, serologic, or genomic consensus sequence da…
View article: Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks
Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks Open
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response …
View article: Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity
Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity Open
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…
View article: Understanding dengue virus evolution to support epidemic surveillance and counter-measure development
Understanding dengue virus evolution to support epidemic surveillance and counter-measure development Open
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbaniz…
View article: <i>Rickettsia asembonensis</i> Characterization by Multilocus Sequence Typing of Complete Genes, Peru
<i>Rickettsia asembonensis</i> Characterization by Multilocus Sequence Typing of Complete Genes, Peru Open
While studying rickettsial infections in Peru, we detected Rickettsia asembonensis in fleas from domestic animals. We characterized 5 complete genomic regions (17kDa, gltA, ompA, ompB, and sca4) and conducted multilocus sequence typing and…
View article: Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread
Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread Open
View article: Complete Genome Sequences of Zika Virus Strains Isolated from the Blood of Patients in Thailand in 2014 and the Philippines in 2012
Complete Genome Sequences of Zika Virus Strains Isolated from the Blood of Patients in Thailand in 2014 and the Philippines in 2012 Open
Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, Zika virus/ Homo sapiens -tc/THA/2014/SV0127-14 and Zika virus/ H. sapiens -tc/PHL/2012/CPC-0740, isolated from the blood of patients collected in Thailand, 2…
View article: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia
Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia Open
Little is known about circulation of influenza and other respiratory viruses in remote populations along the Thai-Cambodia border in western Cambodia. We screened 586 outpatients (median age 5, range 1-77) presenting with influenza-like-il…
View article: ngs_mapper: v1.3.0 - Filter Reads
ngs_mapper: v1.3.0 - Filter Reads Open
Introduces new stage where you can filter reads out based on some criteria First release that should be on Zenodo See Changelog for all changes
View article: Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat
Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat Open
Recent studies of bacterial speciation have claimed to support the biological species concept-that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery tha…
View article: Additional file 4: of Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread
Additional file 4: of Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread Open
Separate segment and full genome ML phylogenetic trees in machine readable (Newick) formats (9 sheets). (XLSX 267 kb)
View article: Additional file 6: of Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread
Additional file 6: of Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread Open
Reassortant lineage passaging information. (XLSX 14 kb)
View article: Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform
Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform Open
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. …
View article: Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country
Feasibility and effectiveness of a brief, intensive phylogenetics workshop in a middle-income country Open
There is an increasing role for bioinformatic and phylogenetic analysis in tropical medicine research. However, scientists working in low- and middle-income regions may lack access to training opportunities in these methods. To help addres…
View article: Additional file 1: of Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform
Additional file 1: of Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform Open
(zip 23 kb)