Search results
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Title
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A new strategy to infer circularity applied to four new complete frog mitogenomes
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Author
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Machado, Denis Jacob, Janies, Daniel, Brouwer, Cory, Grant, Taran
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Date Created
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2018
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Subjects--Topical
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Genomics, Amphibians, Bioinformatics
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Description
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We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae (Melanophryniscus moreirae), Dendrobatidae (Hyloxalus subpunctatus and Phyllobates terribili...
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Title
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Active Notch signaling is required for arm regeneration in a brittle star
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Author
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Janies, Daniel, Machado, Denis Jacob, Reid, Robert
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Date Created
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2020
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Subjects--Topical
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Genomics, Biology
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Description
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Cell signaling pathways play key roles in coordinating cellular events in development. The Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including pr...
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Title
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Comparative phylogenetic studies on Schistosoma japonicum and its snail intermediate host Oncomelania hupensis : origins, dispersal and coevolution
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Author
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Attwood, Stephen W., Ibaraki, Motomu, Saitoh, Yasuhide, Janies, Daniel
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Subjects--Topical
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Parasites, Coevolution, Public health
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Description
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Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite, which is transmitted by freshwater snails of the species Oncomelania hupen- sis, causes the disease intestinal schistosomiasis in humans and cat...
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Title
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Content and sentiment surveillance (CSI) : A critical component for modeling modern epidemics
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Author
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Janies, Daniel, Chen, Shi, Zhang, Dongsong
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Date Created
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2023
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Subjects--Topical
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Communicable diseases, Biology
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Description
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Comprehensive surveillance systems are the key to provide accurate data for effective modeling. Traditional symptom-based case surveillance has been joined with recent genomic, serologic, and environment surveillance to provide more integrated dis...
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Title
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EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
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Author
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Janies, Daniel, Witter, Zachary, Linchangco, Gregorio V., Jr.
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Date Created
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2016
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Subjects--Topical
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Genomics, Biology
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Description
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Background: One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echin...
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Title
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Exploring feasibility of multivariate deep learning models in predicting COVID-19 epidemic
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Author
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Thill, Jean-Claude, Janies, Daniel, Chen, Shi, Paul, Rajib
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Date Created
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2021
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Subjects--Topical
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Deep learning (Machine learning), COVID-19 (Disease)
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Description
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Background: Mathematical models are powerful tools to study COVID-19. However, one fundamental challenge in current modeling approaches is the lack of accurate and comprehensive data. Complex epidemiological systems such as COVID-19 are especially...
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Title
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FLAVi : an enhanced annotator for viral genomes of Flaviviridae
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Author
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Machado, Denis Jacob, Schneider, Adriano, Guirales, Sayal, Janies, Daniel
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Subjects--Topical
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Viruses, Phylogeny
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Description
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Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phyl...
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Title
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Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses : SARS-CoV, MERS-CoV and SARS-CoV-2
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Author
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Machado, Denis Jacob, Scott, Rachel, Guirales, Sayal, Janies, Daniel
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Subjects--Topical
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Coronaviruses, SARS (Disease), MERS (Disease), COVID-19 (Disease)
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Description
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The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emerg...
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Title
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Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions
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Author
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Machado, Denis Jacob, White, Richard Allen, III, Kofsky, Janice, Janies, Daniel
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Subjects--Topical
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COVID-19 (Disease), Epidemiology
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Description
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The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronav...
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Title
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Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions
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Author
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Janies, Daniel, Rush, Nathaniel, Witter, Zachary, Williams, John
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Date Created
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2018
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Subjects--Topical
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Genomics, Biology
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Description
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Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale...
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Title
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Patch dynamics modeling framework from pathogens' perspective : Unified and standardized approach for complicated epidemic systems
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Author
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Janies, Daniel, Chen, Shi, Lo, Eugenia, Dulin, Michael
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Date Created
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2020
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Subjects--Topical
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Communicable diseases, Biology
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Description
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Mathematical models are powerful tools to investigate, simulate, and evaluate potential interventions for infectious diseases dynamics. Much effort has focused on the Susceptible-Infected-Recovered (SIR)-type compartment models. These models consi...
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Title
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Phylogeny of echinoderm hemoglobins
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Author
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Janies, Daniel, Linchangco, Gregorio V., Jr.
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Date Created
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2015
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Subjects--Topical
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Genomics, Biology
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Description
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Background Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and alpha-globin/beta-globin tetramer hemoglobin, and ...
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Title
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Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination
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Author
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Thill, Jean-Claude, Janies, Daniel, Chen, Shi
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Date Created
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2022
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Subjects--Topical
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COVID-19 (Disease), Vaccination
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Description
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In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increa...