Search results | J. Murrey Atkins Library

Title: Exploring feasibility of multivariate deep learning models in predicting COVID-19 epidemic
Author: Thill, Jean-Claude, Janies, Daniel, Chen, Shi, Paul, Rajib
Date Created: 2021
Subjects--Topical: Deep learning (Machine learning), COVID-19 (Disease)
Description: 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...

Title: 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
Author: Thill, Jean-Claude, Janies, Daniel, Chen, Shi
Date Created: 2022
Subjects--Topical: COVID-19 (Disease), Vaccination
Description: 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...

Title: Comparative phylogenetic studies on Schistosoma japonicum and its snail intermediate host Oncomelania hupensis : origins, dispersal and coevolution
Author: Attwood, Stephen W., Ibaraki, Motomu, Saitoh, Yasuhide, Janies, Daniel
Subjects--Topical: Parasites, Coevolution, Public health
Description: 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...

Title: FLAVi : an enhanced annotator for viral genomes of Flaviviridae
Author: Machado, Denis Jacob, Schneider, Adriano, Guirales, Sayal, Janies, Daniel
Subjects--Topical: Viruses, Phylogeny
Description: 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...

Title: A novel machine learning framework for comparison of viral COVID-19–related Sina Weibo and Twitter posts : workflow development and content analysis
Author: Chen, Shi, Zhou, Lina, Song, Yunya, Xu, Qian, Wang, Ping, Wang, Kanlun, Ge, Yaorong, Janies, Daniel
Date Created: 2021
Subjects--Topical: COVID-19 (Disease), Twitter (Firm), Social media, Machine learning
Description: Background: Social media plays a critical role in health communications, especially during global health emergencies such as the current COVID-19 pandemic. However, there is a lack of a universal analytical framework to extract, quantify, and comp...

Title: A new strategy to infer circularity applied to four new complete frog mitogenomes
Author: Machado, Denis Jacob, Janies, Daniel, Brouwer, Cory, Grant, Taran
Date Created: 2018
Subjects--Topical: Genomics, Amphibians, Bioinformatics
Description: 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...

Title: Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses : SARS-CoV, MERS-CoV and SARS-CoV-2
Author: Machado, Denis Jacob, Scott, Rachel, Guirales, Sayal, Janies, Daniel
Subjects--Topical: Coronaviruses, SARS (Disease), MERS (Disease), COVID-19 (Disease)
Description: 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...

Title: Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions
Author: Machado, Denis Jacob, White, Richard Allen, III, Kofsky, Janice, Janies, Daniel
Subjects--Topical: COVID-19 (Disease), Epidemiology
Description: 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...

Title: Tracking a serial killer : integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks
Author: Janies, Daniel, Galac, Madeline R., Kilianski, Andrew
Date Created: 2018
Subjects--Topical: Communicable diseases, Biology
Description: Background While overall rates of meningococcal disease have been declining in the United States for the past several decades, New York City (NYC) has experienced two serogroup C meningococcal disease outbreaks in 2005-2006 and in 2010-2013. The o...

Title: Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022 : A multi-model study
Author: Janies, Daniel, Chen, Shi, Thill, Jean-Claude
Date Created: 2023
Subjects--Topical: Communicable diseases, COVID-19 (Disease)
Description: Background The COVID-19 Scenario Modeling Hub convened nine modeling teams to project the impact of expanding SARS-CoV-2 vaccination to children aged 5-11 years on COVID-19 burden and resilience against variant strains. Methods Teams contributed s...

Title: Active Notch signaling is required for arm regeneration in a brittle star
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert
Date Created: 2020
Subjects--Topical: Genomics, Biology
Description: 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...

Title: Phylogeny of echinoderm hemoglobins
Author: Janies, Daniel, Linchangco, Gregorio V., Jr.
Date Created: 2015
Subjects--Topical: Genomics, Biology
Description: 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 ...

Title: Tracing origins of the Salmonella bareilly strain causing a food-borne outbreak in the United States
Author: Janies, Daniel
Date Created: 2016
Subjects--Topical: Communicable diseases, Salmonella
Description: Background. Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associate...

Title: Changing of the genomic pattern of Salmonella enteritidis strains isolated in Brazil over a 48 year-period revealed by whole genome SNP analyses
Author: Janies, Daniel
Date Created: 2018
Subjects--Topical: Genomics, Salmonella
Description: Salmonella Enteritidis became the main serovar isolated from gastroenteritis cases in Brazil after the 90's. In this study we used whole genome sequence analysis to determine the phylogenetic relationships among a collection of strains isolated in...

Title: The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida)
Author: Janies, Daniel, Machado, Denis Jacob
Date Created: 2020
Subjects--Topical: Genomics, Biology
Description: Morphologic and molecular data often lead to different hypotheses of phylogenetic relationships. Such incongruence has been found in the echinoderm class Echinoidea. In particular, the phylogenetic status of the order Clypeasteroida is not well re...

Title: Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms
Author: Janies, Daniel, Clouse, Ronald M., Linchangco, Gregorio V., Jr.
Date Created: 2015
Subjects--Topical: Genomics, Biology
Description: Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been exte...

Title: EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Author: Janies, Daniel, Witter, Zachary, Linchangco, Gregorio V., Jr.
Date Created: 2016
Subjects--Topical: Genomics, Biology
Description: 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...

Title: Zika virus : medical countermeasure development challenges
Author: Janies, Daniel, Damodaran, Lambodhar, Schneider, Adriano
Date Created: 2016
Subjects--Topical: Communicable diseases, Zika virus
Description: Introduction Reports of high rates of primary microcephaly and Guillain-Barre syndrome associated with Zika virus infection in French Polynesia and Brazil have raised concerns that the virus circulating in these regions is a rapidly developing neu...

Title: Gene polymorphisms among Plasmodium vivax geographical isolates and the potential as new biomarkers for gametocyte detection
Author: Janies, Daniel, Lo, Eugenia, Ford, Anthony
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: The unique biological features of Plasmodium vivax not only make it difficult to control but also to eliminate. For the transmission of the malaria parasite from infected human to the vector, gametocytes play a major role. The transmission potenti...

Title: Patch dynamics modeling framework from pathogens' perspective : Unified and standardized approach for complicated epidemic systems
Author: Janies, Daniel, Chen, Shi, Lo, Eugenia, Dulin, Michael
Date Created: 2020
Subjects--Topical: Communicable diseases, Biology
Description: 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...