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: Modeling Plasmodium falciparum diagnostic test sensitivity using machine learning with histidine-rich protein 2 variants
Author: Ford, Colby, Janies, Daniel, Alemayehu, Gezahegn, Lo, Eugenia, Blackburn, Kayla, Lopez, Karen, Dieng, Cheikh Cambel, Golassa, Lemu
Subjects--Topical: Malaria, Plasmodium falciparum
Description: Malaria, predominantly caused by Plasmodium falciparum, poses one of largest and most durable health threats in the world. Previously, simplistic regression-based models have been created to characterize malaria rapid diagnostic test performance, ...

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: 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: Sequence-based identification of Anopheles species in eastern Ethiopia
Author: Janies, Daniel, Lopez, Karen
Date Created: 2019
Subjects--Topical: Communicable diseases, Malaria
Description: Background: The recent finding of a typically non-African Anopheles species in eastern Ethiopia emphasizes the need for detailed species identification and characterization for effective malaria vector surveillance. Molecular approaches increase t...

Title: Geographical distribution of Anopheles stephensi in eastern Ethiopia
Author: Janies, Daniel, Lopez, Karen
Date Created: 2020
Subjects--Topical: Communicable diseases, Malaria
Description: Background The recent detection of the South Asian malaria vector Anopheles stephensi in Ethiopia and other regions in the Horn of Africa has raised concerns about its potential impact on malaria transmission. We report here the findings of a surv...

Title: Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes
Author: Janies, Daniel, Lo, Eugenia, Ford, Anthony, Kepple, Daniel
Date Created: 2020
Subjects--Topical: Communicable diseases, Malaria
Description: Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. R...

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: Insecticide resistance in Anopheles stephensi in Somali Region, eastern Ethiopia
Author: Janies, Daniel, Lopez, Karen
Date Created: 2020
Subjects--Topical: Communicable diseases, Malaria
Description: Background The movement of malaria vectors into new areas is a growing concern in the efforts to control malaria. The recent report of Anopheles stephensi in eastern Ethiopia has raised the necessity to understand the insecticide resistance status...

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: 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: Selection and utility of single nucleotide polymorphism markers to reveal fine-scale population structure in human malaria parasite Plasmodium falciparum
Author: Janies, Daniel, Lo, Eugenia, Ford, Anthony
Date Created: 2018
Subjects--Topical: Communicable diseases, Malaria
Description: Single nucleotide polymorphisms (SNPs) have been shown to be useful in revealing population structure with continental-and regional-scale samples. In epidemiological study, a careful selection of SNPs to track disease spread in local communities w...

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...

Title: Four challenges associated with current mathematical modeling paradigm of infectious diseases and call for a shift
Author: Janies, Daniel, Chen, Shi, Robinson, Patrick, Dulin, Michael
Date Created: 2020
Subjects--Topical: Communicable diseases, Biology
Description: Mathematical models are critical tools to characterize COVID-19 dynamics and take action accordingly. We identified 4 major challenges associated with the current modeling paradigm (SEIR) that hinder the efforts to accurately characterize the emer...

Title: Detection of high prevalence of Plasmodium falciparum histidine-rich protein 2/3 gene deletions in Assosa zone, Ethiopia : implication for malaria diagnosis
Author: Janies, Daniel, Blackburn, Kayla, Lopez, Karen, Lo, Eugenia
Date Created: 2021
Subjects--Topical: Communicable diseases, Malaria
Description: Background Rapid diagnostic tests (RDTs) targeting histidine rich protein 2(HRP2) are widely used for diagnosis of Plasmodium falciparum infections. Besides PfHRP2, the PfHRP3 antigen contributes to the detection of P. falciparum infections in PfH...