Search results | J. Murrey Atkins Library

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: Venomix : a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data
Author: Janies, Daniel, Reitzel, Adam M., Macrander, Jason
Date Created: 2018
Subjects--Topical: Genomics, Biology
Description: The advent of next-generation sequencing has resulted in transcriptome-based approaches to investigate functionally significant biological components in a variety of non-model organism. This has resulted in the area of venomics: a rapidly growing ...

Title: Updated phylogeny of chikungunya virus suggests lineage-specific RNA architecture
Author: Janies, Daniel
Date Created: 2019
Subjects--Topical: Communicable diseases, Biology
Description: Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both...

Title: Twinkle twinkle brittle star : the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert, Kofsky, Janice
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: Background Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the f...

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions
Author: Janies, Daniel, Rush, Nathaniel, Witter, Zachary, Williams, John
Date Created: 2018
Subjects--Topical: Genomics, Biology
Description: 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...

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: 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: 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: Genetic variation of Plasmodium falciparum histidine-rich protein 2 and 3 in Assosa zone, Ethiopia : its impact on the performance of malaria rapid diagnostic tests
Author: Janies, Daniel, Blackburn, Kayla, Lopez, Karen, Lo, Eugenia
Date Created: 2021
Subjects--Topical: Communicable diseases, Malaria
Description: Background Rapid diagnostic tests (RDT) are commonly used for the diagnosis of malaria caused by Plasmodium falciparum. However, false negative results of RDT caused by genetic variation of P. falciparum histidine-rich protein 2 and 3 genes (pfhrp...

Title: Genetic diversity of Anopheles stephensi in Ethiopia provides insight into patterns of spread
Author: Janies, Daniel, Lopez, Karen
Date Created: 2021
Subjects--Topical: Communicable diseases, Malaria
Description: Background: The recent detection of the South Asian malaria vector Anopheles stephensi in the Horn of Africa (HOA) raises concerns about the impact of this mosquito on malaria transmission in the region. Analysis of An. stephensi genetic diversity...