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: 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: 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: 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: 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: 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: 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: A subterminal growth zone at arm tip likely underlies life-long indeterminate growth in brittle stars
Author: Janies, Daniel, Machado, Denis Jacob, Reid, Robert, Kofsky, Janice
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: Background Echinoderms are a phylum of marine invertebrates with close phylogenetic relationships to chordates. Many members of the phylum Echinodermata are capable of extensive post-traumatic regeneration and life-long indeterminate growth. Diffe...

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: 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: 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: 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: 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...