Search results | J. Murrey Atkins Library

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: 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: 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: 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: 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: Content and sentiment surveillance (CSI) : A critical component for modeling modern epidemics
Author: Janies, Daniel, Chen, Shi, Zhang, Dongsong
Date Created: 2023
Subjects--Topical: Communicable diseases, Biology
Description: 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...

Title: EchinoDB : an update to the web-based application for genomic and transcriptomic data on echinoderms
Author: Janies, Daniel
Date Created: 2022
Subjects--Topical: Genomics, Biology
Description: Background: Here we release a new version of EchinoDB, EchinoDB v2.0 (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralog...

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: 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: 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: Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance
Author: Janies, Daniel, Lo, Eugenia, Kepple, Daniel
Date Created: 2019
Subjects--Topical: Communicable diseases, Malaria
Description: Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the ex...

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: 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: 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: 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: 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: 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: 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: 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...