Jason Caravas - Academia.edu (original) (raw)

Papers by Jason Caravas

Carolina Digital Repository (University of North Carolina at Chapel Hill), 2012

In scientific research, integration and synthesis require a common understanding of where data co... more In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

Textnames

This file resolves the identity of taxon name codes used in the phylogenetic data sets below. You... more This file resolves the identity of taxon name codes used in the phylogenetic data sets below. You can also find information about all of these name codes at : http://www.inhs.uiuc.edu/research/flytreephp/flytree/index.ph

Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages — United States, January 2022–May 2023

MMWR. Morbidity and Mortality Weekly Report

JAMA Network Open

ImportanceFew studies have prospectively assessed SARS-CoV-2 community infection in children aged... more ImportanceFew studies have prospectively assessed SARS-CoV-2 community infection in children aged 0 to 4 years. Information about SARS-CoV-2 incidence and clinical and virological features in young children could help guide prevention and mitigation strategies.ObjectiveTo assess SARS-CoV-2 incidence, clinical and virological features, and symptoms in a prospective household cohort and to compare viral load by age group, symptoms, and SARS-CoV-2 lineage in young children, older children, and adults.Design, Setting, and ParticipantsThis prospective cohort study enrolled 690 participants from 175 Maryland households with 1 or more children aged 0 to 4 years between November 24, 2020, and October 15, 2021. For 8 months after enrollment, participants completed weekly symptom questionnaires and submitted self-collected nasal swabs for SARS-CoV-2 qualitative real-time reverse transcriptase polymerase chain reaction (RT-PCR) testing, quantitative RT-PCR testing, and viral lineage determinat...

Concatenated mitochondial gene alignment (Gblock)

Mitochondrial genes used in this study, Gblock data set. See Supplemental Table S2. ATP6, 1, 666;... more Mitochondrial genes used in this study, Gblock data set. See Supplemental Table S2. ATP6, 1, 666; ATP8, 667, 747; Cox1, 748, 2274; Cox2, 2275, 2955; Cox3, 2956, 3738; CytB, 3739, 4869; ND1, 4870, 5793; ND2, 5794, 6651; ND3, 6652, 6999; ND4, 7000, 8307; ND4L, 8308, 8601; ND5, 8602, 10305; ND6, 10306, 10812

PEPCK_alnFLYTREE

Alignment of dipteran PEPCK gene sequences from the FLYTREE project in fasta format

GART_alnFLYTREE

Alignment of dipteran GART gene sequences from the FLYTREE project in fasta format

CAD_noIntrons.alnFLYTREE

Alignment of dipteran CAD (= CPSase, rudimentary) gene sequences from the FLYTREE project in fast... more Alignment of dipteran CAD (= CPSase, rudimentary) gene sequences from the FLYTREE project in fasta format

AATS_Exon1alnFLYTREE

Alignment of dipteran AATS1 gene sequences from the FLYTREE project in fasta format

Small_rRNA12S-alnFLYTREE

Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in ... more Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format

Nad4L-alnFLYTREE

Alignment of dipteran mitochondrial NADH4L gene sequences from the FLYTREE project in fasta format

Cytb-alnFLYTREE

Alignment of dipteran mitochondrial cyt-b gene sequences from the FLYTREE project in fasta format

Cox3-alnFLYTREE

Alignment of dipteran mitochondrial CO-III (Cox3) gene sequences from the FLYTREE project in fast... more Alignment of dipteran mitochondrial CO-III (Cox3) gene sequences from the FLYTREE project in fasta format

Cox1-alnFLYTREE

Alignment of dipteran mitochondrial CO1 gene sequences from the FLYTREE project in fasta format

SYX1A_alnFLYTREE

Alignment of dipteran SYX1A gene sequences from the FLYTREE project in fasta format

Supplemental material for: Characterization of Legionella from watersheds in British Columbia, Canada

Supplemental material for the paper: Characterization of Legionella from watersheds in British Co... more Supplemental material for the paper: Characterization of Legionella from watersheds in British Columbia, Canada. Contains Tables S1-S3 and Figures S1-S3.

Mitochondrial genome phylogeny of the Schizophora

6th International Congress of Dipterology, 2006

IntroductoryThe evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has res... more IntroductoryThe evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of many new variant lineages that have exacerbated the COVID-19 pandemic. Some of those variants were designated as variants of concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact on vaccines. To ascertain and rank the risk of VOCs and VOIs, we analyzed their ability to escape from vaccine-induced antibodies. The variants showed differential reductions in neutralization and replication titers by post-vaccination sera. Although the Omicron variant showed the most escape from neutralization, sera collected after a third dose of vaccine (booster sera) retained moderate neutralizing activity against that variant. Therefore, vaccination remains the most effective strategy to combat the COVID-19 pandemic.

Data from: Shaking the Diptera tree of life: performance analysis of nuclear and mitochondrial sequence data partitions

The value of mitochondrial versus nuclear gene sequence data in phylogenetic analysis has receive... more The value of mitochondrial versus nuclear gene sequence data in phylogenetic analysis has received much attention without yielding definitive conclusions. Theoretical arguments and empirical data suggest a lower phylogenetic utility than equivalent nuclear gene sequences, but there are many examples of important progress made using mitochondrial sequences. We undertook a systematic performance analysis of mitochondrial and nuclear sequence partitions taken from a representative sample of dipteran species. When analysed alone, mitochondrial genes generally performed less well than nuclear genes; however, these genes resolved some branches for which nuclear genes failed. Moreover, the combined use of mitochondrial and nuclear sequences produced superior results without artifacts for nodes where mitochondrial and nuclear gene data generated conflicting topologies. These findings strongly advocate the inclusion of mitochondrial sequences, even in deep phylogeny reconstruction. Comparison of tree support between our and previous analyses identified robustly supported high-confidence clades in the Diptera, but also revealed problematic groupings in need of further analysis

Fatima all contributed to this project. iv TABLE OF CONTENTS Dedication__________________________... more Fatima all contributed to this project. iv TABLE OF CONTENTS Dedication__________________________________________________________ ii Acknowledgements___________________________________________________ iii List of Tables________________________________________________________ vi List of Figures _______________________________________________________ vii Chapter 1 "Introduction"_______________________________________________ Mitochondrial and nuclear gene biology_____________________________ Mitochondrial and nuclear genes in phylogeny reconstruction____________ Divergence time estimation_______________________________________ Dipteran diversification: a Gordian superknot on wings_________________ Chapter 2 "Shaking the fly tree of life: performance analysis of nuclear and mitochondrial sequence data partitions"__________________________