Browsing Faculty Works, Biocomplexity Institute by Title
Now showing items 1-20 of 252
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A Network Biology Approach to Denitrification in Pseudomonas aeruginosa
(2015-02-23)Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of ... -
A Simulation Optimization Approach to Epidemic Forecasting
(PLOS, 2013-06-27)Reliable forecasts of influenza can aid in the control of both seasonal and pandemic outbreaks. We introduce a simulation optimization (SIMOP) approach for forecasting the influenza epidemic curve. This study represents ... -
Accuracy of epidemiological inferences based on publicly available information: retrospective comparative analysis of line lists of human cases infected with influenza A(H7N9) in China
(2014-05-28)Background Appropriate public health responses to infectious disease threats should be based on best-available evidence, which requires timely reliable data for appropriate analysis. During the early stages of epidemics, ... -
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
(2011-07-20)Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The ... -
Adaptive Imaging Cytometry to Estimate Parameters of Gene Networks Models in Systems and Synthetic Biology
(PLOS, 2014-09-11)The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists ... -
Age-related variations in the methylome associated with gene expression in human monocytes and T cells
(Springer Nature, 2014-11)Age-related variations in DNA methylation have been reported; however, the functional relevance of these differentially methylated sites (age-dMS) are unclear. Here we report potentially functional age-dMS, defined as ... -
An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors
(Public Library of Science, 2009-01-09)Nucleoside analogs used in antiretroviral treatment have been associated with mitochondrial toxicity. The polymerase-gamma hypothesis states that this toxicity stems from the analogs' inhibition of the mitochondrial DNA ... -
Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype
(Nature Publishing Group, 2014-05)Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse ... -
Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing
(PLoS, 2012-03-12)Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this ... -
Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions
(2007-11-08)Background: Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite ... -
Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages
(2008-03-04)Background Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence ... -
An analytical framework for optimizing variant discovery from personal genomes
(Springer Nature, 2015-02)The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of genome-wide sequencing, particularly in the clinic. However, performance testing is currently complicated by the ... -
An anomalous type IV secretion system in Rickettsia is evolutionarily conserved
(Public Library of Science, 2009-03-12)Background: Bacterial type IV secretion systems (T4SSs) comprise a diverse transporter family functioning in conjugation, competence, and effector molecule (DNA and/or protein) translocation. Thirteen genome sequences from ... -
Antimicrobial Resistance Prediction in PATRIC and RAST
(Springer Nature, 2016-06-14)The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic ... -
Arlington County Emergency Alerts: Enhancing Enrollment and Effectiveness
(Virginia Tech, 2017)Emergency alerts are an efficient tool for keeping populations well informed during high-risk situations. In collaboration with Arlington County, our laboratory conducted a pilot study to identify messaging patterns that ... -
Assessing Glucose Uptake through the Yeast Hexose Transporter 1 (Hxt1)
(PLOS, 2015-03-27)The transport of glucose across the plasma membrane is mediated by members of the glucose transporter family. In this study, we investigated glucose uptake through the yeast hexose transporter 1 (Hxt1) by measuring ... -
An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications
(PLOS, 2009-10-23)The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. ... -
An attenuated Lassa vaccine in SIV-infected rhesus macaques does not persist or cause arenavirus disease but does elicit Lassa virus-specific immunity
(2013-02-12)Background Lassa hemorrhagic fever (LHF) is a rodent-borne viral disease that can be fatal for human beings. In this study, an attenuated Lassa vaccine candidate, ML29, was tested in SIV-infected rhesus macaques for its ... -
Bayesian estimation of genetic parameters for multivariate threshold and continuous phenotypes and molecular genetic data in simulated horse populations using Gibbs sampling
(2007-05-09)Background Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties ... -
BioFlow: a web based workflow management software for design and execution of genomics pipelines
(2014-09-18)Background Bioinformatics data analysis is usually done sequentially by chaining together multiple tools. These are created by writing scripts and tracking the inputs and outputs of all stages. Writing such scripts require ...
