Research articles, presentations, and other scholarship

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  • Can long-term historical data from electronic medical records improve surveillance for epidemics of acute respiratory infections? A systematic evaluation 

    Zheng, Hongzhang; Woodall, William H.; Carlson, Abigail L.; DeLisle, Sylvain (PLOS, 2018-01-31)
    Background As the deployment of electronic medical records (EMR) expands, so is the availability of long-term datasets that could serve to enhance public health surveillance. We hypothesized that EMR-based surveillance ...
  • Effect of Using Mobile Phones on Driver’s Control Behavior Based on Naturalistic Driving Data 

    Zhang, Lanfang; Cui, Boyu; Yang, Minhao; Guo, Feng; Wang, Junhua (MDPI, 2019-04-25)
    Distracted driving behaviors are closely related to crash risk, with the use of mobile phones during driving being one of the leading causes of accidents. This paper attempts to investigate the impact of cell phone use ...
  • Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles 

    Highnam, Gareth; Franck, Christopher; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David (2013-01)
    Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping ...
  • XTALKDB: a database of signaling pathway crosstalk 

    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T. M. (2017-01-04)
    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents ...
  • Two-phase Monte Carlo simulation for partitioning the effects of epistemic and aleatory uncertainty in TMDL modeling 

    Mishra, A.; Ahmadisharaf, E.; Benham, B.L.; Gallagher, D.L.; Reckhow, K.H.; Smith, E.P. (American Society of Civil Engineers (ASCE), 2018-10-29)
    A two-phase Monte Carlo simulation (TPMCS) uncertainty analysis framework is used to analyze epistemic and aleatory uncertainty associated with simulated exceedances of an in-stream fecal coliform (FC) water quality criterion ...
  • Profile monitoring based quality control method for fused deposition modeling process 

    He, K.; Zhang, Q.; Hong, Y. (Springer New York LLC, 2018-05-26)
    In order to monitor the quality of parts in printing, the methodology to monitor the geometric quality of the printed parts in fused deposition modeling process is researched. A non-contact measurement method based on ...
  • Panamanian frog species host unique skin bacterial communities 

    Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibanez, Roberto; Harris, Reid N. (Frontiers, 2015-10-27)
    Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, ...
  • System and method for genotyping using informed error profiles 

    Virginia Tech Intellectual Properties, Inc.; Mittelman, David A.; Franck, Christopher T. (United States Patent and Trademark Office, 2018-03-13)
    A system and method for genotyping tandem repeats in sequencing data. The invention uses Bayesian model selection guided by an empirically-derived error model that incorporates properties of sequence reads and reference ...
  • vi-HMM: a novel HMM-based method for sequence variant identification in short-read data 

    Tang, Man; Hasan, Mohammad Shabbir; Zhu, Hongxiao; Zhang, Liqing; Wu, Xiaowei (2019-02-13)
    Abstract Background Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), ...
  • Age-related variations in the methylome associated with gene expression in human monocytes and T cells 

    Reynolds, Lindsay M.; Taylor, Jackson R.; Ding, Jingzhong; Lohman, Kurt; Johnson, Craig; Siscovick, David; Burke, Gregory L.; Post, Wendy; Shea, Steven; Jacobs, David R., Jr.; Stunnenberg, Hendrik; Kritchevsky, Stephen B.; Hoeschele, Ina; McCall, Charles E.; Herrington, David M.; Tracy, Russell P.; Liu, Yongmei (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 ...
  • Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis 

    Liu, Yongmei; Reynolds, Lindsay M.; Ding, Jingzhong; Hou, Li; Lohman, Kurt; Young, Tracey; Cui, Wei; Huang, Zhiqing; Grenier, Carole; Wan, Ma; Stunnenberg, Hendrik G.; Siscovick, David; Hou, Lifang; Psaty, Bruce M.; Rich, Stephen S.; Rotter, Jerome I.; Kaufman, Joel D.; Burke, Gregory L.; Murphy, Susan; Jacobs, David R., Jr.; Post, Wendy; Hoeschele, Ina; Bell, Douglas A.; Herrington, David; Parks, John S.; Tracy, Russell P.; McCall, Charles E.; Stein, James H. (Springer Nature, 2017-08-30)
    Little is known regarding the epigenetic basis of atherosclerosis. Here we present the CD14+ blood monocyte transcriptome and epigenome signatures associated with human atherosclerosis. The transcriptome signature includes ...
  • The effect of temporal aggregation level in social network monitoring 

    Zhao, Meng J.; Driscoll, Anne R.; Sengupta, Srijan; Stevens, Nathaniel T.; Fricker, Ronald D., Jr.; Woodall, William H. (PLOS, 2018-12-19)
    Social networks have become ubiquitous in modern society, which makes social network monitoring a research area of significant practical importance. Social network data consist of social interactions between pairs of ...
  • Cell Cycle Model System for Advancing Cancer Biomarker Research 

    Lazar, Iulia M.; Hoeschele, Ina; de Morais, Juliana; Tenga, Milagros J. (Springer Nature, 2017-12-21)
    Progress in understanding the complexity of a devastating disease such as cancer has underscored the need for developing comprehensive panels of molecular markers for early disease detection and precision medicine applications. ...
  • Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma 

    Connolly, Nina P.; Shetty, Amol C.; Stokum, Jesse A.; Hoeschele, Ina; Siegel, Marni B.; Miller, C. Ryan; Kim, Anthony J.; Ho, Cheng-Ying; Davila, Eduardo; Simard, J. Marc; Devine, Scott E.; Rossmeisl, John H.; Holland, Eric C.; Winkles, Jeffrey A.; Woodworth, Graeme F. (Springer Nature, 2018-01-19)
    Glioma is a unique neoplastic disease that develops exclusively in the central nervous system (CNS) and rarely metastasizes to other tissues. This feature strongly implicates the tumor-host CNS microenvironment in gliomagenesis ...
  • Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models 

    Tegge, Allison N.; Rodrigues, Richard R.; Larkin, Adam L.; Vu, Lucas; Murali, T. M.; Rajagopalan, Padmavathy (Springer Nature, 2018-07-27)
    Liver homeostasis requires the presence of both parenchymal and non-parenchymal cells (NPCs). However, systems biology studies of the liver have primarily focused on hepatocytes. Using an organotypic three-dimensional (3D) ...
  • Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells 

    Luo, Yanting; He, Jianlin; Xu, Xiguang; Sun, Ming-an; Wu, Xiaowei; Lu, Xuemei; Xie, Hehuang (PLOS, 2018-03)
    Embryonic stem cells (ESCs) consist of a population of self-renewing cells displaying extensive phenotypic and functional heterogeneity. Research towards the understanding of the epigenetic mechanisms underlying the ...
  • Changing measurements or changing movements? Sampling scale and movement model identifiability across generations of biologging technology 

    Johnson, Leah R.; Boersch-Supan, Philipp H.; Phillips, Richard A.; Ryan, Sadie J. (Wiley-Blackwell, 2017-10-03)
    Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. Over time, sensor technology for measuring movement ...
  • Regret Expression and Social Learning Increases Delay to Sexual Gratification 

    Quisenberry, Amanda J.; Eddy, Celia R.; Patterson, David L.; Franck, Christopher T.; Bickel, Warren K. (PLOS, 2015-08-17)
    Objective Modification and prevention of risky sexual behavior is important to individuals’ health and public health policy. This study employed a novel sexual discounting task to elucidate the effects of social learning ...
  • Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus 

    Walke, Jenifer B.; Becker, Matthew H.; Loftus, Stephen C.; House, Leanna L.; Teotonio, Thais L.; Minbiole, Kevin P. C.; Belden, Lisa K. (PLOS, 2015-10-07)
    The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian ...
  • Stuck in Time: Negative Income Shock Constricts the Temporal Window of Valuation Spanning the Future and the Past 

    Bickel, Warren K.; Wilson, A. George; Chen, Chen; Koffarnus, Mikhail N.; Franck, Christopher T. (PLOS, 2016-09-15)
    Insufficient resources are associated with negative consequences including decreased valuation of future reinforcers. To determine if these effects result from scarcity, we examined the consequences of acute, abrupt changes ...

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