Research articles, presentations, and other scholarship

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  • 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, ...
  • 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 ...
  • 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 ...
  • 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. ...
  • 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 ...
  • Setting development goals using stochastic dynamical system models 

    Ranganathan, Shyam; Nicolis, Stamatios C.; Swain, Ranjula Bali; Sumpter, David J. T. (PLOS, 2017-02-27)
    The Millennium Development Goals (MDG) programme was an ambitious attempt to encourage a globalised solution to important but often-overlooked development problems. The programme led to wide-ranging development but it has ...
  • Jaccard distance based weighted sparse representation for coarse-to-fine plant species recognition 

    Zhang, Shanwen; Wu, Xiaowei; You, Zhuhong (PLOS, 2017-06-07)
    Leaf based plant species recognition plays an important role in ecological protection, however its application to large and modern leaf databases has been a long-standing obstacle due to the computational cost and feasibility. ...
  • The CCP Selector: Scalable Algorithms for Sparse Ridge Regression from Chance-Constrained Programming 

    Xie, W; Deng, X
    Sparse regression and variable selection for large-scale data have been rapidly developed in the past decades. This work focuses on sparse ridge regression, which considers the exact $L_0$ norm to pursue the sparsity. We ...
  • A Statistical Framework for the Adaptive Management of Epidemiological Interventions 

    Merl, Daniel; Johnson, Leah R.; Gramacy, Robert B.; Mangel, Marc (PLOS, 2009)
    Background: Epidemiological interventions aim to control the spread of infectious disease through various mechanisms, each carrying a different associated cost. Methodology: We describe a flexible statistical framework for ...

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