Research articles, presentations, and other scholarship

Recent Submissions

  • Cyber War Game in Temporal Networks 

    Cho, Jin-Hee; Gao, Jianxi (PLOS, 2016-02-09)
    In a cyber war game where a network is fully distributed and characterized by resource constraints and high dynamics, attackers or defenders often face a situation that may require optimal strategies to win the game with ...
  • 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) ...
  • EpiViewer: an epidemiological application for exploring time series data 

    Thorve, Swapna; Wilson, Mandy L.; Lewis, Bryan L.; Swarup, Samarth; Vullikanti, Anil Kumar S.; Marathe, Madhav V. (2018-11-22)
    Abstract Background Visualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers ...
  • Burst of Young Retrogenes and Independent Retrogene Formation in Mammals 

    Pan, Deng; Zhang, Liqing (PLOS, 2009-03-27)
    Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes ...
  • An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications 

    Pan, Deng; Zhang, Liqing (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. ...
  • Discovering Networks of Perturbed Biological Processes in Hepatocyte Cultures 

    Lasher, Christopher D.; Rajagopalan, Padmavathy; Murali, T. M. (PLOS, 2011-01-05)
    The liver plays a vital role in glucose homeostasis, the synthesis of bile acids and the detoxification of foreign substances. Liver culture systems are widely used to test adverse effects of drugs and environmental ...
  • Prediction of Disease and Phenotype Associations from Genome-Wide Association Studies 

    Lewis, Stephanie N.; Nsoesie, Elaine; Weeks, Charles; Qiao, Dan; Zhang, Liqing (PLOS, 2011-11-04)
    Background Genome wide association studies (GWAS) have proven useful as a method for identifying genetic variations associated with diseases. In this study, we analyzed GWAS data for 61 diseases and phenotypes to elucidate ...
  • User-elicited dual-hand interactions for manipulating 3D objects in virtual reality environments 

    Nanjappan, Vijayakumar; Liang, Hai-Ning; Lu, Feiyu; Papangelis, Konstantinos; Yue, Yong; Man, Ka L (2018-10-29)
    Abstract Virtual reality technologies (VR) have advanced rapidly in the last few years. Prime examples include the Oculus RIFT and HTC Vive that are both head-worn/mounted displays (HMDs). VR HMDs enable a ...
  • Connecting the Dots between PubMed Abstracts 

    Hossain, M. Shahriar; Gresock, Joseph; Edmonds, Yvette; Helm, Richard; Potts, Malcolm; Ramakrishnan, Naren (PLOS, 2012-01-03)
    Background There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but ...
  • A Partition Function Approximation Using Elementary Symmetric Functions 

    Anandakrishnan, Ramu (PLOS, 2012-12-12)
    In statistical mechanics, the canonical partition function can be used to compute equilibrium properties of a physical system. Calculating however, is in general computationally intractable, since the computation scales ...
  • Point Charges Optimally Placed to Represent the Multipole Expansion of Charge Distributions 

    Anandakrishnan, Ramu; Baker, Charles; Izadi, Saeed; Onufriev, Alexey V. (PLOS, 2013-07-04)
    We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge ...
  • Network Effects of Risk Behavior Change Following Prophylactic Interventions 

    Rajaraman, Rajmohan; Sun, Zhifeng; Sundaram, Ravi; Vullikanti, Anil Kumar S. (PLOS, 2013-08-01)
    We formulated a network-based model to understand how risk behavior change in conjunction with failure of prophylactic interventions can lead to unintended outcomes where “less (intervention) is more (effective).” Our model ...
  • What to know before forecasting the flu 

    Chakraborty, Prithwish; Lewis, Bryan; Eubank, Stephen; Brownstein, John S.; Marathe, Madhav; Ramakrishnan, Naren (PLOS, 2018-10-12)
    Accurate and timely influenza (flu) forecasting has gained significant traction in recent times. If done well, such forecasting can aid in deploying effective public health measures. Unlike other statistical or machine ...
  • Protein Complex Identification by Integrating Protein-Protein Interaction Evidence from Multiple Sources 

    Xu, Bo; Lin, Hongfei; Chen, Yang; Yang, Zhihao; Liu, Hongfang (PLOS, 2013-12-27)
    Background Understanding protein complexes is important for understanding the science of cellular organization and function. Many computational methods have been developed to identify protein complexes from experimentally ...
  • The Abridgment and Relaxation Time for a Linear Multi-Scale Model Based on Multiple Site Phosphorylation 

    Wang, Shuo; Cao, Yang (PLOS, 2015-08-11)
    Random effect in cellular systems is an important topic in systems biology and often simulated with Gillespie’s stochastic simulation algorithm (SSA). Abridgment refers to model reduction that approximates a group of ...
  • Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling 

    Zhang, Yonggang; Arango, Gustavo; Li, Fang; Xiao, Xiao; Putatunda, Raj; Yu, Jun; Yang, Xiao-Feng; Wang, Hong; Watson, Layne T; Zhang, Liqing; Hu, Wenhui (2018-09-10)
    Abstract Background CRISPR/CAS9 (epi)genome editing revolutionized the field of gene and cell therapy. Our previous study demonstrated that a rapid and robust reactivation of ...
  • Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data 

    Badr, Eman; ElHefnawi, Mahmoud; Heath, Lenwood S. (PLOS, 2016-11-18)
    Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors ...
  • Personal Anomaly Detection and Smart-Phone Security 

    Xiong, Huijun; Yao, Danfeng (Daphne) (Virginia Tech, 2010-04-22)
    Mobile devices increasingly become the computing platform for networked applications such as Web and email. This development requires strong guarantees on the system integrity and data security of mobile devices against ...
  • Keystroke-Dynamics Authentication Against Synthetic Forgeries 

    Stefan, Deian; Yao, Danfeng (Daphne) (IEEE, 2010)
    We describe the use of keystroke-dynamics patterns for authentication and detecting infected hosts, and evaluate its robustness against forgery attacks. Specifically, we present a remote authentication framework called ...
  • A Declarative Approach to Hardening Services Against QoS Vulnerabilities 

    Kwon, Young-Wo; Tilevich, Eli (IEEE, 2011)
    The Quality of Service (QoS) in a distributed service-oriented application can be negatively affected by a variety of factors. Network volatility, hostile exploits, poor service management, all can prevent a service-oriented ...

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