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The Department of Computer Science has an accredited undergraduate program that offers specialized ‘tracks’ of study in key areas. Undergraduates are prepared by graduation for pursuing a computing career or for graduate study. Our active corporate partners program offers internships and permanent employment to our students. Students are encouraged to participate in research experiences during their studies. Capstone courses provide significant team project experiences. The graduate program offers M.S. and Ph.D. degrees, emphasizing thesis work both at the main campus in Blacksburg and at the Northern Virginia Center. About two-thirds of the graduate students are pursuing the Ph.D. degree. The faculty, among whom there are 12 NSF or DOE CAREER Award winners, are active researchers who are visible contributors to the profession and have achieved significant honors.

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Recent Submissions

  • Efficient Synthesis of Mutants Using Genetic Crosses 

    Pratapa, Aditya; Jalihal, Amogh P.; Ravi, S. S.; Murali, T. M. (2018-06-29)
    The genetic cross is a fundamental, flexible, and widely-used experimental technique to create new mutant strains from existing ones. Surprisingly, the problem of how to efficiently compute a sequence of crosses that can ...
  • Large-scale protein function prediction using heterogeneous ensembles 

    Wang, Linhua; Law, Jeffrey; Kale, Shiv D.; Murali, T. M.; Pandey, Gaurav (F1000Research, 2018-09-28)
    Heterogeneous ensembles are an effective approach in scenarios where the ideal data type and/or individual predictor are unclear for a given problem. These ensembles have shown promise for protein function prediction (PFP), ...
  • The PathLinker app: Connect the dots in protein interaction networks 

    Gil, Daniel P.; Law, Jeffrey N.; Murali, T. M. (F1000Research, 2017-01-20)
    PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors ...
  • Computational prediction of host-pathogen protein–protein interactions 

    Dyer, Matthew D.; Murali, T. M.; Sobral, Bruno W. (Oxford University Press, 2007)
    Motivation: Infectious diseases such as malaria result in millions of deaths each year. An important aspect of any host-pathogen system is the mechanism by which a pathogen can infect its host. One method of infection is ...
  • Automating the PathLinker app for Cytoscape 

    Huang, Li Jun; Law, Jeffrey N.; Murali, T. M. (F1000Research, 2018-06-12)
    PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network ...
  • Accurate and Efficient Gene Function Prediction using a Multi-Bacterial Network 

    Law, Jeffrey N.; Kale, Shiv D.; Murali, T. M. (2019-05-24)
    The rapid rise in newly sequenced genomes requires the development of computational methods to supplement experimental functional annotations. The challenge that arises is to develop methods for gene function prediction ...
  • Connectivity Measures for Signaling Pathway Topologies 

    Franzese, Nicholas; Groce, Adam; Murali, T. M.; Ritz, Anna (Virginia Tech, 2019-03-30)
    Characterizing cellular responses to different extrinsic signals is an active area of research, and curated pathway databases describe these complex signaling reactions. Here, we revisit a fundamental question in signaling ...
  • Identifying Human Interactors of SARS-CoV-2 Proteins and Drug Targets for COVID-19 using Network-Based Label Propagation 

    Law, Jeffrey N.; Akers, Kyle; Tasnina, Nure; Santina, Catherine M. Della; Kshirsagar, Meghana; Klein-Seetharaman, Judith; Crovella, Mark; Rajagopalan, Padmavathy; Kasif, Simon; Murali, T. M. (Virginia Tech, 2020-06-22)
    Motivated by the critical need to identify new treatments for COVID- 19, we present a genome-scale, systems-level computational approach to prioritize drug targets based on their potential to regulate host- virus interactions ...
  • Teaching Natural Language Processing through Big Data Text Summarization with Problem-Based Learning 

    Li, Liuqing; Geissinger, Jack; Ingram, William A.; Fox, Edward A. (Sciendo, 2020)
    Natural language processing (NLP) covers a large number of topics and tasks related to data and information management, leading to a complex and challenging teaching process. Meanwhile, problem-based learning is a teaching ...
  • SBML Level 3: an extensible format for the exchange and reuse of biological models 

    Keating, Sarah M.; Waltemath, Dagmar; Koenig, Matthias; Zhang, Fengkai; Draeger, Andreas; Chaouiya, Claudine; Bergmann, Frank T.; Finney, Andrew; Gillespie, Colin S.; Helikar, Tomas; Hoops, Stefan; Malik-Sheriff, Rahuman S.; Moodie, Stuart L.; Moraru, Ion I.; Myers, Chris J.; Naldi, Aurelien; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Swat, Maciej J.; Thieffry, Denis; Watanabe, Leandro; Wilkinson, Darren J.; Blinov, Michael L.; Begley, Kimberly; Faeder, James R.; Gomez, Harold F.; Hamm, Thomas M.; Inagaki, Yuichiro; Liebermeister, Wolfram; Lister, Allyson L.; Lucio, Daniel; Mjolsness, Eric; Proctor, Carole J.; Raman, Karthik; Rodriguez, Nicolas; Shaffer, Clifford A.; Shapiro, Bruce E.; Stelling, Joerg; Swainston, Neil; Tanimura, Naoki; Wagner, John; Meier-Schellersheim, Martin; Sauro, Herbert M.; Palsson, Bernhard; Bolouri, Hamid; Kitano, Hiroaki; Funahashi, Akira; Hermjakob, Henning; Doyle, John C.; Hucka, Michael (2020-08)
    Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We ...
  • Cell cycle control and environmental response by second messengers in Caulobacter crescentus 

    Xu, Chunrui; Weston, Bronson R.; Tyson, John J.; Cao, Yang (2020-09-30)
    Abstract Background Second messengers, c-di-GMP and (p)ppGpp, are vital regulatory molecules in bacteria, influencing cellular processes such as biofilm formation, transcription, ...
  • Crossing complexity of space-filling curves reveals entanglement of S-phase DNA 

    Kinney, Nick; Hickman, Molly; Anandakrishnan, Ramu; Garner, Harold R. (2020-08-31)
    Space-filling curves have been used for decades to study the folding principles of globular proteins, compact polymers, and chromatin. Formally, space-filling curves trace a single circuit through a set of points (x,y,z); ...
  • Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants 

    Gallegos, Jenna E.; Adames, Neil R.; Rogers, Mark F.; Kraikivski, Pavel; Ibele, Aubrey; Nurzynski-Loth, Kevin; Kudlow, Eric; Murali, T. M.; Tyson, John J.; Peccoud, Jean (2020-05-06)
    Over the last 30 years, computational biologists have developed increasingly realistic mathematical models of the regulatory networks controlling the division of eukaryotic cells. These models capture data resulting from ...
  • Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator 

    Xiong, Yeyue; Onufriev, Alexey V. (PLOS, 2019-11-14)
    Rigid n-point water models are widely used in atomistic simulations, but have known accuracy drawbacks. Increasing the number of point charges, as well as adding electronic polarizability, are two common strategies for ...
  • DeepMicro: deep representation learning for disease prediction based on microbiome data 

    Oh, Min; Zhang, Liqing (Nature Research, 2020)
    Human microbiota plays a key role in human health and growing evidence supports the potential use of microbiome as a predictor of various diseases. However, the high-dimensionality of microbiome data, often in the order ...
  • Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro 

    Mahalak, Karley K.; Firrman, Jenni; Lee, Jung-Jin; Bittinger, Kyle; Nunez, Alberto; Mattei, Lisa M.; Zhang, Huanjia; Fett, Bryton; Bobokalonov, Jamshed; Arango-Argoty, Gustavo; Zhang, Liqing; Zhang, Guodong; Liu, Lin Shu (2020-06-25)
    The recent ban of the antimicrobial compound triclosan from use in consumer soaps followed research that showcased the risk it poses to the environment and to human health. Triclosan has been found in human plasma, urine ...
  • Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates 

    Pan, Deng; Zhang, Liqing (BioMed Central, 2007-08-02)
    Background: The rate of gene duplication is an important parameter in the study of evolution, but the influence of gene conversion and technical problems have confounded previous attempts to provide a satisfying estimate. ...
  • MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement 

    Shi, Guanqun; Zhang, Liqing; Jiang, Tao (BioMed Central, 2010)
    Background: Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions ...
  • ClaMS: A Classifier for Metagenomic Sequences 

    Pati, Amrita; Heath, Lenwood S.; Kyrpides, Nikos C.; Ivanova, Natalia (Springer, 2011)
    ClaMS – “Classifier for Metagenomic Sequences” – is a Java application for binning assembled contigs in metagenomes using user-specified training sets and initial parameters. Since ClaMS trains on sequence composition-based ...
  • LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa 

    Tian, Long; Huang, Chengjie; Mazloom, Reza; Heath, Lenwood S.; Vinatzer, Boris A. (Oxford University Press, 2020-03-30)
    High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues ...

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