{"id":65,"date":"2024-03-24T21:46:53","date_gmt":"2024-03-24T21:46:53","guid":{"rendered":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/?page_id=65"},"modified":"2024-03-24T21:46:53","modified_gmt":"2024-03-24T21:46:53","slug":"t-m-muralis-research-group","status":"publish","type":"page","link":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/t-m-muralis-research-group\/","title":{"rendered":"T. M. MURALI’S RESEARCH GROUP"},"content":{"rendered":"\n

Graduate students<\/h2>\n\n\n\n
    \n
  1. Blessy Antony, Ph. D., Computer Science, co-advised with Dr. Anuj Karpatne, predictive models of viral evolution<\/li>\n\n\n\n
  2. Maryam Haghani, Ph. D., Computer Science, co-advised with Dr. Debswapna Bhattacharya, prediction of protein complex structures<\/li>\n\n\n\n
  3. Parker Niccum, Ph. D., Genetics Bioinformatics and Computational Biology, co-advised with Dr. Padma Rajagopalan<\/li>\n\n\n\n
  4. Yiqi Su, Ph. D., Computer Science, inference of gene regulatory networks<\/li>\n\n\n\n
  5. Nure Tasnina, Ph.D., Computer Science, drug-drug interactions<\/li>\n<\/ol>\n\n\n\n

    Former Post-doctoral researchers<\/h2>\n\n\n\n
      \n
    1. Hyunju Kim<\/a>, Ph.D., Physics, University of Notre Dame, 2011. Currently a post-doctoral researcher with Prof. Paul Davies<\/a>, Arizona State University.<\/li>\n\n\n\n
    2. Anna Ritz<\/a>, Ph.D., Computer Science, Brown University, 2012. Currently an Associate Professor in the Department of Biology, Reed College.<\/li>\n\n\n\n
    3. Allison Tegge<\/a>, Ph.D., Informatics, University of Missouri, Columbia, 2012. Co-advised by Padma Rajagopalan. Supported by an F32 fellowship from the National Institute for Environmental Health Sciences. Currently a Research Assistant Professor in the Department of Statistics, Virginia Tech.<\/li>\n<\/ol>\n\n\n\n

      Former Ph. D. students<\/h2>\n\n\n\n
        \n
      1. Jeffrey N. Law<\/a>, Ph.D., Genetics, Bioinformatics, and Computational Biology, 2020, Development and Application of Network Algorithms for Prediction of Gene Function and Response to Viral Infection and Chemicals<\/em>. Currently a post-doctoral fellow at the National Renewable Energy Laboratory.<\/li>\n\n\n\n
      2. Aditya Bharadwaj<\/a>, Ph.D., Computer Science, 2020, Mixed-initiative methods for following design guidelines in creative tasks<\/em>. Currently at B12 Solutions.<\/li>\n\n\n\n
      3. Aditya Pratapa<\/a>, Ph.D., Computer Science, experiment design, 2020, Algorithms for regulatory network inference and experiment planning in systems biology<\/em>. Currently a post-doctoral fellow at the Broad Institute of Harvard and MIT.<\/li>\n\n\n\n
      4. Amogh Jalihal<\/a>, Ph.D., Genetics, Bioinformatics, and Computational Biology, 2020, co-advised with John Tyson, Mathematical modeling of macronutrient signaling in Saccharomyces cerevisiae<\/em>. Currently a post-doctoral fellow in the Department of Systems Biology at the Harvard Medical School.<\/li>\n\n\n\n
      5. Ahsanur Rahman<\/a>, Ph.D., Computer Science, 2015, Unstable Communities in Network Ensembles<\/em>. Currently an Assistant Professor in the Department of Electrical and Computer Engineering Department in North South University, Dhaka, Bangladesh.<\/li>\n\n\n\n
      6. Christopher L. Poirel<\/a>, Ph. D., Computer Science, 2013, Bridging Methodological Gaps in Network-Based Systems Biology<\/a><\/em>, supported by a National Science Foundation Graduate Research Fellowship. Currently a senior data scientist at RedOwl Analytics.<\/li>\n\n\n\n
      7. Yared Kidane, Ph.D., Genetics, Bioinformatics, and Computational Biology, 2012, co-advised with Christopher Lawrence<\/a>, The Landscape of Host Transcriptional Response Programs Commonly Perturbed by Infectious Pathogens: Towards Host-Oriented Broad-Spectrum Drug Targets<\/a><\/em>, supported in 2011-2012 by a Dissertation Fellowship Award from the Southern Regional Education Board and in 2008-2010 by Virginia Tech’s Intiative to Maximize Student Diversity Program<\/a>. Currently a research scientist at the Universities Space Research Association<\/a>, working at the NASA\/Johnson Space Center.<\/li>\n\n\n\n
      8. Christopher D. Lasher<\/a>, Ph. D., Genetics, Bioinformatics, and Computational Biology, 2011, co-advised with Padma Rajagopalan<\/a>, Discovering contextual connections between biological processes using high-throughput data<\/a><\/em>. Currently a bioinformatics analyst at 5AM Solutions.<\/li>\n\n\n\n
      9. Matthew D. Dyer<\/a>, Ph.D. Genetics, Bioinformatics, and Computational Biology, 2008, co-advised with Bruno Sobral<\/a>, Pathosystems Biology: Computational Prediction and Analysis of Host-Pathogen Protein Interaction Networks<\/a><\/em>. Currently the Associate Director for Bioinformatics and Community at Life Technologies. The Virginia Tech Graduate School selected Dyer for the “Outstanding Dissertation in Science and Engineering” award in March 2009.<\/strong><\/li>\n\n\n\n
      10. Corban G. Rivera<\/a>, Ph. D., Computer Science, 2008, Automatic Reconstruction of the Building Blocks of Molecular Interaction Networks<\/em><\/a>. Currently a bioinformatics research scientist at DuPont Inc.<\/li>\n<\/ol>\n\n\n\n

        Former M. S. students<\/h2>\n\n\n\n
          \n
        1. Malabika Sen, M.S., Computer Science, 2021, Supervised Inference of Gene Regulatory Networks<\/em>.<\/li>\n\n\n\n
        2. Tanya Tyagi, M.S., Computer Science, 2020, Benchmarking Methods For Predicting Phenotype Gene Associations<\/em>. Currently at Amazon.<\/li>\n\n\n\n
        3. Dhruva Sahasrabudhe, M.S., Computer Science, 2020, A Multimodal Graph Convolutional Approach to Predict Genes Associated with Rare Genetic Diseases<\/em>. Currently at Amazon.<\/li>\n\n\n\n
        4. Mitchell Wagner<\/a>, M.S., Computer Science, 2018, Reconstructing Signaling Pathways Using Regular-Language Constrained Paths<\/em><\/li>\n\n\n\n
        5. Phillip Summers, M.S., Computer Science, 2017, pathway reconstruction algorithms<\/li>\n\n\n\n
        6. Divit Singh, M.S., Computer Science, 2016, co-advised with Kurt Luther, “GraphCrowd: Harnessing the Crowd to Lay Out Graphs with Applications to Signaling Pathways”<\/a>. Now at Bloomberg.<\/li>\n\n\n\n
        7. Naveed Massjouni, M. S., Computer Science, 2012, GraphSpace<\/a>. Now at Rackspace.<\/li>\n\n\n\n
        8. Clifford Conley Owens (aka the tree ninja<\/a>), M. S., Computer Science, 2009, co-advised with Naren Ramakrishnan<\/a>, Mining Truth Tables and Straddling Biclusters in Binary Datasets<\/em><\/a>. Now at Google<\/li>\n\n\n\n
        9. Gregory A. Grothaus, M. S., Computer Science, 2005, biologically interpretable disease classifiers. Now at Google.<\/li>\n\n\n\n
        10. Srinivas Venkataraghavan, M. S. (Computer Science), 2005, co-advised with Brett Tyler<\/a>, biclustering algorithms for promotor analysis<\/li>\n\n\n\n
        11. Shivaram Narayanan, M. S., Computer Science, 2005, betweenness centrality of biological networks. Now at SWIFT.<\/li>\n<\/ol>\n\n\n\n

          Former undergraduate students<\/h2>\n\n\n\n
            \n
          1. Jacqueline Addesa, Computer Science and Mathematics, Summer and Fall 2010, Cellular response networks, supported in Summer 2010 by a Summer Research Fellowship from the Fralin Life Sciences Institute<\/a>.<\/li>\n\n\n\n
          2. Brendan Avent<\/a>, Computer Science, Economics, Mathematics, Statistics, 2014-2015, hypergraph algorithms (now a Ph.D. student in the Department of Computer Science at the University of Southern California<\/li>\n\n\n\n
          3. David Badger, Computer Science, 2006-2007, gene function prediction<\/li>\n\n\n\n
          4. Peter Burnham, Biochemistry, 2011-2015, viral dependency factors, now a Ph.D. student in molecular microbiology at the University of Texas Southwestern Medical Center<\/li>\n\n\n\n
          5. Andrew Chan, B.S., Computer Science, 2022, prediction of viral hosts<\/li>\n\n\n\n
          6. Daniel Gil, Computer Science, 2015-2016, PathLinker app for Cytoscape<\/a><\/li>\n\n\n\n
          7. Akshay Goel, Computer Science, 2017, Yeast mutant database<\/li>\n\n\n\n
          8. Li Huang<\/a>, Computer Science, 2017-2018, PathLinker app for Cytoscape,<\/li>\n\n\n\n
          9. Rupin Khera, Computer Science, PathLinker, 2016–2017<\/li>\n\n\n\n
          10. Yoonjin Kim, Computer Science, 2017, Pathway reconstruction algorithms<\/li>\n\n\n\n
          11. Milap Lavani, Biological Sciences and Neuroscience, 2016-2017, XTalkDB<\/a><\/li>\n\n\n\n
          12. Zach Layman, Computer Science, 2008, the VIRGO web server<\/li>\n\n\n\n
          13. Zoya Mahajan, Biochemistry, 2014-2015, signaling pathways<\/li>\n\n\n\n
          14. Naveed Massjouni, Computer Science, 2005-2006, the VIRGO web server, now at Rackspace, after an M. S. in the Department of Computer Science at Virginia Tech<\/li>\n\n\n\n
          15. Anthony McNevin, Computer Science, 2006-2007, compositional data mining<\/li>\n\n\n\n
          16. Adeel Mufti<\/a>, Computer Science, 2005-2006, automatic layout and visualisation of biclusters, now at Information Delivery Systems<\/li>\n\n\n\n
          17. Clifford Conley Owens, Computer Science, 2006-2007, co-advised with Naren Ramakrishnan<\/a>, pursuit of truthiness and mining truth tables, now at Google, after an M. S. in the Department of Computer Science at Virginia Tech<\/li>\n\n\n\n
          18. Neel Patel, B.S., Computer Science, 2021–2022, BoolODE<\/li>\n\n\n\n
          19. Larissa Perara, Computer Science, 2017, yeast mutant database<\/li>\n\n\n\n
          20. Arif Khokhar, Computer Science, 2006-2007, biclustering algorithms<\/li>\n\n\n\n
          21. Paul Robertson, Computer Science, Summer and Fall 2011, databases for systems biology, now at Rackspace<\/li>\n\n\n\n
          22. Sarah Sam, Biological Sciences and Neuroscience, 2014-2016, Pathway crosstalk and XTalkDB<\/a>, now a Ph.D. student in the Department of Neuroscience at Caltech<\/li>\n\n\n\n
          23. Nick Sharp<\/a>, Computer Science, Engineering Physics, Mathematics, k<\/em>-shortest path algorithms, 2014-2015 (now a Ph.D. student in Computer Science at CMU)<\/li>\n\n\n\n
          24. Rajat Singhania<\/a> 2004-2005, co-advised with Brett Tyler<\/a>, algorithms for physical map assembly, now a PhD student in the GBCB programme at Virginia Tech<\/li>\n\n\n\n
          25. Peter Steele, Computer Science, shortest-path algorithms, 2015-2016<\/li>\n\n\n\n
          26. Anika Thatavarthy, B.S., Computer Science, 2023, prediction of viral hosts<\/li>\n\n\n\n
          27. Joelle Teel, Biological Sciences, XTalkDB<\/a>, 2015-2016<\/li>\n\n\n\n
          28. Shomir Wilson<\/a> (Computer Science, Mathematics, and Philosophy, 2004-2005, Honours thesis, co-advised with Brett Tyler<\/a>, gene function prediction using functional linkage networks, now a post-doctoral research associate in the School for Computer Science at CMU, after a PhD in the Department of Computer Science at the University of Maryland<\/li>\n\n\n\n
          29. Amelia Whithead, B.S., Computer Science, 2021–2022, BoolODE<\/li>\n\n\n\n
          30. Mike Woods, Computer Science, the VIRGO web server, 2008<\/li>\n\n\n\n
          31. Shuaicheng Zhang, Computer Science, 2017, cycles in signaling pathways<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

            Graduate students Former Post-doctoral researchers Former Ph. D. students Former M. S. students Former undergraduate students<\/p>\n","protected":false},"author":447,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-65","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/65","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/users\/447"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/comments?post=65"}],"version-history":[{"count":1,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/65\/revisions"}],"predecessor-version":[{"id":66,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/65\/revisions\/66"}],"wp:attachment":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/media?parent=65"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}