T. M. Murali's Research Group

Graduate students

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

Former Post-doctoral researchers

  1. Hyunju Kim, Ph.D., Physics, University of Notre Dame, 2011. Currently a post-doctoral researcher with Prof. Paul Davies, Arizona State University.
  2. Anna Ritz, Ph.D., Computer Science, Brown University, 2012. Currently an Associate Professor in the Department of Biology, Reed College.
  3. Allison Tegge, 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.

Former Ph. D. students

  1. Jeffrey N. Law, 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. Currently a post-doctoral fellow at the National Renewable Energy Laboratory.
  2. Aditya Bharadwaj, Ph.D., Computer Science, 2020, Mixed-initiative methods for following design guidelines in creative tasks. Currently at B12 Solutions.
  3. Aditya Pratapa, Ph.D., Computer Science, experiment design, 2020, Algorithms for regulatory network inference and experiment planning in systems biology. Currently a post-doctoral fellow at the Broad Institute of Harvard and MIT.
  4. Amogh Jalihal, Ph.D., Genetics, Bioinformatics, and Computational Biology, 2020, co-advised with John Tyson, Mathematical modeling of macronutrient signaling in Saccharomyces cerevisiae. Currently a post-doctoral fellow in the Department of Systems Biology at the Harvard Medical School.
  5. Ahsanur Rahman, Ph.D., Computer Science, 2015, Unstable Communities in Network Ensembles. Currently an Assistant Professor in the Department of Electrical and Computer Engineering Department in North South University, Dhaka, Bangladesh.
  6. Christopher L. Poirel, Ph. D., Computer Science, 2013, Bridging Methodological Gaps in Network-Based Systems Biology, supported by a National Science Foundation Graduate Research Fellowship. Currently a senior data scientist at RedOwl Analytics.
  7. Yared Kidane, Ph.D., Genetics, Bioinformatics, and Computational Biology, 2012, co-advised with Christopher Lawrence, The Landscape of Host Transcriptional Response Programs Commonly Perturbed by Infectious Pathogens: Towards Host-Oriented Broad-Spectrum Drug Targets, 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. Currently a research scientist at the Universities Space Research Association, working at the NASA/Johnson Space Center.
  8. Christopher D. Lasher, Ph. D., Genetics, Bioinformatics, and Computational Biology, 2011, co-advised with Padma Rajagopalan, Discovering contextual connections between biological processes using high-throughput data. Currently a bioinformatics analyst at 5AM Solutions.
  9. Matthew D. Dyer, Ph.D. Genetics, Bioinformatics, and Computational Biology, 2008, co-advised with Bruno Sobral, Pathosystems Biology: Computational Prediction and Analysis of Host-Pathogen Protein Interaction Networks. 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.
  10. Corban G. Rivera, Ph. D., Computer Science, 2008, Automatic Reconstruction of the Building Blocks of Molecular Interaction Networks. Currently a bioinformatics research scientist at DuPont Inc.

Former M. S. students

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

Former undergraduate students

  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.
  2. Brendan Avent, 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
  3. David Badger, Computer Science, 2006-2007, gene function prediction
  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
  5. Andrew Chan, B.S., Computer Science, 2022, prediction of viral hosts
  6. Daniel Gil, Computer Science, 2015-2016, PathLinker app for Cytoscape
  7. Akshay Goel, Computer Science, 2017, Yeast mutant database
  8. Li Huang, Computer Science, 2017-2018, PathLinker app for Cytoscape,
  9. Rupin Khera, Computer Science, PathLinker, 2016--2017
  10. Yoonjin Kim, Computer Science, 2017, Pathway reconstruction algorithms
  11. Milap Lavani, Biological Sciences and Neuroscience, 2016-2017, XTalkDB
  12. Zach Layman, Computer Science, 2008, the VIRGO web server
  13. Zoya Mahajan, Biochemistry, 2014-2015, signaling pathways
  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
  15. Anthony McNevin, Computer Science, 2006-2007, compositional data mining
  16. Adeel Mufti, Computer Science, 2005-2006, automatic layout and visualisation of biclusters, now at Information Delivery Systems
  17. Clifford Conley Owens, Computer Science, 2006-2007, co-advised with Naren Ramakrishnan, pursuit of truthiness and mining truth tables, now at Google, after an M. S. in the Department of Computer Science at Virginia Tech
  18. Neel Patel, B.S., Computer Science, 2021--2022, BoolODE
  19. Larissa Perara, Computer Science, 2017, yeast mutant database
  20. Arif Khokhar, Computer Science, 2006-2007, biclustering algorithms
  21. Paul Robertson, Computer Science, Summer and Fall 2011, databases for systems biology, now at Rackspace
  22. Sarah Sam, Biological Sciences and Neuroscience, 2014-2016, Pathway crosstalk and XTalkDB, now a Ph.D. student in the Department of Neuroscience at Caltech
  23. Nick Sharp, Computer Science, Engineering Physics, Mathematics, k-shortest path algorithms, 2014-2015 (now a Ph.D. student in Computer Science at CMU)
  24. Rajat Singhania 2004-2005, co-advised with Brett Tyler, algorithms for physical map assembly, now a PhD student in the GBCB programme at Virginia Tech
  25. Peter Steele, Computer Science, shortest-path algorithms, 2015-2016
  26. Anika Thatavarthy, B.S., Computer Science, 2023, prediction of viral hosts
  27. Joelle Teel, Biological Sciences, XTalkDB, 2015-2016
  28. Shomir Wilson (Computer Science, Mathematics, and Philosophy, 2004-2005, Honours thesis, co-advised with Brett Tyler, 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
  29. Amelia Whithead, B.S., Computer Science, 2021--2022, BoolODE
  30. Mike Woods, Computer Science, the VIRGO web server, 2008
  31. Shuaicheng Zhang, Computer Science, 2017, cycles in signaling pathways
T. M. Murali (murali at cs dot vt dot edu)