T. M. Murali
(murali at cs dot vt dot edu)
T. M. Murali's Research Group
- Kyle T. Akers, Ph.D., Genetics, Bioinformatics, and Computational Biology, inference of gene regulatory networks
- Blessy Antony, M.S., Computer Science
- Joseph D'Anna, B.S./M.S., Computer Science, GraphSpace
- Malabika Sen, M.S., Computer Science, bee bioinformatics
- Nure Tasnina, Ph.D., Computer Science, drug-drug interactions
- Neel Patel, B.S., Computer Science
- Amelia Whithead, B.S., Computer Science
Former Post-doctoral researchers
- Hyunju Kim, Ph.D., Physics, University of Notre Dame,
2011. Currently a post-doctoral researcher with Prof. Paul
Davies, Arizona State University.
Ritz, Ph.D., Computer Science, Brown University,
2012. Currently an Associate Professor in the Department of
Biology, Reed College.
- 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
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.
- Aditya Bharadwaj, Ph.D., Computer Science, 2020, Mixed-initiative methods for following design guidelines in creative tasks. Currently at B12 Solutions.
- 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.
- 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.
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.
- 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.
- 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.
- 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.
- 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.
Tech Graduate School selected Dyer for the "Outstanding
Dissertation in Science and Engineering" award in March 2009.
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
- Tanya Tyagi, M.S., Computer Science, 2020, Benchmarking Methods For Predicting Phenotype Gene Associations. Currently at Amazon.
- Dhruva Sahasrabudhe, M.S., Computer Science, 2020, A Multimodal Graph Convolutional Approach to Predict Genes Associated with Rare Genetic Diseases. Currently at Amazon.
- Mitchell Wagner, M.S., Computer Science, 2018, Reconstructing Signaling Pathways Using Regular-Language Constrained Paths
- Phillip Summers, M.S., Computer Science, 2017, pathway reconstruction algorithms
- 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.
- Naveed Massjouni, M. S., Computer Science, 2012,
GraphSpace. Now at Rackspace.
- Clifford Conley Owens (aka the
ninja), M. S., Computer Science, 2009, co-advised with Naren
Truth Tables and Straddling Biclusters in Binary
Datasets. Now at Google
- Gregory A. Grothaus, M. S., Computer Science, 2005, biologically interpretable disease
classifiers. Now at Google.
- Srinivas Venkataraghavan, M. S. (Computer Science), 2005,
co-advised with Brett
Tyler, biclustering algorithms for
- Shivaram Narayanan, M. S., Computer Science, 2005, betweenness centrality of biological
networks. Now at SWIFT.
Former undergraduate students
- 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
- 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
- David Badger, Computer Science, 2006-2007, gene function prediction
- Peter Burnham, Biochemistry, 2011-2015, viral dependency factors, now a Ph.D. student in molecular microbiology at the University of Texas Southwestern Medical Center
- Daniel Gil, Computer Science, 2015-2016, PathLinker app for Cytoscape
- Akshay Goel, Computer Science, 2017, Yeast mutant database
- Li Huang, Computer Science, 2017-2018, PathLinker app for Cytoscape,
- Rupin Khera, Computer Science, PathLinker, 2016--2017
- Yoonjin Kim, Computer Science, 2017, Pathway reconstruction algorithms
- Milap Lavani, Biological Sciences and Neuroscience, 2016-2017, XTalkDB
- Zach Layman, Computer Science, 2008, the VIRGO web server
- Zoya Mahajan, Biochemistry, 2014-2015, signaling
- 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
- Anthony McNevin, Computer Science, 2006-2007, compositional data mining
- Adeel Mufti, Computer Science, 2005-2006, automatic layout and visualisation of biclusters, now at Information Delivery Systems
- 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
- Larissa Perara, Computer Science, 2017, yeast mutant database
- Arif Khokhar, Computer Science, 2006-2007, biclustering algorithms
- Paul Robertson, Computer Science, Summer and Fall 2011,
databases for systems biology, now at Rackspace
Sarah Sam, Biological Sciences and Neuroscience, 2014-2016,
and XTalkDB, now a
Ph.D. student in the Department of Neuroscience at Caltech
- Nick Sharp, Computer Science, Engineering Physics,
Mathematics, k-shortest path algorithms, 2014-2015
(now a Ph.D. student in Computer Science at CMU)
- Rajat Singhania 2004-2005, co-advised with Brett
Tyler, algorithms for physical map assembly, now a PhD student in the GBCB programme at Virginia
- Peter Steele, Computer Science, shortest-path algorithms, 2015-2016
- Joelle Teel, Biological Sciences, XTalkDB, 2015-2016
- 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
- Mike Woods, Computer Science, the VIRGO web server, 2008
- Shuaicheng Zhang, Computer Science, 2017, cycles in signaling pathways