T. M. Murali
(murali at cs dot vt dot edu)
- March 23, 2021 Kyle Akers receives an "Honorable Mention" from the National Science Foundation for his graduate research fellowship application.
- October 21, 2020, Jeffrey
N. Law defends his Ph.D. on Development and Application of Network Algorithms for Prediction of Gene Function and Response to Viral Infection and Chemicals. He is joining the National Renewable Energy Laboratory as a post-doctoral fellow.
- August 13, 2020, Tanya Tyagi defends her M.S. research on Benchmarking Methods For Predicting Phenotype Gene Associations. His next position is at Amazon.
- August 13, 2020, Dhruva Sahasrabudhe defends his M.S. research on A Multimodal Graph Convolutional Approach to Predict Genes Associated with Rare Genetic Diseases. His next position is at Amazon.
- July 29, 2020, Aditya Bharadwaj defends his doctoral research on Mixed-initiative methods for following design guidelines in creative tasks. He will be joining B12 Solutions.
- June 18, 2020, Aditya Pratapa defends his Ph.D. thesis on Algorithms for regulatory network inference and experiment planning in systems biology. Next stop: a post-doctoral position at the Broad Institute of Harvard and MIT.
- May 12, 2020, Amogh Jalihal defends his Ph.D. thesis on Mathematical modeling of macronutrient signaling in Saccharomyces cerevisiae. He will be joining the Department of Systems Biology at the Harvard Medical School as a post-doctoral fellow.
- April 30, 2020 Aditya Pratapa received the "Ph.D. Student of the Year" award from the Department of Computer Science.
- December 10, 2018Aditya Bharadwaj successfully completes his preliminary examination.
- September 1, 2018, Murali is part of a group that has received a grant from the NSF's Molecular and Cellular Biology program to study host-microbiome-pathogen interactions in the honeybee. Lisa Belden in the Department of Biological Sciences is the PI of this four-year $960,000 award.
- August 14, 2018, Mitch Wagner defends his Master's thesis on "Reconstructing Signaling Pathways Using Regular-Language Constrained Paths."
- July 20, 2018, Murali and John Tyson receive a grant from NSF to
to develop a new approach to dramatically speed up the process of
developing mathematical models in systems biology. This research
is in collaboration with Jean Peccoud.
- May 30, 2018 Anna Ritz receives the NSF CAREER award for
Signaling Pathway Analysis: Methods and Tools for Turning
Theory into Practice. Anna is an assistant professor in
the Biology Department at Reed College and was a post-doctoral fellow in our group.
- May 16, 2018, Aditya Pratapa successfully completes his Ph.D. preliminary examination.
- Apr 25, 2018, Jahan Daniyal selected as a 2018
Google Summer of Code student to work on the "GraphSpace: Git for Graphs" project.
- November 9, 2016, The PathLinker paper is one of the "Top 10 papers in regulatory and systems genomics" in 2016.
- August 11, 2016, The National Cancer Institute
awards Kurt Luther and
T. M. Murali a grant on
"GraphCrowd: Using Crowdsourced Design to Visualize Effects of
Environmental Chemicals on Signaling Networks", as part of the
Big Data to Knowledge (BD2K) initiative.
- May 25, 2016, The National Science Foundation
awards John Kececioglu and T. M. Murali a three-year grant on
Signaling Hypergraphs: Algorithms and Applications". This
project will develop a new representation called signaling
hypergraphs that naturally describes the relationships between
multiple groups of proteins as complexes, reactants, products,
and regulators. The project will also develop novel algorithms for fundamental computational challenges in the analysis of signaling hypergraphs, and apply this new representation and these algorithms to widely-used databases of cellular reactions.
- May 13, 2016, Sarah Sam graduates from Virginia
Tech with majors in neuroscience and biological sciences. She will join the Ph.D. programme in
Neuroscience at Caltech in
Fall 2016, after spending the summer in our group working on XTalkDB.
- May 4, 2016, Divit Singh defends his Master's thesis
on "GraphCrowd: Harnessing the Crowd to Lay Out Graphs with
Applications to Signaling Pathways". He will start working at
Bloomberg in New York City.
Apr 22, 2016, GraphSpace is part of the 2016 Google Summer of Code! Follow Mridul Seth's progress on his blog.
- March 31, 2016, Nick Sharp, a former undergraduate researcher in the group,
receives the NSF Graduate Research Fellowship.
- December 14, 2015, Murali receives the Senior
Member designation from the International Society of
- September 25, 2015, Ahsanur Rahman defends his
Ph.D. research on "Unstable
Communities in Network Ensembles". He will join the Department of Electrical and Computer
Engineering Department in North South University, Dhaka,
Bangladesh as an Assistant Professor.
- August 26, 2015, Our collaboration with John Tyson and Jean Peccoud on experimental
validation and refinement of a dynamic model of the budding
yeast cell cycle
appears in a special issue on Quantitative Biology of
Molecular Biology of the Cell.
- Aug 1, 2015, Post-doctoral fellow Anna Ritz starts as
Assistant Professor in the Department of Biology at Reed College.
- May 15, 2015, Nick Sharp graduates from Virginia
Tech with majors in computer science, engineering physics, and
mathematics. He will join the Ph.D. programme in
Computer Science at CMU in
Fall 2015, after spending his summer at Facebook/Oculus.
- May 15, 2015, Peter Burnham graduates from Virginia
Tech in biochemistry. He will join the Ph.D. programme in
Molecular Microbiology at the University of Texas Southwestern
Medical Center in Dallas in
- May 15, 2015, Brendan Avent graduates from Virginia
Tech with majors in computer science, economics, mathematics,
and statistics. He will join the Ph.D. programme in
Computer Science at the University of Southern California in
Fall 2015, after spending his summer at Facebook.
- February 5, 2015, Nick Sharp receives the
distinction of finalist in
National Computing Research Association Undergraduate Research
Award competition. Nick is also a member of the
Tech programming team that will participate in the 2015
ACM-ICPC World Finals in Morocco in May 2015.
- August 25, 2014, Allison Tegge receives an F32 fellowship from the National Institute of Environmental Health Sciences.
- July 11, 2014, Anna Ritz wins the second place for her poster in the NetBio SIG meeting at ISMB 2014.
- April 25, 2014, The Department of Computer Science selects Chris Poirel as the recipient of the Outstanding Research by a PhD Student award for
- December 20, 2013, Chris Poirel selected as the student speaker at the Fall 2013 Graduate Student Commencement ceremonies.
- December 14, 2013,
The American Society of Cell Biology created a video on
computational cell biology research at Virginia Tech including our
group's collaboration with John Tyson. Murali talks about
our research around 3 minutes into the video. The video also
of GraphSpace and networks computed by LINKER.
- December 4, 2013, Ahsanur Rahman successfully completes his Ph.D. preliminary examination.
- November 11, 2013. Murali receives the ACM
Distinguished Scientist award.
- August 30, 2013, Chris Poirel defends his Ph.D. research on "Bridging Methodological Gaps in Network-Based Systems Biology". Chris will be joining RedOwl Analytics as a Senior Data Scientist.
- October 7, 2012, Ahsanur Rahman's paper on Reverse
Engineering Molecular Hypegraphs wins the Best Paper
Award at the ACM conference on Bioinformatics, Computational Biology, and Biomedicine, 2012. Chris Poirel and David Badger also contributed to this paper.
- April 30, 2012, Murali receives the College of Engineering Faculty Fellow award.
- April 6, 2012, Chris Poirel successfully completes his Ph.D. preliminary examination.
- March 27, 2012, Yared Kidane defends his Ph.D. research on "The landscape of host transcriptional response programs commonly perturbed by infectious pathogens: towards host-oriented broad-spectrum drug targets".
- March 1, 2012, Computer, the flagship journal of the IEEE Computer Society, publishes a special issue on Computationally Driven Experimental Biology guest edited by
- February 6, 2012, the Virginia Tech Graduate School
selects the Computational
Tissue Engineering (CTE) interdisciplinary graduate education program (IGEP) for funding. Our collaborator Padma Rajagopalan directs this IGEP. Murali is one of its members. The goal of the CTE IGEP is to fruitfully exploit the natural synergy between tissue engineering and systems biology to define a new synthesis of these area, using the computational sciences as the driving force.
- January 1, 2012, Applications are open for an undergraduate
summer research institute on "Computationally-Driven Experimental Biology in Engineered Tissues." The application deadline is February 6, 2012.
- September 22, 2011, Our work on predicting
HIV dependency factors, performed in collaboration with
Michael Katze and Brett Tyler, appears
in PLoS Computational Biology.
- September 11, 2011, Chris Lasher defends his Ph.D. research on "Discovering contextual connections between biological processes using high-throughput data".
- July 8, 2011, Yared Kidane receives a Dissertation
Fellowship Award from the Southern Regional Education Board.
- June 1, 2011, NSF's Advances in Bioinformatics
program awards Murali, Padma Rajagopalan, and Rich Helm a grant
intercellular signaling in liver mimics. The Collegiate
Times carried an
article about this project.
- May 1, 2011, Murali and colleagues Jean Peccoud
and John Tyson receive a grant from NIGMS to
connect top-down and bottom-up models in systems biology.
- May 1, 2011, Padma Rajagopalan, Murali, and
Marion Ehrich receive a STAR grant from the
EPA. The project will develop systems biology approaches to unearth
toxicity pathways in bioengineered livers.
- December 16, 2010, Yared Kidane successfully completes his
Ph.D. preliminary examination.
- November 30, 2010, Jacqueline Addesa recieves
an Honorable Mention in the Computing
Research Association's Outstanding Undergraduate Researcher
Award competition for
- July 1, 2010, ICTAS
Center for Systems Biology of Engineered Tissues
formed. Murali is the co-director of the center. The goal of the
center is to develop integrated computational and experimental
models of bioengineered tissues by defining a synthesis between
systems biology and tissue engineering.
- May 10, 2010, Chris Lasher successfully completes his
Ph.D. preliminary examination.
- April 4, 2010, Chris Poirel is awarded the National Science
Foundation's Graduate Research Fellowship.
- March 11, 2010, Jacqueline Addessa is awarded a 10-week
Summer Research Fellowship by the Fralin Life Sciences
Institute. She will develop algorithms to compute
similarities and differences between cellular reponse
December 2008, Nucleic Acids Research publishes our paper on the
- October 2008, Murali co-organises an iPlant Grand
Challenges Workshop on Impacts of Climate Change on Plant
Productivity World-Wide. Prediction of Phenotype from
Genotype. Data Integration for Analysis and Prediction
Across Process Scales.
- August 2008, Murali conducts an invited tutorial
on Host-Pathogen Protein Interaction
Networks at the 9th International Conference on
- August 2008, Murali teaches an invited week-long course on
Systems Biology at the Chalmers Graduate
School of Bioscience, Chalmers University, Sweden.
- August 2008, Ph.D. student Corban G. Rivera successfully
Reconstruction of the Building Blocks of Molecular Interaction
Networks. He will be joining the Dept. of Biomedical
Engineering, the Johns Hopkins University as a post-doctoral
S. Bader and Aleksander S. Popel.
- July 2008, Murali and former Ph.D. student Matthew D. Dyer
organise a special session on Challenges and Opportunities in
Host-Pathogen Systems Biology
Cuomo, and Brett Tyler speak at the special session on their
work on human, animal, and plant pathogens.
- July 2008, PNAS publishes our paper that sheds new light on
the 50-year mystery of how ligands move inside
release that accompanied this paper.
- June 2008, Ph.D. student Matthew D. Dyer, co-advised by
Bruno Sobral and Murali, successfully defends his
thesis on Pathosystems Biology: Computational
Prediction and Analysis of Host-Pathogen Protein Interaction
Networks. He is joining Michael G. Katze's group in the
Department of Microbiology at the University of Washington
as a computational research scientist.
- January 2008, PLoS Pathogens publishes Matt Dyer's paper on
landscape of human proteins that interact with
pathogens. Read a related press release.
- May 2007, Murali is invited to speak at
Biology Workshop held in Bertinoro, Italy.
- Murali is a member of the programme committee for the 2007
IEEE International Conference on Data Mining.