News about ISBET

ISBET News

2018

  • October 2018, ISBET faculty member Padma Rajagopalan's group's article "Measuring Cytoplasmic Stiffness of Fibroblasts as a Function of Location and Substrate Rigidity Using Atomic Force Microscopy" has been selected to be featured in ACS Editors' Choice. This honor is given to only one article from the entire ACS portfolio each day of the year and is based on recommendations by ACS journals' editors.
  • June 2018, Chemical Engineering Ph.D. student Andrew Ford successfully defends his Ph.D. thesis on "Investigating the Interplay between Inflammation and Matrix Stiffness: Evaluation of Cell Phenotype and Cytoplasmic Stiffness In Vitro". ISBET faculty member Padma Rajagopalan was his doctoral advisor. Andrew will be a post-doctoral fellow in the Department of Bioengineering at Tufts University.
  • June 1, 2018, ISBET faculty member T. M. 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.
  • February 2018, Congratulations to Sophia Orbach for successfully defending her Ph.D. thesis on "Multi-Cellular Organotypic Liver Models for the Investigation of Chemical Toxicity and Liver Fibrosis". Sophia was co-advised by ISBET faculty members Padma Rajagopalan and Marion Ehrich. Sophia is joining the Department of Biomedical Engineering at the University of Michigan, Ann Arbor as a post-doctoral fellow.
  • August 14, 2018, Computed Science student Mitch Wagner defends his Master's thesis on "Reconstructing Signaling Pathways Using Regular-Language Constrained Paths."
  • July 20, 2018, T. M. Murali and John Tyson receive a $1.5M 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, a former ISBET faculty member who is now at Colorado State University.
  • May 30, 2018 Anna Ritz receives the NSF CAREER award for Network-Based 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 with T. M. Murali from 2013-2015.

2017

  • December 9, 2017, Computer Science Ph.D. student Aditya Pratapa wins the first position in the Multiple Myeloma DREAM Challenge for predicting clinical progression using DNA-based features.

2016

  • May 4, 2016, Divit Singh defends his Master's thesis on "GraphCrowd: Harnessing the Crowd to Lay Out Graphs with Applications to Signaling Pathways". T. M. Murali and Kurt Luther co-advised him. He will start working at Bloomberg in New York City.
  • April 2016, ISBET director Padma Rajagopalan has been appointed the Robert E. Hord, Jr. Professor of Chemical Engineering by the Virginia Tech Board of Visitors.
  • March 31, 2016, Nick Sharp, a former undergraduate researcher in T. M. Murali's group, receives the NSF Graduate Research Fellowship. Nick is currently a Ph.D. student in computer science at CMU.
  • January 4, 2016, ISBET faculty member Jean Peccoud is joining Colorado State University as the Abell Chair in Synthetic Biology in the Department of Chemical & Biological Engineering. We are sorry to see him leave but wish him the very best in his new position!
  • January 1, 2016, ISBET faculty members Rafael Davalos and Scott Verbridge receive a $380,000 award from Virginia Biosciences Health Research Corporation to develop new technologies to fight brain cancer.

2015

  • November 2015, Congratulations to Sophia Orbach for being awarded the 2015-2016 Sigma Xi Ph.D. Research Award from the Virginia Tech Sigma Xi Scientific Research Society. This award recognizes outstanding researchers across the university. This year, the society's focus was on the environment. Sophia was nominated for her innovative research on investigating the toxicity of environmental chemicals on liver function.
  • October 2015, Congratulations to Sophia Orbach for being selected by the Society of Toxicology to be a "Gold Level Award Recipient" based on her meritorious abstract titled "Hepatotoxicity Testing in Multi-cellular 3D Organotypic Liver Models and Their Potential for High-Throughput Studies" submitted to FutureTox III: Bridges for Translation-Transforming 21st Century Science into Risk Assessment and Regulatory Decision-Making.
  • September 2015, Congratulations to Maggie Cassin for successfully defending her M.S. thesis on "The Design of Antimicrobial Detachable Thin Films for the Study of Hepatic Infections". Maggie is a Chemical Engineering student advised by Padma Rajagopalan.
  • September 29, 2015, The NIGMS BioBeat blogs about Jean Peccoud and John Tyson's research on stochastic models of the regulatory network controlling cell division. Read How Cells Manage Chance.
  • September 25, 2015, Ahsanur Rahman successfully defends his PhD thesis in "Unstable Communities in Network Ensembles." Ashanur is a student in the Department of Computer Science advised by T. M. Murali. He will join the Department of Electrical and Computer Engineering Department in North South University, Dhaka, Bangladesh as an Assistant Professor.
  • September 15, 2015, Lucas Vu successfully defends his PhD thesis on "Investigation of Hepatocyte Proteomes using Three Dimensional Organotypic Liver Models". Lucas is a Chemical Engineering student advised by ISBET faculty members Richard Helm and Padma Rajagopalan.
  • September 12, 2015, NSF's Chemical, Bioengineering, Environmental, and Transport Systems (CBET) Division awards Padma Rajagopalan a three-year grant for $350,000 to study integrated tissue engineering. This project focuses on engineering an integrated GI and liver tissue to obtain information on how these organs work in unison to metabolize chemicals.
  • August 26, 2015 A collaborative publication between John Tyson, Jean Peccoud, and T. M. Murali 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.
  • May 14, 2015 ISBET faculty member Jean Peccoud and collaborator John Tyson receive a $2M award from the National Institute of General Medical Sciences (NIGMS) to develop stochastic models of the regulatory network controlling the cell division cycles in eukaryotes.
  • March 27, 2015, Sophia Orbach receives the "Outstanding Interdisciplinary Doctoral Student" award from the Virginia Tech Graduate School.
  • February 1, 2015, ISBET faculty members Rafael Davalos and Scott Verbridge are leading a two-year, $386,000 award from the National Cancer Institute to develop targeted electric field therapies for malignant brain tumors.

2014

  • September 23, 2014, Gaurav Jain successfully defends his PhD thesis on "Cell migration on opposity rigidity-protein gradients: single cell and co-culture studies". Gaurav is an SBES student working with Padma Rajagopalan.
  • September 1, 2014, Padma Rajagopalan joins the Editorial Board of ACS Biomaterials Science and Engineering.
  • September 1, 2014, ISBET faculty member Scott Verbridge and collaborator Chang Lu receive a two-year, $406,000 award from the National Institute of Biomedical Imaging and Bioengineering to develop 3D tissue models in order to understand spatiotemporal heterogeneity in transcriptional regulation.
  • August 25, 2014, Allison Tegge receives an F32 fellowship from the National Institute of Environmental Health Sciences for $250,000. She will collaborate with ISBET faculty Murali and Rajagopalan to develop computational models of signaling between liver cells exposed to environmental chemicals.
  • July 29, 2014, Rebekah Less, a first-year Ph.D. student in the Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, has been awarded a Science, Mathematics, and Research for Transformation (SMART) graduate fellowship from the Department of Defense. Less was selected for this $150,000 fellowship based on her proposed research in integrating liver and gastrointestinal tissues.
  • June 27, 2014, NSF's Chemical, Bioengineering, Environmental, and Transport Systems (CBET) Division awards Padma Rajagopalan a three-year $390,000 grant to study transitional tissue engineering. This project focuses on engineering a liver tissue that exhibits a gradient in both mechanical and chemical properties. The goal of the project is to use such a tissue to determine to what extent must chemical and mechanical profiles vary in the liver in order to sustain hepatic fibrosis and to understand how the major hepatic cells respond to stiffer matrices and varying chemical concentrations.
  • May 7, 2014, Padma Rajagopalan receives the Dean's Award for Excellence in Research.
  • April 25, 2014, The Department of Computer Science selects Chris Poirel as the recipient of the Outstanding Research by a PhD Student award for 2013-2014. Chris completed his Ph.D. thesis under the guidance of T. M. Murali in August 2013. In his thesis, Chris developed novel graph algorithms to connect top-down and bottom-up approaches in systems biology.

2013

  • December 20, 2013, The Virginia Tech Graduate School selects Chris Poirel as the student speaker at its 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 the collaboration of ISBET faculty T. M. Murali and Jean Peccoud with John Tyson.
  • November 11, 2013, T. M. Murali receives the ACM Distinguished Scientist award.
  • September 5-6, 2013, Rajagopalan and Murali organize Workshop on Computational Toxicology.
  • 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. Chris was a student in T. M. Murali's group.
  • August 1, 2013, Dr. Shiv Kale joins ISBET. He has been a VBI independence fellow since 2011. He focuses on characterizing novel human-fungal molecular interactions during invasive infections.
  • July 25, 2013, Padma Rajagopalan invited to serve on National Institutes of Health study section on biomaterials.
  • July 15, 2013 ISBET faculty member Jean Peccoud gives a keynote lecture titled "The A-Myth: why you should run your lab as a business" at Junior PI Meeting at ISMB/ECCB 2013.

2012

  • 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. Ahsanur is a Computer Science Ph.D. student in T. M. Murali's group.
  • August 2012, Adam Larkin defends his PhD thesis on "The design of three dimensional multicellular liver models using detachable, nanoscale polyelectrolyte multilayers". Adam is a Chemical Engineering Ph.D. student in Padma Rajagopalan's group. He is joining Celanese Corporation as a Research Engineer.
  • July 7, 2012, Jean Peccoud and colleagues receive a $1,000,000 INSPIRE award from the NSF to model and optimize DNA manufacturing processes.
  • April 2012, Cigdem Arca defends her Master's thesis on "The design of polyelectrolyte multilayers using galactosylated chitosan". Cigdem is a Chemical Engineering student in Padma Rajagopalan's group.
  • April 23, 2012, T. M. Murali gives a highlight presentation at RECOMB 2012 on "Network-Based Prediction and Analysis of HIV Dependency Factors".
  • March 26, 2012, Naren Ramakrishnan named the Thomas L. Phillips Professor of Engineering.
  • March 26, 2012, Padma Rajagopalan receives the Robert H. Hord Jr. Chemical Engineering Fellowship.
  • March 1, 2012, Computer, the flagship journal of the IEEE Computer Society, publishes a special issue on Computationally Driven Experimental Biology guest edited by T. M. Murali.
  • February 6, 2012, the Virginia Tech Graduate School selects the Computational Tissue Engineering (CTE) interdisciplinary graduate education program (IGEP) for funding. ISBET director Padma Rajagopalan will direct this IGEP. Several ISBET faculty are affiliated with CTE. The goal of the CTE IGEP is to train a new generation of scientists at the nexus of tissue engineering, systems biology, and computational science.
  • January 2, 2012, Renee Prater is the new Associate Dean for Medical Education at the Edward Via College of Osteopathic Medicine.
  • 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.
  • January 1, 2012, Prof. Scott Verbridge joins ISBET. He is a primary faculty member in the Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences. Prof. Verbridge leads the Laboratory of Integrative Tumor Ecology. He is an expert on engineering the cancer microenvironment.

2011

  • September 12, 2011, Chris Lasher defends his Ph.D. in Genetics, Bioinformatics, and Computational Biology on "Discovering contextual connections between biological processes using high-throughput data". ISBET director Rajagopalan and co-director Murali co-advised Lasher.
  • August 28, 2011, Jean Peccoud gives the opening keynote lecture on "Learning DNA as a Second Language" at the 12th International Conference on Systems Biology held at Heidelberg/Mannheim, Germany.
  • July 25, 2011, Padma Rajagopalan's research is featured in an article titled The Quest for an Artificial Liver in the Indian newspaper The Telgraph.
  • June 1, 2011, NSF's Advances in Bioinformatics program awards ISBET researchers T. M. Murali, Padma Rajagopalan, and Rich Helm a $1.13M grant to study intercellular signaling in liver mimics. The investigators will use the 3-D liver mimic developed by Rajagopalan to understand how different cell types within the mimic communicate with each other. The project will analyze transcriptional measurements to prioritize proteomic experiments. It will combine both types of data to construct an integrated model of intercellular signaling in liver mimics.
  • May 1, 2011, ISBET researchers T. M. Murali and Jean Peccoud and collaborator John Tyson receive $2.13M grant from NIGMS to connect top-down and bottom-up models in systems biology. This project will fuse representations of the budding yeast cell cycle are constructed from large-scale high-throughput datasets with ODE-based models and simulation of the cell cycle protein regulatory network.
  • May 1, 2011, ISBET researchers Padma Rajagopalan, T. M. Murali, and collaborator Marion Ehrich receive $750,000 STAR grant from the EPA. The project will develop systems biology approaches to unearth toxicity pathways in bioengineered livers.

2010

2009

  • September 2009, Padma Rajagopalan and collaborators T. M. Murali and Richey Davis receive three grants totaling more than $1M from the NSF and the NIH to investigate 3D liver mimics.