Drs Pedro Mendes, Reinhard Laubenbacher, Anna Dongari-Bagtzoglou awarded $1.69 million from National Institutes of Health (NIH)

Drs. Reinhard Laubenbacher and Pedro Mendes of Center for Quantitative Medicine, and Dr. Anna Dongari-Bagtzoglou of The Division of Periodontology UConn School of Dental Medicine, have been awarded over $1.69 million over the next four years from the National Institutes of Health (NIH) for “Control of heterogeneous microbial communities using model-based multi-objective optimization” (1R01GM127909-01).  A novel mathematical approach to an important use of Agent-based models (ABMs) as a means to model-based control biological system. Rather than viewing the ABM as a model, it is to be viewed as a surrogate for the actual system.

ggalluvial v0.5.0: A ggplot2 Extension for Alluvial Diagrams, an R package by Cory Brunson, is now available on CRAN

ggplot2 is a very popular R package for data visualization.  When Dr. Jason (Cory) Brunson, a postdoctoral fellow, engaged in a data analysis project with the State Comptroller’s office, he began developing an extension to ggplot2 to create so-called alluvial diagrams, like the one used by Bergstrom and Rosvall in their PLOS One paper.[1]  Dr. Brunson kept working on it intermittently, and a couple of months ago he submitted it to CRAN, which is the primary repository for stable R packages.[2].

Alluvial diagrams can be used to represent repeated categorical measures, classifications that evolve over time, and multi-dimensional categorical data. ggalluvial produces alluvial diagrams using the principles and syntax of the tidyverse packages, including ggplot2 and tidyr.

Please click on the link to an introduction/tutorial that he wrote.[3]

[1]: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008694

[2]: https://cran.r-project.org/package=ggalluvial

[3]: https://cran.r-project.org/web/packages/ggalluvial/vignettes/ggalluvial.html

UConn Health/JAX faculty member, Dr. Reinhard Laubenbacher, wins $2.7M grant to develop better tools for biomedical modeling

UConn Health/JAX faculty member, Dr. Reinhard Laubenbacher, has been awarded over $2.7 million over the next four years from the National Institutes of Health (NIH) for “Modular design of multiscale models, with an application to the innate immune response to fungal respiratory pathogens” (1U01EB024501-01). The project aims to develop a novel modular approach to model architecture to improve the usability of multiscale mathematical models. Such tools have emerged as essential tools in the life sciences, especially biomedicine.






Dr. Reinhard Laubenbacher has been named an inaugural Fellow of the Society for Mathematical Biology

Dr. Reinhard Laubenbacher, director of the Center for Quantitative Medicine at the UConn School of Medicine and The Jackson Laboratory for Genomic Medicine, has been named an inaugural Fellow of the Society for Mathematical Biology. The Society promotes the development and dissemination of research and education at the interface between the mathematical and biological sciences. The Society serves a diverse community of researchers and educators in academia, industry, and government agencies throughout the world. Dr. Laubenbacher was honored at the Society’s annual meeting in Salt Lake City last month.

Society for Mathematical Biology announces inaugural Fellows of the Society




Dr. Thomas Agresta Featured in The Pulse on Discussion of State Health Information Exchange

Dr. Thomas Agresta, director of clinical informatics at the Center for Quantitative Medicine at UConn Health, was asked about his work with the Health IT Advisory Council and the upcoming roundtables.

A series of health information technology community stakeholder roundtables is taking place next week at UConn Health and five other locations throughout the state. Allan Hackney, Connecticut’s health information technology (HIT) officer, will lead the discussions and review the findings of a report prepared for the Health IT Advisory Council.

The UConn Health roundtable is scheduled for Thursday, July 20, from 8 to 9:30 a.m. in the Cell and Genome Sciences Building.

Stakeholder groups include physician, nursing, patient advocacy, consumer-oriented, business, academic health center, health care delivery network, insurer, government agency, business and others. Attendees are asked to register in advance, as space is limited.

Read the Full Article


Brianna Kozemzak, REU Class of 2016, Named Recipient of the NSF Graduate Research Fellowship Program

Brianna Kozemzak of Saint Mary’s College, Notre Dame, IN receives The National Science Foundation Graduate Research Fellowship Program.  The NSF Graduate Research Fellowship Program (GRFP) helps ensure the vitality of the human resource base of science and engineering in the United States and reinforces its diversity. The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master’s and doctoral degrees at accredited United States institutions. Fellows benefit from a three-year annual stipend of $34,000 along with a $12,000 cost of education allowance for tuition and fees (paid to the institution), opportunities for international research and professional development, and the freedom to conduct their own research at any accredited U.S. institution of graduate education they choose.

For more information, visit http://www.nsfgrfp.org.

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Paola Vera-Licona, Ph.D., Has Been Accepted to Participate in the Interstellar Initiative Mentoring Workshop at the New York Academy of Sciences from March 17–19, 2017.

vera-liconaPaola Vera-Licona, Ph.D., faculty at Center for Quantitative Medicine, has been accepted to participate in the Interstellar Initiative mentoring workshop at the New York Academy of Sciences from March 17-19, 2017. The Interstellar Initiative — presented jointly by the Japan Agency for Medical Research and Development and the New York Academy of Sciences — will recognize the world’s most promising Early Career Investigators in the fields of cancer, regenerative medicine, and neuroscience. Individuals accepted into the Interstellar Initiative will participate in a three-day conference at the New York Academy of Sciences, where they will be grouped within teams of three and asked to propose a solution to a major research question, guided by mentors who are at the peak of their respective disciplines.”

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