Blog

Co-authored by senior associate Tebeb Gebretsadik and research professor Pingsheng Wu.

The Department of Biostatistics' Statistical Computing Series focuses on the implementation of statistical models and methods, statistical computation and graphics. These informal meetings allow experienced statisticians and developers to share their expertise on computing topics with practitioners across Vanderbilt. On Thursday, May 23, at 2:30 p.m., principal application developer Zhouwen Liu (MS, computer science, MTSU; MA, biology and biochemistry, Binghamton University), will present "Cloud, StatComp3, and ACCRE computation":

Cloud computing enables users to access computing resources such as servers, storage, databases, and software applications via the internet, offering scalability, flexibility, and cost-effectiveness. Users can easily adjust resources based on demand, avoiding upfront costs and infrastructure management.

The StatComp3 system caters to statistical analysis needs, handling large-scale tasks unsuitable for local workstations due to high memory or runtime requirements. In this way, our StatComp3 system functions as a CQS cloud.

Vanderbilt University's ACCRE provides computational resources and support, including high-performance clusters and storage systems, for research in bioinformatics, engineering, physics, and social sciences. These resources facilitate complex tasks and data analysis, accelerating research discovery.

This presentation introduces the ACCRE system and provides guidance on setting up and running parallel processing jobs.

For access to this Teams presentation, contact Ryan Moore. 

Senior biostatistician Elizabeth McNeer (a graduate of our program) and professor Bill Dupont co-authored this study.

We are thrilled to share the news that Fei Ye, professor of biostatistics and medicine on the Basic Science Educator track, has been selected as a 2024 Fellow of the American Statistical Association. The designation of ASA Fellow honors members of the association who have made outstanding contributions to statistical science. The process of being considered for ASA fellowship is exceptionally competitive, with very few honorees chosen among many highly qualified nominees. Dr. Ye, whose induction will take place during the Joint Statistical Meetings in Portland, Oregon, this August, is being recognized "for pioneering contributions to biomedical research, including statistical and bioinformatic methods, innovations in clinical trial design and analysis, and a deeper understanding of biomarkers, plus impactful collaborations and mentoring."

Dr. Ye earned her MSPH and PhD from the University of South Carolina and joined Vanderbilt University Medical Center as a staff biostatistician in 2006. Her current roles include serving as vice chair of collaborative studies for the department of biostatistics, and assistant editor for statistics with JAMA Oncology. Her statistical prowess has been a game-changer for dozens of research programs, both in terms of securing large grants and providing predictive models, diagnostic algorithms, and sophisticated data analyses to the investigations in question. In the words of Dr. Vivian Weiss, head of the high-impact translational research Weiss Lab, Dr. Ye's contributions "are paving the way for dramatic changes in the way we take care of thyroid cancer patients"; these include validating a commercial molecular diagnostic assay for children, developing a molecular assay for outcome prediction in adults, and setting in motion other novel strategies for assessing malignancies and their potential origins. Dr. Ye has also been at the forefront of discussions on liver allocation, with an eye toward addressing health inequity concerns in organ transplant policy and practice, as well as a go-to collaborator for a wide range of topics and conditions, from original research on atherosclerosis, atrial fibrillation, diverticulitis, multiple sclerosis, and more, to observations on surgical practice and ethics. She is also a trusted expert on statistical considerations for the design and implementation of clinical trials.

With Vanderbilt epidemiologist Dr. Jirong Long, Dr. Ye is Multiple Principal Investigator (MPI) of a pioneering investigation—the first large multi-racial methylation-wide association study (MeWAS)—that combines integrative bioinformatics, functional experiments, and high statistical power to expand and refine our understanding of the role DNA methylation plays in cancer development. Dr. Ye has also designed advanced modules for Vanderbilt’s Epidemiology PhD program, and she is on the faculty of the Vanderbilt Molecular and Genetic Epidemiology of Cancer (MAGEC) Training Program. International initiatives that have called on Dr. Ye’s experience include the Vietnam National Cancer Institute (VNCI) and Vinmec International Hospital, as well as the Vanderbilt-Zambia Cancer Research Training Program. A past president of the ASA's Middle Tennessee chapter, Dr. Ye is currently program chair of the ASA's Statistics in Epidemiology Section and poster chair for the 2024 International Chinese Statistical Association's Applied Statistics Symposium, which will convene in Nashville this June.

Fei Ye (center), flanked by lead biostatistician Amy Perkins and application developer Hui Wu at the department's January 2024 winter celebration.

Congratulations to data scientist assistant Hua-Chang Chen on the publication of "EVPsort: An atlas of small ncRNA profiling and sorting in extracellular vesicles and particles." The pre-proof was published online in the Journal of Molecular Biology on April 10, with research assistant professor Jing Wang as a co-author, and professors Yu Shyr and Qi Liu as corresponding authors, along with colleagues in Vanderbilt's Departments of Cell and Developmental Biology, Medicine, Biological Sciences, and Pathology, Microbiology and Immunology. EVP stands for "extracellular vesicles and particles." The EVPsort database "not only provides an extensive overview of ncRNA [non-coding RNAs] profiling in 3,162 samples across various biofluids, cell lines, and disease contexts but also seamlessly integrates 19 external databases and tools" and is freely accessible at bioinfo.vanderbilt.edu/evpsort. 

Panpan Zhang (right, in Vanderbilt hoodie), assistant professor of biostatistics and neurology, has been named the first-ever Early Career Representative on the Data Core Steering Committee of the National Alzheimer's Coordinating Center, which is the Alzheimer's disease research center program of the National Institute on Aging. Committee members serve three-year terms. Dr. Zhang is on the Vanderbilt Memory & Alzheimer's Center faculty, Local Committee co-chair for the 2024 International Chinese Statistical Association's Applied Statistics Symposium, co-chair of the 2025 Institute of Mathematical Statistics' New Researchers Conference, and associate editor of Journal of Data Science and Methodology and Computing in Applied Probability.  

The Department of Biostatistics' Statistical Computing Series focuses on the implementation of statistical models and methods, statistical computation and graphics. These informal meetings allow experienced statisticians and developers to share their expertise on computing topics with practitioners across Vanderbilt. On Thursday, April 25, at 2:30 p.m., assistant professor Panpan Zhang will present "Fundamentals of building R packages."

From Dr. Zhang:

This presentation targets audiences with zero or limited knowledge of building R packages. In this presentation, I will introduce some fundamentals of building an R package, including but not limited to the generations of NAMESPACE, DESCRIPTION, and R Documents. With the increasing demand for intensive computation (e.g., numerical integration), I will also discuss how to interface CPP files (primarily based on Rcpp and Rcpp Armadillo) into an R package. Lastly, I will show a few fundamental techniques for testing R packages.

For access to this Teams presentation, contact Ryan Moore.