First-authored paper in Genome Biology by Jia Li
Congratulations to postdoctoral fellow Jia Li on the publication of "aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph" in Genome Biology on August 1, with professors Yu Shyr and Qi Liu as corresponding authors. The paper offers a new method "to simultaneously identify abundant and rare cell types based on an adaptive k-nearest neighbor graph with optimization," doing so "more accurately than general and specialized methods." {aKKNO} and related tutorials are free and available on GitHub and Zenodo.
Figure 1 in the paper provides an overview of how aKNNO works.
First-authored paper in Journal of Heart and Lung Transplantation by Tatsuki Koyama
Congratulations to professor Tatsuki Koyama on the publication of "Long-term air pollution exposure and the risk of primary graft dysfunction after lung transplantation" in The Journal of Heart and Lung Transplantation on July 15. Co-authors include assistant in biostatistics Zhiguo "Alex" Zhao, plus colleagues at the University of California, San Francisco, and the University of Pennsylvania, along with corresponding author Lorraine Ware at Vanderbilt. The study explored whether "long-term exposure of the lung donor and recipient to high levels of ambient air pollutants would increase the risk of PGD in lung transplant recipients."
Figure 2 in the paper: "Location of transplantation recipients in the primary analytical cohort (N = 1,524)."
First-authored paper in JMIR Research Protocols by Amber Hackstadt
Congratulations to assistant professor Amber Hackstadt on the publication of "Effects of a Patient Portal Intervention to Address Diabetes Care Gaps: Protocol for a Pragmatic Randomized Controlled Trial" in JMIR Research Protocols on June 28. Co-authors include senior biostatistician Zhihong Yu, as well as colleagues in Vanderbilt's Division of General Internal Medicine, Department of Ophthalmology and Visual Sciences, and Department of Biomedical Informatics. The study seeks to address consistency in preventive care among people with diabetes by applying "user-centered design sprint methodology to develop a patient portal intervention.
Figure 2 in the paper depicts the study recruitment results as a flow chart.
First-authored paper in American Journal of Epidemiology by Andrew Spieker
Congratulations to associate professor Andrew Spieker on the publication of "The impact of different strategies for modeling associations between medications at low doses and health outcomes: a simulation study and practical application to postpartum opioid use." This article was published online ahead of print on June 21 in the American Journal of Epidemiology. Co-authors include recently retired associate Sharon Phillips, plus colleagues in Vanderbilt's Departments of Health Policy and Obstetrics and Gynecology. It reports on the simulation study conducted by Dr. Spieker and his collaborators "to assess the performance of several regression approaches to model the drug dose-response curve at low doses in a setting where no safe range exists" and to "demonstrate and empirically assess the use of these regression strategies in a practical scenario."
Figure S1 in the paper features graphical representations of various models.
Panels (A) and (B) illustrate the simple linear model in the absence and presence (respectively) of a spike effect. Panel (C) illustrates the case in which dose group is categorized (with zero included as a category). Panels (C) and (D) illustrate the natural cubic spline model in the absence and presence (respectively) of a spike effect. Panel (F) illustrates the “slab-and-spline” model that is piecewise constant over the low-dose range but otherwise shares the properties of a natural cubic spline. Of note, the models presented in panels (A) and (D) invoke the safe-dose assumption as no spike effect is present.
Yajing Li promoted to senior biostatistician
We are pleased to announce the promotion of Yajing Li to senior biostatistician, in effect as of June 28. Li earned a bachelor's degree in statistics at East China Normal University in Shanghai, followed by her MS in statistics at the University of Michigan. Since joining our department in 2021, Li has contributed her analytical expertise to studies of the correlation between genetic/environmental factors and the risk of clonal hematopoiesis (CH) transformation; the likelihood of CH mutations among patients undergoing radiation therapy; genotypic-phenotypic links; the interplay between JAK2-V617F mutation and aUPD and their impact on blood cancers; the correlation between human leukocyte antigens, CHIP mutations, and specific diseases in BioVU and UK Biobank cohorts, and more. Her programming experience includes the creation of an R package to facilitate the efficient extraction and processing of data from large data platforms, and her peer-reviewed publications include papers in Blood Cancer Journal, Genetics in Medicine Open, and Transplantation and Cellular Therapy.
Figure 5 from Li's recent paper in Annals of Allergy, Asthma & Immunology: Adrenal steroid metabolites associated with childhood asthma within Kyoto Encyclopedia of Genes and Genomes molecular pathways. Metabolites that were significantly associated with childhood asthma are highlighted in yellow. Green diamonds indicate enzymes involved in the pathway and gray boxes indicate progenitor or downstream steroid metabolites.
Cara Lwin promoted to biostatistician
We are pleased to announce the promotion of Cara Lwin to biostatistician, in effect as of June 1. Lwin earned a bachelor's degree in microbiology from the University of Pittsburgh in 2017, with minors in chemistry, computer science, neuroscience, and economics, followed by three years as a senior research associate at eyeGENE and the Ophthalmic Genetics Laboratory at the National Eye Institute. Lwin entered our graduate training program in 2020, began working for the department as an associate biostatistician in 2022, and earned her master's degree in biostatistics this May. Her thesis was titled "Bayesian Survival Analysis Using Data from Electronic Health Records: A Study on Cardiovascular Outcomes Leveraging Information from Randomized Clinical Trials" and can be accessed via Vanderbilt's Institutional Repository. Her activities as a student included serving as Biostatistics Graduate Student Association vice president As a staff biostatistician, she is a member of the Vanderbilt Biostatistics Data Coordinating Center Design & Analysis Unit. See her staff profile for links to her peer-reviewed publications on influenza and COVID-19.
Elisa Yazdani and Cara Lwin listen to speeches in their honor at the department reception for MS graduates, April 16, 2024