All-department team publishes paper in Computational and Structural Biotechnology Journal
Congratulations to former visiting student Chia-Jung "Charlene" Chang (PhD candidate in biomedical engineering at National Cheng Kung University), research assistant professor Chih-Yuan Hsu, and professors Qi Liu and Yu Shyr on the publication of "VICTOR: Validation and inspection of cell type annotation through optimal regression." The article on this new method appeared online ahead of print on October 15 and will go to press as part of Computational and Structural Biotechnology Journal's December issue. As described in the paper's abstract:
Single-cell RNA sequencing provides unprecedent opportunities to explore the heterogeneity and dynamics inherent in cellular biology. An essential step in the data analysis involves the automatic annotation of cells. Despite development of numerous tools for automated cell annotation, assessing the reliability of predicted annotations remains challenging, particularly for rare and unknown cell types. Here, we introduce VICTOR: Validation and inspection of cell type annotation through optimal regression. VICTOR aims to gauge the confidence of cell annotations by an elastic-net regularized regression with optimal thresholds. We demonstrated that VICTOR performed well in identifying inaccurate annotations, surpassing existing methods in diagnostic ability across various single-cell datasets, including within-platform, cross-platform, cross-studies, and cross-omics settings.
Figure 1 in the paper provides an " One example in diagnosing the reliability of cell annotations. a) diagnostic performance of singleR, scmap, SCINA, scPred, CHETAH, scClassify, and Seurat. b) diagnostic performance of VICTOR when applied to annotations from singleR, scmap, SCINA, scPred, CHETAH, scClassify, and Seurat.
First-authored paper in JAMIA by Andrew Guide
Congratulations to senior biostatistician Andrew Guide on first-authorship of "Balancing efficacy and computational burden: weighted mean, multiple imputation, and inverse probability weighting methods for item non-response in reliable scales," an article published in JAMIA: A Scholarly Journal of Informatics in Health and Biomedicine on August 13. Co-authors include assistant in biostatistics Shawn Garbett, senior biostatistician Xiaoke (Sarah) Feng, and professor Qingxia (Cindy) Chen, who is the paper's corresponding author, with colleagues in VICTR, DBMI, and Ohio State's Department of Internal Medicine. The study examined ways of interpreting non-responses to the Physical Activity Neighborhood Environment Scale (PANES) in the All of Us Social Determinants of Health survey and to what degree computationally intensive approaches are advisable. In the words of Guide and his co-authors, their goal is "to inform researchers on considerations for handling incomplete data in participant surveys, utilize the data received as efficiently and accurately as possible, and better understand how to use surveys with missingness to conduct accurate research." Guide, Garbett, Chen, and some other team members published another paper on interpreting All of Us data earlier this year; Guide, Garbett, and Feng also served as teaching asistants in this year's Summer Institute short course on the All of Us research program.
Figure 1 in Guide et al., "Balancing efficacy..." For the full caption, view the figure at its journal page or within the full paper.
First-authored paper in Nature Communications by Jia Li
Congratulations to postdoctoral fellow Jia Li, professor and chair Yu Shyr, and professor Qi Liu on the August 22 publication of Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn’s disease (CD) in Nature Communications. Dr. Li is first author of the paper and Dr. Liu its corresponding author. The team's study of terminal ileum and ascending colon (LND) cells in CD patients has led to findings that "suggest a potential pathogenic role" for such cells in inflammatory bowel disease (IBD).
Figure 1 from the paper. Visit it at the publication site for the full caption.
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.