Research Areas
Research Areas
Yale rotation projects thus far
Fine-tuning single-cell foundational models for novel generative tasks
Conventional computational approaches to identify virus-associated patterns in TCR sequencing data
Northwestern research areas
Predictive modeling in the ICU (preprint)
Developed machine learning models to predict successful extubation in the ICU intensive care unit (ICU) using routinely collected electronic health records (EHR) features in patients with severe pneumonia.
Models temporally trained and validated using data from Northwestern Memorial Hospital, including external validation with Central DuPage Hospital.
SHAP analysis reveals measures previously demonstrated to be important in determining readiness for extubation were found to be most informative using. Additionally, the model proposes potential opportunities to alter extubation decisions to reduce adverse outcomes.
Pathogen-specific responses in single-cell data
Large collaborative effort between the Northwestern Division of Pulmonary and Critical Care Medicine and Ewa Szczurek's group at Helmholtz Munich. Data includes the integration of a large collection of single-cell RNA sequencing data from bronchoalveolar lavage (BAL) fluid in patients with severe pneumonia accompanied with valuable EHR data including pathogen information.
Performed unsupervised tensor decomposition with multi-omics factor analysis (MOFA) to identify drivers of patient response in single-cell data.
Identified factors and specific EHR and RNA features that are associated with pathogens and pneumonia outcomes.
Manuscript is currently under development.
General sequencing support
Managed large-scale single-cell sequencing efforts projects including quality assessment, planning, and data-driven sequencing design, and automation.
Performed integration and analysis of single-cell data spanning small disease-specific datasets to large cross-disease atlases.
Contributed to division projects through analysis of bulk and single-cell differential analysis RNA sequencing datasets, as well as development of machine learning-based classification tasks of cells and samples.
Bailey J.I., Puritz, C.H., Senkow, K.J. et al. Profibrotic monocyte-derived alveolar macrophages are expanded in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19. Nat Immunol 25, 2097–2109 (2024). https://doi.org/10.1038/s41590-024-01975-x
Fenske S, Peltekian AK et al. Developing and validating a machine learning model to predict successful next-day extubation in the ICU. medRxiv (2024). https://doi.org/10.1101/2024.06.28.24309547
Grudzinski KM, Fenske S, Markov NS, Pickens CI, Walter JM, Nadig N, Singer BD, Wunderink RG, Gao CA, NU SCRIPT Study Investigators. Neutrophil percentages in bronchoalveolar lavage fluid: Implications for diagnosing bacterial pneumonia in patients with immunocompromise and neutropenia. medRxiv (2024). https://doi.org/10.1101/2024.05.04.24306709
See updated Google Scholar here
Grudzinski KM, Fenske S, Markov NS, Pickens CI, Walter JM, Nadig N, Singer BD, Wunderink RG, Gao CA, NU SCRIPT Study Investigators. Neutrophil percentages in BAL fluid: implications for diagnosing bacterial pneumonia in patients with immunocompromise and neutropenia. Submitted to American Thoracic Society 2024.
Fenske S,* Peltekian AK, et al. Machine Learning with Time Series Data: Modeling Successful Extubation in the ICU. Poster presentation at Chicago-Munich Molecular Mechanisms of Lung Disease Conference, NIAID Systems Biology Annual Meeting, and 17th Annual Lewis Landsberg Research Day at Northwestern University Feinberg School of Medicine, Chicago IL, Sept 2023.
Akpuokwe M, Markov NS, Fenske S, Gao CA, NU SCRIPT Study Investigators. Using machine learning to predict prolonged intubation in patients with suspected pneumonia. Oral and poster presentation at Kimberly Querrey Summer Research Program Presentations, Northwestern University Feinberg School of Medicine, Chicago IL. July 2023. Poster presentation at Northwestern University Landsberg Research Day, Chicago IL, Sept 2023.
Lin S, Fenske S, Markov NS, Gao CA, NU SCRIPT Study Investigators. Predictive Modeling for ECMO Utilization in ICU Patients. Oral and poster presentation at Kimberly Querrey Summer Research Program (KQSRP) Presentations, Northwestern University Feinberg School of Medicine, Chicago IL. July 2023. Poster presentation (selected as finalist from >450 abstracts) at Northwestern University Landsberg Research Day, Chicago IL, Sept 2023.