Seminars
2022-2023 CBM Seminar Series
Tuesdays 3:00-4:00 PM
Virtual via Zoom
Updated 5/5/2023
Tuesday, May 16, 2023
Natasha Gurevich, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell and Lab of Stefano Monti Junxiang Xu, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell and Lab of Ruben Dries
Tuesday, May 23, 2023
“Recontextualizing Gene Expression Signatures” Andrew Chen, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti
Tuesday, June 6, 2023
Whitney Souery, MD/PhD student, Bioinformatics Program, Lab of Ehab Billatos and Lab of Avrum Spira and Marc Lenburg Amulya Shastry, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell, Lab of Jay Mizgerd and Lab of Stefano Monti
Tuesday, June 20, 2023
Yulia Shaykhutdinova, M.Sc, Research Fellow, Lab of Ignaty Leshchiner
“Bronchial and Nasal gene expression alterations associated with Sulforaphane” Yohana Kefella, Bioinformatics Analyst, Lab of Jennifer Beane
Past Seminars
Tuesday, September 6, 2022
“CaDrA: A Containerized and Cloud-Deployable Open-Source Software Package for Candidate Driver Analysis of Multi-Omics Data” Reina Chau, Bioinformatician, Lab of Stefano Monti
“Characterization of early lung adenocarcinoma immune microenvironment through single cell sequencing” Yusuke Koga, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell
Tuesday, September 20, 2022
“Joint estimation of signatures across mutation modalities using Multi-Modal NMF” Kelly Geyer, Ph.D. Candidate, Mathematics and Statistics Program, Lab of Joshua Campbell
“Learning system-level dependency from human multi-omics data” Ziwei Huang, Ph.D. Candidate, Physics Program, Lab of Stefano Monti
Tuesday, October 4, 2022
“Batch Effect Correction of Metagenomic Data and its Effectiveness in Improving Microbiome Studies” Howard Fan, Ph.D. Candidate, Bioinformatics Program, Lab of Evan Johnson
“Spatial Transcriptomics Highlights a Field of Invasion in Early Stage Lung Adenocarcinoma” Dylan Steiner, Ph.D. Candidate, Genetics and Genomics Program, Lab of Jennifer Beane and Lab of Avrum Spira and Marc Lenburg
Tuesday, October 18, 2022
“An integrated framework for multi-scale and multi-omic spatial analysis” Jiaji (George) Chen, Ph.D. Candidate, Graduate Program in Genetics and Genomics, Lab of Ruben Dries (Hematology and Oncology)
“A meta-analysis of 12 NSCLC single-cell RNA-seq datasets reveals gene co-expression programs across cancer cells” Rui Hong, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell
Tuesday, November 1, 2022
“Multiplexed immune phenotyping and miRNA-ISH in bronchial premalignant lesions reveals a mechanism of immune suppression” Darren Chiu, Ph.D., Postdoctoral Associate, Lab of Jennifer Beane and Lab of Sarah Mazzilli
“Exploring the cellular heterogeneity of 4NQO-induced tumors in mice and their treatment with Wnt/b-cat/CBP inhibitor, E7386” Muzamil Khan, Ph.D. Candidate, Bioinformatics Program, Lab of Ruben Dries and Lab of Stefano Monti
“Gene expression signatures of aging and extreme human longevity using data from Long Life Family Study” Mengze (Vanessa) Li, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti
“Cell type localization of gene signatures defining bronchial premalignant lesion molecular subtypes implicates reduced dendritic and B cell antigen presentation in lesion progression” Conor Shea, M.D./Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane and Lab of Avrum Spira and Marc Lenburg
Tuesday, December 6, 2022
“Comparison of the tumor and lymph node immune microenvironment in early non-small cell lung cancer through multimodal single cell sequencing” Zhan Hao (Charley) Xi, Ph.D. Candidate, Molecular and Translational Medicine, Lab of Sarah Mazzilli and Lab of Jennifer Beane
Tuesday, January 10, 2023
“Improving the predictive ability of existing TB signatures via ensemble learning” Xutao Wang, Ph.D. Candidate, Biostatistics Program, Lab of Evan Johnson
Tuesday, January 17, 2023
“Comparing transcriptomic alterations from endobronchial biopsies and brushes to determine how cancer alters the airway field” Kelley Anderson, Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane and Lab of Avrum Spira and Marc Lenburg
“Evaluating the Robustness of Single Cell Integration Methods through Creation of a Human Atlas of Head and Neck Squamous Cell Carcinoma” Lina Kroehling, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti
Tuesday, January 24, 2023
“Exploring the immune contribution to progression of carcinogen-induced lung squamous cell carcinoma premalignancy in an NTCU-sensitive and NTCU-resistant mouse strain” Táchira Pichardo, Ph.D. Candidate, Molecular Translational Medicine, Lab of Sarah Mazzilli, Computational Biomedicine
“Microbial dysbiosis and epithelial dysmorphism in Vitamin A-Deficient Lungs” Kiloni Quiles-Franco, Ph.D. Candidate, Molecular and Translational Medicine, Lab of Evan Johnson and Lab of Felicia Chen (Pulmonary Center)
Tuesday, February 7, 2023
“The TBSignatureProfiler: A Novel R Package for Comparing Tuberculosis Gene Expression Signatures” Aubrey Odom-Mabey, Ph.D. Student, Bioinformatics Program, Lab of Evan Johnson
Tuesday, February 14, 2023
“Data driven analysis of single nucleus RNA-seq data of brain samples associated with Chronic Traumatic Encephalopathy (CTE) disease” Nida Pervaiz, M.S., Bioinformatics Analyst, Lab of Joshua Campbell
Tuesday, February 21, 2023
“Cancer-Associated Gene Expression Alterations in the Nasal Epithelium of Never Smokers” Minyi Lee, Ph.D. Candidate, Bioinformatics Program, Lab of Avrum Spira and Marc Lenburg
“A graph-transformer for whole slide image classification” Yi Zheng, Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane and Lab of Vijaya Kolachalama
Tuesday, February 28, 2023
“Integrated multi-omics approach to reveal underlying protective mechanisms of delaying cognitive decline in centenarians” Anastasia Leshchyk, Ph.D. Candidate, Bioinformatics Program, Lab of Paola Sebastiani & Lab of Stefano Monti
“Towards the interpretability of “good” models – A review of SHAP framework” Chonghua Xue, Ph.D. Candidate, Electrical Engineering, Lab of Vijaya Kolachalama
Tuesday, March 7, 2023
“Disease-driven Domain Generalization for Neuroimaging-based Classification of Alzheimer’s Disease” Diala Lteif, Ph.D. Candidate, Computer Science Graduate Program, Lab of Vijaya Kolachalama
Tuesday, March 21, 2023
“Cell segmentation in IMC data” Roxana Pfefferkorn, Ph.D., Postdoctoral Fellow, Lab of Joshua Campbell and Lab of Sarah Mazzilli
“Spatial transcriptomics analysis of Calciphylaxis, a dread complication in CKD patients, reveals mechanistic leads” Yichi Zhang, Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane and Lab of Vijaya Kolachalama
Tuesday, April 4, 2023
“Single cell RNA-seq of the airway field of injury associated with lung squamous premalignant lesions” Regan Conrad, Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane
“Panel Design for MERFISH Spatial Transcriptomics” Jason Weis, Ph.D. Candidate, Molecular and Translational Medicine Program, Lab of Ruben Dries and Lab of Sarah Mazzilli
Tuesday, May 2, 2023
“Deep Graphical Modeling for Mild Cognitive Impairment Risk Subtyping” Meagan Lauber, Ph.D. Candidate, Neuroscience Program, Lab of Vijaya Kolachalam