Seminars

CBM Seminar Series 2023-2024

72 East Concord Street

Evans Building, 6th Floor

Room 605 – Hybrid

Tuesdays from 3:00-4:00pm


Updated April 8, 2024

Tuesday, March 26, 2024 – Postponed
“Deep Learning-Based Quantification of Glomerular Ultrastructure in Kidney TEM Images”
Anqi Zou, Ph.D., Postdoctoral Associate, Lab of Chao Zhang
Jason Wong, M.D., Postdoctoral Associate, Pulmonary Fellow, Lab of Marc Lenburg and Ehab Bilatos
Moderators: Yi Zheng, Yohana Kefella

Tuesday, April 2, 2024 – Postponed
Cailyn Kirkaldy, MS Candidate, Pathology Program, Lab of Sarah Mazzilli
Yohana Kefella, MS, Bioinformatics Analyst, Lab of Jennifer Beane
Moderators: Jason Wong, Irzam Sarfraz

Tuesday, April 16, 2024
Amulya Shastry, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell, Lab of Jay Mizgerd (Pulmonary), and Lab of Stefano Monti
Natasha Gurevich, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell
Moderators: Cailyn Kirkaldy, Tao Guo

Tuesday, May 7, 2024
Irzam Sarfraz, Ph.D. Candidate, Bioinformatics Program, Lab of Josh Campbell
Ming Liu, MS, Bioinformatics Analyst, Lab of Joshua Campbell
Moderators: Osman Berke Guney, Amulya Shastry

Tuesday, May 21, 2024
Eliezer Lichter, Ph.D., Postdoctoral Associate, Lab of Ignaty Leshchiner
Osman Berke Guney, Ph.D. Candidate, Electrical & Computer Engineering Program, Lab of Ruben Dries (Hematology and Oncology)
Moderators: Yibing Michelle Wu, Natasha Gurevich

Tuesday, June 4, 2024
Anna Parfenenkova, M.S., Research Fellow, Lab of Ignaty Leshchiner
Yibing Michelle Wu, Ph.D. Candidate, Molecular and Translational Medicine Program, Lab of Ruben Dries (Hematology and Oncology)
Moderators: Natasha Gurevich, Eliezer Lichter

Past Seminars

Tuesday, September 5, 2023
“Effect of mucus plugging on bronchial gene expression”
Whitney Souery, Ph.D. Candidate, Bioinformatics Program, Lab of Marc Lenburg and Lab of Ehab Billatos
“Molecular Characterization of Premalignant Lung Adenocarcinoma Lesions
Kelley Anderson, Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane and Lab of Avrum Spira and Marc Lenburg

Tuesday, September 19, 2023
“Analyze Cell-Type Proportion Changes with Age Using Cell-Type Deconvolution in LLFS Whole Blood RNAseq Data”
Mengze (Vanessa) Li, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti
“Learning 3D Medical Image Representations with Self-supervised Pre-Training”
Diala Lteif, Ph.D. Candidate, Computer Science Graduate Program, Lab of Vijaya Kolachalama

Tuesday, October 3, 2023
“Comparison and characterization of the tumor and lymph node immune microenvironment in early non-small cell lung cancer through multimodal single cell sequencing
Yusuke Koga, Ph.D. Candidate, Bioinformatics Program, Lab of Joshua Campbell
“Graph neural diffusion in scRNA-seq analysis”
Yu-Chen Liu, Ph.D., Postdoctoral Associate, Lab of Chao Zhang

Tuesday, October 17, 2023
“Elucidating age-specific characteristics of Head and Neck Squamous Cell Carcinoma through a single-cell atlas”
Lina Kroehling, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti

Tuesday, November 7, 2023
“Utilizing computational tools for single-cell RNA sequencing data analysis reveals a novel molecular mechanism of kidney fibrosis”
Simon Lu, Bioinformatics Analyst, Lab of Chao Zhang

Tuesday, November 21, 202
“Characterization of the persistent effects of smoking on nasal gene expression”
Minyi Lee, Ph.D. Candidate, Bioinformatics Program, Lab of Avrum Spira and Marc Lenburg
“The role of the B-cell receptor repertoire in lung squamous premalignant lesions”
Darren Chiu, Ph.D., Postdoctoral Associate, Lab of Jennifer Beane and Lab of Sarah Mazzilli

Tuesday, December 5, 2023
“Spatially informed profiling of stage I lung adenocarcinoma reveals a gene expression signature of extensive vascular invasion”
Dylan Steiner, Ph.D. Candidate, Genetics and Genomics Program, Lab of Jennifer Beane and Lab of Avrum Spira and Marc Lenburg
“Investigating the cellular heterogeneity of carcinogen-induced murine oral tumors via targeted therapy”
Mohammed Muzamil Khan
, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti

Tuesday, December 19, 2023
Single cell gene expression analysis of the field of precancerous LUSC”
Regan Conrad
, Ph.D. Candidate, Bioinformatics Program, Lab of Jennifer Beane
“Assessing Local Ancestry Inference Using Different Sequencing Assays and Depth of Coverage”
Tomoki Motegi, Ph.D., Postdoctoral Associate, Lab of Joshua Campbell

Tuesday, January 9, 2024
“Inferring historic genotypes and progression of common cancer models”Tayeb Jamali, Ph.D., Postdoctoral Associate, Lab of Ignaty Leshchiner
Association of acoustic perturbation measures with dementia status
Chonghua Xue
, Ph.D. Candidate, Electric and Computer Engineering, Lab of Vijaya Kolachalama

Tuesday, January 16, 2024
“Immunophenotyping of the murine premalignant lesion microenvironment reveal immune differences that may underpin strain-dependent carcinogen response”
Táchira Pichardo,
Ph.D. Candidate, Molecular and Translational Medicine, Lab of Sarah Mazzilli
“Identifying gene programs related to metastatic prostate cancer via a meta-analysis of single cell RNAseq datasets”
Junxiang Xu, Ph.D. Candidate, Molecular and Translational Medicine, Lab of Joshua Campbell and Lab of Ruben Dries (Hematology and Oncology)

Tuesday, February 6, 2024
dbverse: scalable data analysis in R”
Edward Ruiz, PhD Student, Genetics and Genomics program, Lab of Ruben Dries
“Dynamic Identification of Cancer Tissue Neighborhoods in Whole Slide Images Using a Graph-Based Approach”
Yichi Zhang, Ph.D. Candidate, Bioinformatics Program, Labs of Jennifer Beane and Vijaya Kolachalama

Tuesday, February 13, 2024
“Characterizing tumor’s and tumor surrounding lymph node’s (TSLN) immune microenvironment in early non-small cell lung cancer through multimodal single-cell analysis”
Zhan Hao (Charley) Xi, Ph.D. Candidate, Molecular and Translational Medicine, Lab of Sarah Mazzilli
“Limitations of the omics-based aging clock models”
Anastasia Leshchyk, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti

Tuesday, February 20, 2024
“Improving pre-cancer phenotype prediction through multimodal learning”
Lingyi Xu, Ph.D. Candidate, Computing & Data Sciences Program, Lab of Vijaya Kolachalama
Varuna Jasodanand, Ph.D. Candidate, Neuroscience Program, Lab of Vijaya Kolachalama

Tuesday, February 27, 2024
“Benchmarking Visium Spatial Transcriptomics using Lung Cancer Biopsies”
Jason Weis
, Ph.D. Candidate,  Program in Genetics and Genomics, Lab of Sarah Mazzilli

Tuesday, March 5, 2024
“Metabolically Annotated Single Cell Atlas for Breast Cancer”
Andrew Chen, Ph.D. Candidate, Bioinformatics Program, Lab of Stefano Monti

Tuesday, March 19, 2024
“Graphical Models to Analyze Statistical Relationships in Regional Tau Across the Amyloid Continuum”
Meagan Lauber, Ph.D. Candidate, Neuroscience. Lab of Vijaya Kolachalama
“Giotto Suite & 10x Genomics”
Jiaji (George) Chen, Ph.D. Candidate, Graduate Program in Genetics and Genomics, Lab of Ruben Dries (Hematology and Oncology)