Studying the transcriptional heterogeneity in kidney tumor cells

הרקע לפרויקט:

Single-cell RNA sequencing (scRNA-seq) is a cutting-edge molecular biology technique that allows researchers to analyze gene expression at the single-cell level. It enables the identification and profiling of individual cells within a complex tissue or organism, providing insights into cellular diversity, heterogeneity, and functional states. By capturing the transcriptome of individual cells, scRNA-seq has revolutionized our understanding of cell biology, developmental processes, disease mechanisms, and has immense potential for personalized medicine and therapeutic discovery.

מטרת הפרויקט:

In this project we will use published scRNA-seq datasets to study the heterogeneity between different tumor cells from renal cell carcinoma (RCC) and Wilms’ tumor patients. We will use unsupervised machine learning algorithms to cluster tumor cells based on latent biological signals as well as to infer the different gene expression regulatory networks (GERN) operating in different tumor cells.

תכולת הפרויקט:

• Survey of the relevant literature
• Application of existing and new machine learning and data analysis tools on scRNA-seq datasets
• Analysis of results

קורסי קדם:

At least one of the following (can be taken in parallel):

• Computational Biology (83665)
• Introduction to Machine Learning (83622)
• Neuro-Genomics (83675)
•  Biological data science (83414)

דרישות נוספות:

A basic first course in biology is recommended for this project.

מקורות:

1. Trink, Y.; Urbach, A.; Dekel, B.; Hohenstein, P.; Goldberger, J.; Kalisky, T. Characterization of Continuous Transcriptional Heterogeneity in High-Risk Blastemal-Type Wilms’ Tumors Using Unsupervised Machine Learning. Int. J. Mol. Sci. 2023, 24, 3532. https://doi.org/10.3390/ijms24043532
2. Heumos, L., Schaar, A.C., Lance, C. et al. Best practices for single-cell analysis across modalities. Nat Rev Genet 24, 550–572 (2023). https://doi.org/10.1038/s41576-023-00586-w
3. https://www.sc-best-practices.org/preamble.html