What are the distinct paths for nonmalignant clones to transform into cancer?
What are the boundaries between a nonmalignant and a malignant clone?
Why do certain accelerated aging diseases increase cancer risk (Werner syndrome) vs. some decreases them (Hutchinson-Gilford progeria syndrome)?
Do people with germline mutations in cancer genes (RAS, BRCA1) have a different rate of the aging clock?
What is the ability of interventions to slow down aging effects to prevent cancer?
Five major intervention targets: Insulin growth factor pathway, the mammalian target of rapamycin (TOR) pathway, the family of sirtuins, the mitochondria and cells undergoing senescence.
What is the best approach to measure biological age in routine clinics? Can these measurements guide cancer treatment? Can changes in these measurements during therapy predict response?
What are the effects of cancer treatment on the aging of various tissues, including highly dividing tissues measured via multiple biological clocks measurements?
What are the links between biological age biomarkers and cancer risk?
Both the definition and our monitoring ability of senescent cells are poor.
How do you monitor and identify senescent cells in aging tissues?
How the efficacy of cellular therapy (CART, T-cell transfer therapy) is dependent on the patient's age?
Does it decrease due to immunosenescence and immune aging?
How the risk-benefit ratio for cancer treatment changes with age, and is there an inflection point?
Can combining senolytic drugs with existing cancer therapies affect the patient's response?
What is the role of pre-existing clonal hematopoiesis in frequently occurring therapy-related leukemia?
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Spending millions of $, Grail created a TCGA-like study to systematically answer the following:
What is the best cell-free DNA method to detect cancer from blood?
17 things we learned.🧵🩸
1. This study was composed of three phases, and today we will only discuss the first phase.
The goal of this phase is to answer which type of assay might give us the most insightful features to detect cancer - methylation, targeted-DNA-seq, or whole genome seq.
2. Before the dive, let's understand the problem.
Multiple current single cancer tests are simply not feasible.
After 3 years of routine cancer screening in three different organs, the cumulative risk of one false positive is 60% for men and 49% for women. No way!
A lot of Machine Learning (ML) I learned during my Ph.D. was from youtube. I didn't have a guide to do this effectively and thus here it is:
A complete guide to studying ML from youtube: 13 best and most recent ML courses available on YouTube. 👩🏫🧵⤵️
We will start with "Stanford CS229: Machine Learning" by Andrew Ng to start and learn the following ML concepts:
Linear & Logistic Regression,
Naive Bayes, SVMs, Kernels
Decision Trees, Introduction to Neural Networks
Debugging ML Models. youtube.com/playlist?list=…
A series of mini-lectures (~5 mins) covering various introductory topics in ML by Cassie Kozyrkov, covering:
Explainability in AI, Precession vs. Recall, Statistical Significance, Clustering and K-means, and finally, Ensemble models. youtube.com/playlist?list=…
I curated a list of 28 common issues one faces while using machine learning for biomedicine research and using different kinds of omics data. I also provided guides on how to best overcome them. 🍉🧵👇
I will cover these issues and how to address them using the following 8 studies.
We will start with the five pitfalls that arise when applying supervised ML models in genetics and genomics and how to best navigate through them. nature.com/articles/s4157…
We will next cover the eight common mistakes we make in deriving and validating predictive statistical models from high-dimensional data. nature.com/articles/s4156…
We will next go onto a brilliant youtube channel -- StatQuest by @joshuastarmer. It is one of the best ways to learn fundamental big data analysis way beyond their statistics. His humor and comedic timing are unmatched. youtube.com/c/joshstarmer
Our understanding of the immune system is quickly growing.
11 resources (videos and papers) covering the fundamentals and computational tools available to study the immune system. 🧵👇🔬🤒
Before we go on to learn the computational tools to quantify and measure the immune system, Let's start with a 15 mins visual overview of the fundamentals of the immune system.
Next is another 15 mins visual. This explains the cells of the immune system and their different functions that provide an immune response to an invading pathogen.
List of 113 major papers that generated big data funded by NIH and direct link to download their processed data. Explore and search through them. gdc.cancer.gov/about-data/pub…