Simona Cristea
@simocristea
Cancer Data Scientist @Harvard & @DanaFarber | Prev @eth | 🇷🇴🇸🇪🇨🇭🇺🇸 I explain complex genomics concepts in-depth & share recent research ♥️🇨🇭🍫
The 2 main forces driving cancer evolution:
1. mutation. new progeny arise, increasing diversity
2. selection. populations with higher fitness (capacity to reproduce) overtake the other lineages by frequency
Tumors evolve via an iteratively malignant dance among these two.
🤔All fields and industries are regularly disrupted. Today, we all own a smartphone.
How will the next disruption change Biology?
Accurate CRISPR editing & designer babies? Fancy prediction models behind medical decisions?
Probably not.
Rather, something totally different 🎁
🤔 Why Biology will have its “AI moment”:
Biology is inherently messy, noisy & complex.
Maths is inherently clean & precise.
Closed-form solutions seldom work for Biology.
The uninterpretable & non-mechanistic “dark” side of Deep Learning might just be the spirit of Biology.
The complex genomics behind predicting immunotherapy response
The science of #immunotherapy can cure a patient's otherwise incurable cancer.
But sometimes immunotherapy fails completely
Shockingly, we hardly know why.
A meta-analysis of #Genomics & #Transcriptomics in >1,000 immunotherapy-treated patients aims to better understand why🧵
Code your own Graph Neural Network for drug prediction
Hands-on weekend learning
Here’s everything you need to know to code your own #GraphNeuralNetworks drug screening predictor from scratch in less than 1 hour 🤯
Code together with @PetarV_93
It will walk you though the basics & learn you how to think.
m.youtube.com/watch?v=e40y0WtRAWM
Why do we say that methods matter in Bioinformatics? An immunotherapy example
‼️Why do we say that #methodsmatter?
Here’s a telling example.
Two very recent studies asked the exact same cancer #immunotherapy prediction question, on the exact same dataset.
They reached contradictory conclusions.
Why?
Slight changes in the #Bioinformatics methods used👇 twitter.com/NCIEytanRuppin/status/1610202233521438721
The changes are:
1.analyze data per cancer type vs. pan-cancer
2.use cutoff of 0.2 vs. 0.1 for calling a copy number alteration
The contradictory conclusions are:
1.aneuploidy score (AS) is not predictive of immunotherapy response
2.a new metric is predictive & outperforms AS
The hidden genetics of fake twins (doppelgängers) hints to shared DNA variants
We all think we're one of a kind.
But sometimes, we come across someone who looks just like us!
A @CellReports study tested the DNA of "fake twins".
Guess what:
They also share 🧬DNA variants related to facial features & behavior 🤯
Surprised or not really? Let’s dig in🧵👇
How contextual learning (Graph Neural Networks & Transformers) is shaping biomedicine
Like it or not, it's happening!
2023 is the year of #DeepLearning in Healthcare.
🚨New editorial @natBME on how Graph Neural Nets & Transformers are shaping Computational Medicine via contextual learning.
Editorial written part by editors, part by #chatGPT🤫
Main takeaways👇
🤔 Science is a deeply creative process.
We literally create knowledge that hasn't previously existed.
Maybe it’s then implicit that creating new knowledge can’t be easy.
To all scientists out there: doing science, in whatever form, is such a unique process.
🧫🧬🔬⚗️🔭🥼🧪🧮