My first month at the Broad Institute

I arrived 🛬 in Boston exactly a month ago. I managed to get my Visa 5 hours🕔 before catching my plane and the next➡️ thing you know. I was in an unfurnished apartment, waiting for it all to start. The Broad Institute is part of these institute a lot of people have never heard👂 of. Backed by billionaire philanthropist. They do cutting edge research and give their members a dream job. In that regard they compete ➕more➕ with the silicon valley unicorn🦄 than any other company.

I came at the broad and did not do a Ph.D. right now for a reason. In this place I am surrounded by people coming from the best schools🎒 in the US, they are driven and all extremely bright. See, I had never been in such an environment before the Flatiron Institute. But last time.. I loved💝 it and felt I had learnt more in a couple of months than in 2 years at school.

I want to do research, I want to have a Ph.D. I want to become an entrepreneur. I want for people to be free from disease😷 and untimely death💀. But what I know is that in order to do that I need to be surrounded with a lot of people with a similar mindset and will. This is what I found🔎 in Boston and at the Broad.

Here I am working on a couple of subjects. I am part of CDS, which work on computational analysis and prediction of Big Biological Dataset in order to better❇️ understand the mechanism of the cell in the context of human🚶 cancer.

We are using Machine Learning, Bioinformatic and High Performance Computing in order to tackle a set of subjects.

The main biological data and technique being used in our group👥 is Perturbation. In a nutshell, we perturb a large amount of Cancer Cell Lines -landmark,ex patient cancerous tissue that has evolved to live and replicate in petri dish since decades- genes by removing❌ them with Crispr tools🔩, by destroying their RNA with RNAi, by submitting the cells to doses of small molecules (drugs and others) and then looking 👀 at their growth📈 rate and sequencing their transcriptome (the quantity of RNA in the cell).

This effort is seconded by CCLE which categorizes via many assays and tools🔭, each cancer cell lines〰️. All of it belong to the DepMap Project, around which a lot (>50) of secondary project gravitate. these projects are made in partnership with research lab at Harvard and MIT and with hospitals in Boston, such as the Dana Farber Cancer Institute, MGH and Boston Children’s hospital🏥. But also with companies such as Novartis and Google.

I have been tasked in taking care of the data💽 processing aspect of CCLE. with each new Cell Line release I will assay a lot of its genetic informationℹ️ and output it for a quarterly🌗 releases.

My second work has to do with the analysis of the epigenome. Which is a set of features on the DNA that can be analyzed and used to understand how the cell is reading📖 and processing DNA at the time of analysis. this can help inferring the program of the cell and differentiate it to any other cells in our body -which all have the same DNA sequence, however not the same function.- In this epigenome I look👀 at networks of regulatory processes which involving enhancers and transcription factors. Some of them create a feed forward process called the Core Regulatory circuitry.

My goal is to understand and analyze it in the context of Acute Myeloid Leukemia in children👶. Understanding it might help in inferring the global cellular program and thus the possible actions that can be undertaken to disrupt or reverse it.

---

Broad Life

Broadies as we are called enjoy, in addition➕ to a life goal, an extremely decent salaries, food 🍦 everywhere (or maybe it is just the US) and talks🗨 twice per day. I know.. I am spoiled.

You will be able to read 📗 much more about my projects and their results in the coming posts 🚩.