People (including me) usually come to DepMap for the synthetic lethalities, the strongly selective dependencies, and the extremely negative gene effect scores (often CERES/Chronos < -1) that scream “this gene is essential for this cell line”; but I have recently found that there is an “Upside Down” view of the data set that is easy to miss. This reversed view is anchored based on a handful of…
Part I Part II Part III (you are reading this) If you have ever watched a crowd surge toward an emergency, sirens blaring and lights flashing, you have seen the good side of a fast response. But the real test of any system is not only how quickly it mobilizes. It is whether it can stand down once the crisis is over. The immune system faces this exact challenge: it can expand armies of lymphocytes…
Part I Part II (you are reading this) Part III Your immune system is a powerful guard dog, but it needs training. From the moment you are born, it has to learn the difference between intruders and you. Most of us never notice that training happening. But in rare cases, the lesson plan goes unexpectedly wrong, and the immune system grows up confused, lashing out at the body while letting some…
Part I (you are reading this) Part II Part III The adaptive immune system depends on a controlled act of genomic violence. To recognize an almost infinite variety of pathogens, developing lymphocytes deliberately break and rejoin their own DNA, assembling antigen receptor genes from modular fragments. For decades, immunologists understood the outcome of this process but not its cause: what enzyme…
If you have ever heard p53 (a protein encoded by the TP53 gene) called “the guardian of the genome,” you might picture a wise molecular sentry that patrols DNA, stops cell cycles, and flips apoptosis switches like a seasoned air-traffic controller. But p53 didn’t make its debut as a heroic gene. p53, actually, began as a mysterious band on a gel as a stubborn ~53 kDa shadow that kept showing up…
Akin to vibe coding, vibe researching is a modern approach to learning where you use LLMs to dive into a topic by prompting, exploring, and iterating—essentially ‘vibing’ your way through the research while the AI handles the deep reading and connects the dots for you. Let’s imagine you are casually exploring DepMap and run into this strange and challenging profile: What is unusual here is that…
On Nov 4, 2025, I received an e-mail from Claude letting me know that I’d been granted $1,000 in credits for the web-based Claude Code environment ( https://claude.ai/code ). The credits were originally set to expire on Nov 18, 2025 (later extended to Nov 23, 2025): Naturally, I decided to make the most of this rare opportunity. I pulled out a few coding projects that had been sitting on the…
Interview Transcript Edited for clarity and readability Sander Wuyts: Hi everyone. A couple of years ago, I became completely obsessed with T cell repertoires—and I know I’m not the only one. That’s why I started this podcast. Welcome to The Repertoire Room . My name is Sander, and I’m the co-founder and CEO of ImmuneWatch, an immunoinformatics company specializing in T cell receptor sequencing…
How adding a few dots and curves to letters became a 3.7‑million‑parameter adventure The “Simple” Problem Picture this: you’re reading Turkish text where someone forgot to add the special characters. “Turkiye” instead of “Türkiye”, “ogrenci” instead of “öğrenci.” Seems simple enough, right? Just add back the missing dots and curves – how hard could it be? Well, buckle up. What looks like a…
Given a software code repository together with all commit history, can you spot potentially problematic parts of the software? This is the question I have been thinking about when I have some extra time left from other projects. As a pet-project, I recently created a proof-of-concept pipeline to show that the answer to this question seems to be yes . I was thinking about writing up a small…
In my earlier post , I talked about what it takes to apply to independent fellowship positions. This is the third post in the series and I am going to talk about my experience with coming up with a reasonable research proposal and CV. Curriculum Vitae (C.V.) When I started working on my application package, the first thing I did was to update my CV. I have previously applied to a few scholarships…
As I wrote earlier, I am interested in becoming an early independent fellow and started a blog series about it. This is the second post in the series. In this post, I am going to talk about what it takes to apply for such a fellowship. And for those of you who want me to cut to the chase, here are things you will be needing for application: Lots of time (and I mean lots) for finding such…
I am a fifth-year graduate student … and considering applying for such and such fellowships… So starts my e-mail messages to program coordinators nowadays. I am now officially a senior student in the Ph.D. program and on average, this is the year I should wrap things up and start thinking about the next step . And I am. And it is taking a lot of time and effort to do these things. And there is…
The Dream Imagine a cancer patient walking into the clinic to learn her therapy options. Her tumor sample was collected some while ago and now it is time to hear the lab results. Results, of course, are from a comprehensive -omics analysis of the tumor sample and are tailored for her. As soon as they pop-up on the physician’s screen, the physician takes a careful look at them and prescribes a drug…
I do terrible when it comes to application for fellowships. I applied to seven different Ph.D. programs, but got officially accepted only by one for which I had to appeal to their initial rejection. I tried applying to HHMI’s International Student Research Fellowship , but my institution did not nominate me for application. I then applied to an internal fellowship at my other institution thinking…
I love preprint services. I love the idea of archiving preprints, short-cutting the painful peer-review process and sharing the results in an easy and quick manner. This is why for our latest paper , I insisted on experimenting with the idea and actually ended up posting the paper on bioRxiv . There are various preprint servers available out there (nicely listed here ) and although the concept is…
As I mentioned earlier , the data available as part of the Cancer Genome Atlas (TCGA) project is incredibly useful for many types of analysis. From a computational biologist point of view, a systematic analysis of all these data sets becomes interesting only when the analysis glues two or more different data types together (remember this post ?). People usually try to show that their analysis is…
Right after I came up with the μ-wheel visualization, people immediately followed up with the obvious question: “ looks nice, but what is next? ” If you, like I do, work in the field of Computational Biology, the chances are that you are already familiar with the following situation: Unbelievable amount of information is publicly available for analysis (e.g. TCGA ). You pick one particular…
I am truly amazed by the abundance of the cancer genomics data and our current knowledge about the genes and the pathways they are involved in. With all these computational-friendly data sets out there, it is not surprising that we see a lot of tools, algorithms, and pipelines that analyze the data sets in their own way and suggest common mechanisms of tumor initiation or progression. Thanks to…
Hi there! This is a blog about various things, but it is mainly about Computational Biology , Systems Biology and Cancer Research . I started this blog, just because I want to share a few humble yet probably interesting observations–I had and hopefully will have– and my experience throughout my research. As many of researchers already are, I am, too, frustated with the current system of publishing…