Embracing Uncertainty in Life, Science

It has been a long time since I wrote a non strictly scientific blog post. The holiday time, often a time of reflection and new resolutions, seems good for getting back to that. But don’t worry, there will be connections to science work as well… 😉 Today’s blog is about uncertainty - in our science, in our lives, in the world.

https://biociphers.wordpress.com/2025/12/28/embracing-uncertainty-in-life-science/

MAJIQ V3 Release

Ever since MAJIQ V2 was released we have been working on V3. It only took us a couple of years, but.... We are (finally!) pleased to announce the release of MAJIQ V3, a major update to our software for detecting, quantifying, and comparing RNA splicing from RNA sequencing. Users can find the software at majiq.biociphers.org Recap: We originally released MAJIQ…

https://biociphers.wordpress.com/2025/06/20/majiq-v3-release/

Tissue-specific splicing prediction – What’s in a name, what’s in a claim, and are target functions all the same?

In today’s blog post, I want to discuss some work/claims related to a topic that has been one of my lab’s focus areas - predicting tissue-specific alternative splicing (AS) of RNA. Some background information on why AS is important/interesting (skip if you know it): I have had much interest in RNA splicing since I started my postdoc with Ben Blencowe and…

https://biociphers.wordpress.com/2025/04/09/tissue-specific-splicing-prediction-whats-in-a-name-whats-in-a-claim-and-are-target-functions-all-the-same/

A Deep Dive into sQTL Modeling – Part 2

In my previous post, I described how, in our recent sQTL preprint, we broke current sQTL pipelines into their basic elements. This led to identifying potential issues/areas we may be able to improve: Read mapping, splicing event representation, handling missing values/imputation, various statistical model assumptions (scaling/transforming of the data as Gaussian with homoskedastic noise, ignoring read depth (point estimate for…

https://biociphers.wordpress.com/2025/01/28/a-deep-dive-into-sqtl-modeling-part-2/

A Deep Dive into sQTL Modeling – Part 1

The next few blog posts will be dedicated to a high level overview of our preprint on splicing QTL (sQTL) modeling: “A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease”. Before we delve into reviewing some of the insights we gained and the new method (MAJIQTL) details, I’d like to take a minute to explain why I believe this work, led by the incredibly talented…

https://biociphers.wordpress.com/2025/01/20/a-deep-dive-into-sqtl-modeling-part-1/

Should I just use long reads for my RNA splicing analysis? 🤔

If you are into studying transcriptomics variations using RNA sequencing you may be weighing your options for the next project in terms of long (ONT, PacBio) or short reads. Indeed, wherever I go for meetings or give talks I inadvertently get the question “Soo…What’s with long reads? Is that what we are supposed to do now?” There are good reasons for that.

https://biociphers.wordpress.com/2024/10/11/should-i-just-use-long-reads-for-my-rna-splicing-analysis-%f0%9f%a4%94/

How to keep up with literature and develop good habits? Try the Journal Club Blitz!

A common problem we all face is that we don’t get to those “important non urgent” tasks. One such task for us scientists is to read papers. We all have our constantly filling pile of interesting papers to read. Yet even as students we already struggle to get to those and PIs I talk with commonly complain they don’t get to read papers anymore.

https://biociphers.wordpress.com/2024/04/28/how-to-keep-up-with-literature-and-develop-good-habits-try-the-journal-club-blitz/