Jaime Abraham Castro-Mondragon

As usual this time of year, started drafting the list of gene regulation conferences for 2026, enjoy! generegulation.org/conferences-...
Know of a relevant event that’s missing? Please reply below

Interested in understanding how epitope recognition specificity is encoded in your TCR sequences? Try our new interactive page for building TCR specificity profiles on the TCR Motif Atlas: tcrmotifatlas.unil.ch/Building_mot....

I’m happy to share that since January, I have started my lab at the @comphealthmunich.bsky.social & Hauner CCRC (LMU) 🎉
We aim to combine single-cell, long-reads, computational modeling, and functional genomics to understand RNA-driven regulation in pediatric diseases.

Ancestry and somatic profile indicate acral melanoma origin and prognosis - Nature Analysis of the somatic and transcriptomic profile of 123 acral melanoma samples from Mexican patients helps understand tumour origins and prognosis, and highlights the importance of including samples...

We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️

www.nature.com/articles/s41...

Bluesky Map Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

I made a map of 3.4 million Bluesky users - see if you can find yourself!

bluesky-map.theo.io

I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

course schedule as a table. Available at the link in the post.

I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.

I will record lectures & all will be found at this link: github.com/rmcelreath/s...

[2025-10-16] What Makes a Good Data Visualization?

Here's a teaser video of @christinezhang.bsky.social's guest lecture for the "140.776 Statistical Computing" 💻 course that I instructed this year at @johnshopkinssph.bsky.social

Watch Christine's full guest lecture for free at youtu.be/SeLucCb05Dk

JASPAR 2026 is out 🎉

The new release massively expands the TF motif collections and adds a dedicated DeepLearning collection of motifs learned from deep learning models.

Database: jaspar.elixir.no
Paper (NAR): doi.org/10.1093/nar/...

🧵1/2

JASPAR goes Deep Learning! - NCMBM - Norwegian Centre for Molecular Biosciences and Medicine A new era for motif resourcesThe team behind JASPAR, led by Anthony Mathelier at NCMBM, has released the 11th update. JASPAR is built and maintained by an international consortium of research groups, ...

Together, these approaches create a uniquely powerful platform for exploring how transcription factors interpret the genome.”

📰 Read the full story: www.med.uio.no/ncmbm/englis...

Congrats to the entire JASPAR community for driving this resource forward to shape the future of regulatory genomics!

#FREECOURSE-announcement
Want to learn about microRNA annotation and differential expression analyses? Within the Oslo Bioinformatics week 2025, we will be teaching a two-day course on the 9th and 10th of December at the University of Oslo. 1/2

Bioconductor Seminar Series flyer. Title: “Deep-learning-based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines.” Event on Dec 2, 2025 at 9 PM CET / 3 PM EST / 12 PM PST. Speakers: Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders. Discussant: Davide Risso. Includes a “Register for Zoom Link” button, QR code, and Bioconductor logo.

📣 Calling Bioconductor users and developers! 🧬 ✨

Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!

Our paper on LARGE-scale benchmarking of motif discovery tools is published! nature.com/articles/s42...

It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.

More results from Codebook about poorly studied TFs are coming soon.

Venn diagrams as jack-o-laterns showing trick/treat logicals: OR, AND, XOR, NOR, NAND, and XNOR

Halloween logicals, still the best 10/31 venn

just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at wizardzines.com#posters

(TPCPA), a proteomic resource that provides proteome-scale quantifications of 999 tumors across 22 cancer types in a unified manner, for discovering tumor biology, biomarkers, and therapeutic targets. hgserver1.amc.nl/cgi-bin/r2/...

I keep stumbling when, in biological data analysis, someone uses the word "noise" as if it represented an objectively existing, tangible thing.
It is not. Noise is just another word for ignorance. Complicated but in principle deterministic stuff that ...
(1/2)

Multiple overlapping binding sites determine transcription factor occupancy - Nature A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

www.nature.com/articles/s41...

Beyond AlphaFold: how AI is decoding the grammar of the genome Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.

I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: www.nature.com/articles/d41...

solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
seeing-theory.brown.edu/index.html

Boromir Meme: One does not simply select the longest ORF

I am super excited to announce the first (brief) pre-print purely from my group:

Start right to end right: authentic open reading frame selection matters

www.biorxiv.org/content/10.1...

This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!

Tomtom-lite: Accelerating Tomtom enables large-scale and real-time motif similarity scoring Summary Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete characters. With the growing prevalence of machine lear...

I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier.

www.biorxiv.org/content/10.1...

Ma main tient un papier carré sur lequel est ecrit 2025 perpendiculairement à un miroir. Avec la symetrie, on peut lire 25 05 2025.

Bonjour, nous sommes le

Our "Atlas of Variant Effects 2030 Roadmap" is live: zenodo.org/records/1542...

1/n

Perspective on recent developments and challenges in regulatory and systems genomics Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul

Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics

An article titled "How the Web Became Unreadable", posted on Medium. There is a soft paywall asking you to sign in, covering most of the article. Screenshot found on Mastodon https://beige.party/@mayintoronto/114497234942335666

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

We have a new preprint out! Led by brilliant PhD student @estefvazquez.bsky.social. here we investigate through transcriptomics and proteomics the microenvironment of ulcerated #acral #melanoma 👇🏾

Thrilled to celebrate 9 rewarding years since founding my group @ncmbm.bsky.social , @uio.no, @nordicembl.bsky.social. Proud of our achievements and honored to now serve as Ass. Director. Deep gratitude to all fantastic team members past & present, collaborators, colleagues. Excited for what's next!

many well-known alternative TF isoforms function as negative regulators of their cognate reference isoforms (e.g. STAT3b), leading us to wonder how widespread this phenomenon may be. we used our data to classify alt TF isoforms into two categories: negative regulators & rewirers

An anti-gata motif ?