Anthony Mathelier

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.

📢 Hiring! Our group @ncmbm.bsky.social seeks a Research Scientist contributing to:
• Reproducible pipelines for large-scale genomics
• cisreg signature analysis in breast cancer
• Continued development of JASPAR
• Cross-disciplinary collaboration

Apply now 👉
www.jobbnorge.no/en/available...

Looking forward to two days of talks and discussions around research and innovation in Life Science in Norway!

@uio.no

Let's get in touch then to see how/if it would work

Let me know if you plan to come to Oslo/Norway.

Looking forward to participating in this symposium! Thanks for the invitation.

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

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AlphaGenome is out in @nature.com today along with model weights! 🧬

📄 Paper: www.nature.com/articles/s41...

💻 Weights: github.com/google-deepm...

Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

Thanks to
@ferhatay.bsky.social
and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io

RECOMB-RSG 2026
Deadline: Feb 15.
Tracks for: Preprints, Highlights (Recent Papers), Lightning talks
Details: recomb-rsg.github.io

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This move supports a "discussion-first" format. As the field moves toward complex genomics and system-level integration, the community needs a venue designed for deep technical exchange and diverse perspectives.

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Excited to see the upcoming new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, it is transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io

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You swear at the code.
You’re sure the computer’s being stupid.
But it’s not the computer. It never was. 🧵

Took this photo 12 years ago

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences AbstractSummary. The accurate development, assessment, interpretation, and benchmarking of bioinformatics frameworks for analyzing transcriptional regulato

inMOTIFin is a modular, user‑friendly Python toolkit for simulating and modifying regulatory DNA sequences. The code is open‑source via PyPI and Docker, with comprehensive docs.
academic.oup.com/bioinformati...

inMOTIFin is now published in Bioinformatics! 🎉

It lets you generate random sequences and TF motifs, and insert motif instances with custom spacing, co‑occurrence and orientation. Use cases for de novo motif discovery, cooperative TF binding, and DL explainability.

academic.oup.com/bioinformati...

Start your independent as an ELISIR fellow right after your PhD, in one of the most terrific places in Europe !

Some interesting points raised here. I'm personally in favor of applications to be evaluated for soundness and feasibility, followed by lottery.

Point of no returns: researchers are crossing a threshold in the fight for funding www.nature.com/articles/d41...

JASPAR recognised as an ELIXIR Core Data Resource - NCMBM - Norwegian Centre for Molecular Biosciences and Medicine ELIXIR has announced the life science data resources selected in its latest evaluation round for ELIXIR Core Data Resources (CDRs) and ELIXIR Deposition Databases. Among the six newly approved Core Da...

@amathelier.bsky.social from NCMBM, says: “ I am very proud to see JASPAR officially recognised as a Core Data Resource by ELIXIR and it is wonderful to see JASPAR join the ranks of other well-established European resources."

Read more about this achievement: tinyurl.com/4r6zntvw

Recognition as an @elixir-europe.org Core Data Resource reinforces JASPAR’s role as a trusted, FAIR reference for TF-based gene regulation research.
Proud of this achieved milestone. A big thanks to all collaborators over the years and to the community.

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism Transcription factors (TFs) may activate or repress gene expression through an interplay of different mechanisms, including RNA polymerase (RNAP) recruitment, exclusion, and initiation. However, depen...

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism | Science www.science.org/doi/10.1126/...

Two new chapters from my free online book in human genetics out this weekend!
These complete Part 3 of the book, on human population structure and history:
3.3: Human prehistory [separate thread]
3.4: Ancient DNA: a genetic time capsule [this thread]
web.stanford.edu/group/pritch...

An integrated view of the structure and function of the human 4D nucleome - Nature The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...

A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!

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

📣 The call for tutorials & workshops at #ECCB2026 is now open! Share your tools, methods or expertise with the community.
🗓️ Deadline: 5 January 2026
👉 Submit: tinyurl.com/tw-eccb26

💡 ECCB will take place on 31 Aug–4 Sept in Geneva, gathering 1,000+ scientists from academia, industry, & healthcare.

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/...

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Glad to have contributed to this work, and big thanks to @amathelier.bsky.social, @damlaob.bsky.social, and @ievarau.bsky.social (and the whole JASPAR crew) for this great effort.

#JASPAR #TFmotifs #DeepLearning #Genomics

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JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models Abstract. JASPAR (https://jaspar.elixir.no/) is an open-access database that has provided high-quality, manually curated, and non-redundant DNA binding pro

From @damlaob.bsky.social & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models | #Bioinformatics #Genomics #Database #OpenScience #TFBS 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/advance-...

It's always exciting when the latest edition of JASPAR comes out. Great leadership by @amathelier.bsky.social and pleased to welcome @anshulkundaje.bsky.social to the journey. #Jaspar2026

academic.oup.com/nar/advance-...

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!

Proud of JASPAR 2026 release with major expansion of PFM profiles and a new collection of deep learning models interpreted to extract learnt motifs!
Work led by @ievarau.bsky.social and @damlaob.bsky.social w/ @anshulkundaje.bsky.social @wywywa.bsky.social @flowerwhatelse.bsky.social labs & more