Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

Meet our newest Research Group Leader: Jess Ewald @ewaldlab.org ‬🇨🇦 Jess’s group takes a multi-disciplinary approach to identify and characterise chemical hazards to humans and ecosystems, using cell profiling data, machine learning, and integrative data analysis. www.ebi.ac.uk/about/news/p... 🖥️🧬

Great talk by Kata Ferenc on improving bioinformatics software quality through teamwork, sharing how we’ve approached this at @ncmbm.bsky.social It sparked discussion on taking action within our Bioinformatics in Life Science initiative at @uio.no @biovitenskap.bsky.social doi.org/10.1093/bioi...

Great read: Beyond AlphaFold: how AI is decoding the grammar of the genome www.nature.com/articles/d41...

Two days left to apply for a 3-year postdoc in #Chromatin #Cancer #Epigenetics at University of Oslo, Norway, co-supervised by @amathelier.bsky.social You will be part of @cancelluio.bosky.social. We focus on #Sarcoma #Epigenome #CRISPR and Drug screen studies. Find out more here: shorturl.at/DtLHM

We are hiring! A 3-year postdoc in #Chromatin #Cancer #Epigenetics at University of Oslo, Norway and co-supervised by @amathelier.bsky.social You will be part of @cancelluio.bosky.social. We focus on #Sarcoma #Epigenome #CRISPR and Drug screen studies. Find out more and apply here: shorturl.at/DtLHM

Only one more week to apply to do a postdoc with our group and this of @thomasdwkim.bsky.social @ncmbm.bsky.social @nordicembl.bsky.social ! If you are interested, contact us or apply directly to the add. Please RT. www.jobbnorge.no/en/available...

We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠 Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels. Take a look at these four open positions 👇

🌟 Looking to launch your independent research career in an environment built for collaboration, clinical relevance, and scientific excellence? 🔗To apply👉 www.jobbnorge.no/en/available... 📅 Deadline: 8 September 2025

📢One month left to apply to our Group Leader position! 🌟A chance to be part of @nordicembl.bsky.social: “The Partnership connects us with an exceptional network of researchers, facilities, and complementary expertise. It opens doors to meaningful scientific exchange”, says @amathelier.bsky.social.

"criteria for retraction have long included major errors that undermine a paper’s findings, not just fabrication and falsification" <- important to emphasize this. Retraction=/ misconduct

It was indeed fantastic! Thank you so much to all the organizers for supporting this community. 🙏

What a fantastic #ISMBECCB2025 conference it has been, with an outstanding #RegSys @iscb-regsys.bsky.social COSI track! Thanks, everyone, for submitting, attending, presenting, and organizing @iscb.bsky.social @eccb-europe.bsky.social

#ISMBECCB2025 It is good to be at a conference in 2025 of a society that reminds us that “equity, diversity and inclusion are essential to how the Society operates, evolves and envisions the future”. www.iscb.org/iscb-news-it... @iscb.bsky.social

Next is @damlaob to talk about putting new Deep learning models of TFs into #Jaspardb #RegSys #ismbeccb2025 @amathelier.bsky.social

Our own Damla @damlaob.bsky.social making a great presentation of the upcoming updates of JASPAR and UniBind with BPnet DL models at #RegSys @iscb-regsys.bsky.social #ISMBECCB2025 Chat with her at her poster D-485.

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: www.nature.com/articles/s42... 📖 News & Views: www.nature.com/articles/s42... 💻 Code: corneto.org 🧵 Thread 👇

Today marks the start of the #RegSys @iscb-regsys.bsky.social track at ##ISMBECCB2025! Very much looking forward to listening to the exciting science that will be presented. Join us in room 11BC today and tomorrow.

🚨 We're hiring! NCMBM @ncmbm.bsky.social is looking for 2 new group leaders to join our vibrant research community. Ready to build your own group with strong support and a solid startup package? Interested and attending #ISMBECCB2025? Let’s connect! 🔗 www.jobbnorge.no/en/available...

Wonderful sunny day in Liverpool for #ISMBECCB2025! Marcelo Hurtado #TransMed talk on CellTFusion tomorrow 3:50, Hugo Chenel #NetBio poster (D-430) on GRNs. I will talk about our paper with Benoît Aliaga and Flavien Raynal in #RegSys on Wednesday. See you there! academic.oup.com/nar/article/...

Thanks for the invitation! Made it to Liverpool and looking forward to the session!

After a long trip and a long sleep, i am ready to enjoy the rich scientific program at #ISMBECCB2025 in Liverpool. This is also the first year of our new COSI in Computational and System Immunology (CSI) happening on Tuesday. And of course looking forward RegSys, as usual with fantastic organizers

Happy to be OMW to #ISMBECCB2025! Looking forward to great science and to seeing old and new friends.

👏Congratulations to Romana Pop, Ping-Han Hsieh, Tatiana Belova, @amathelier.bsky.social and @mkuijjer.bsky.social on their newly published worked! 💡They developed a novel method that integrates patient-specific gene regulatory networks with multi-omics data to improve cancer survival predictions👇.

Fantastic opportunity to launch your research group following the @embl.org model in a great environment with a solid startup package and access to state-of-the-art resources. Join us at the @ncmbm.bsky.social, part of the @nordicembl.bsky.social, at @uio.no Feel free to reach out if you have Qs.

🚨 New preprint from group is now out on arXiv. inMOTIFin: A lightweight, flexible simulation toolkit for regulatory genomics. Simulate, implant, and modify transcription factor binding motifs with ease. 🔗 arxiv.org/abs/2506.20769 🧵👇

Today, we are welcoming @jmschreiber91.bsky.social as part of @ncmbm.bsky.social international seminar series and of the Sven Furberg. @amathelier.bsky.social @uio.no

Exciting to host @jmschreiber91.bsky.social today at @ncmbm.bsky.social! Oslo friends, join at 12PM for the joint NCMBM International and Furberg seminar to hear more about Jacob's research on "Understanding and designing regulatory DNA using machine learning." Looking forward to an exciting talk!

Current genomic deep learning models display decreased performance in cell type-specific accessible regions

Our scientific retreat is starting with Rafal Ciosk from @uio.no! We are looking forward for 2 days of great science and networking! @nordicembl.bsky.social @embl.org @amathelier.bsky.social

Only 4 days left to the deadline: Become our new colleague as associate professor in biostatistical machine learning at Oslo Centre for Biostatistics and Epidemiology @ocbe.bsky.social and our Centre of Knowledge-driven Machine Learning Integreat! www.jobbnorge.no/en/available...

Authors include: @juliazeitlinger.bsky.social, @sroyyors.bsky.social, @ferhatay.bsky.social, @amathelier.bsky.social, @alemedinarivera.bsky.social, @shaunmahony.bsky.social

The paper explores the latest advances in mapping cis-regulatory elements, interpreting sequence-to-function models, and integrating #chromatin architecture and #multiomics data. The authors highlight technical limitations and propose strategies to generalize regulatory models across cell types.

🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics" Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106

Our perspective article is now out

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

Thanks indeed, @alfonsovalencia.bsky.social. What an incredible role you have played in the field and for Bioinformatics! Thank you, Alfonso: An Impactful Bioinformatics Collection url:https://academic.oup.com/bioinformatics/pages/thank-you-alfonso-impactful-bioinformatics-collection?login=false

Europe is well inspired to catch up massively, not just to serve as safe haven for US scientists (and european expats).

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!

<grumble> funding agencies, scoring schemes on “clarity of hypothesis” is quite a straightjacket. There is plenty of v good discovery/ hypothesis generating science which doesn’t have a “narrow” hypothesis

Looking forward to @ewanbirney.bsky.social's visit at @ncmbm.bsky.social on May 5th! The seminar will dive into his current research on "AI modelling of Healthcare trajectories and Scandinavian and UK history with genetics;" exciting! www.med.uio.no/ncmbm/englis...

💡 Our very own postdoc, @damlaob.bsky.social from @amathelier.bsky.social's group, has shared her thoughts on how collaborations between experimental and computational scientists can help solving health-related issues during the 5th @embl.org Partnership conference AI in One Health. 📜 Read more 👇!

🚨 The Sahu group at NCMBM at the University of Oslo is advertising for a lab engineer/lab coordinator position. 📅 Deadline 29th April 2025 See all the details 👉 : www.jobbnorge.no/en/available.... @nordicembl.bsky.social @embl.org @uio.no

🔬 Coming up this May! Three outstanding speakers are taking part in our seminar series: @ewanbirney.bsky.social, @prhsteinmetz.bsky.social, and @afarkkila.bsky.social . 🗓️ Check out all the details 👉 www.med.uio.no/ncmbm/englis... @uio.no @nordicembl.bsky.social

🧬 Happy DNA day 🧬

Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics. Preprint: www.biorxiv.org/content/10.1... GitHub: github.com/jmschrei/led...

Highly recommended 😁

I had such a blast participating in the workshop on Machine Learning In Clinical Research with people working on the European RESCUER project and the Troyanskaya lab at Princeton @princetonupress.bsky.social. Such amazing science going on. Thanks Vessela Kristensen and all organizers!