Associate Professor at University of Oslo. Interested in bioinformatics, 3D Genome, epigenetics, genomics and gene regulation. Postdoc positions available.
Joined February 2011
- Tweets 313
- Following 383
- Followers 1,220
- Likes 95
10 Photos and videos
Pinned Tweet
3 Jul 2024
Struggling with Hi-C data? Meet hictk: a new toolkit revolutionizing working with .hic and .cool files! Seamless interoperability for a range of file formats, and blazing-fast performance, 3D genomics has just gotten a lot easier. Developer: @robomics academic.oup.com/bioinformat…
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Jonas Paulsen retweeted
4 Feb 2025
🚨 PhD in Bioinformatics & Gene Regulation 🚨
Join the Bioinformatics in Life Science initiative through a multidisciplinary project to unravel gene regulation from DNA to proteins, co-supervised by @eviledv @jonnings and me @biovitenskap @NCMMnews!
jobbnorge.no/en/available-jo…
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Jonas Paulsen retweeted
18 Oct 2024
Finally biologists can also use numpy (array programming). Handling e.g. DNA and protein sequences with convenience and speed, like physicists and machine learners for decades have worked with numerical data: nature.com/articles/s41592-0… (1/3)
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Jonas Paulsen retweeted
14 Oct 2024
Epigenetics, gene transcription and cancer research X afficionados...Don't forget to register and join our exciting "nuclear topology and 3D chromatin architecture in cancer" online symposium taking place on Monday November 11th! Organized by @jane_skok and @LabMelnick #epigenetics #cancer @NYUGSOM_Path
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Jonas Paulsen retweeted
2 Sep 2024
🎉 Excited to share the peer-reviewed version of our manuscript describing COBIND, a tool for revealing TF co-binding patterns using non-negative matrix factorization. Great work led by @IevaRau @NCMMnews @NordicEMBL @UniOslo_MED @UniOslo
academic.oup.com/nar/advance…
@NAR_Open
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Jonas Paulsen retweeted
12 Aug 2024
Our lab (papantonislab.eu) is still looking for a PhD candidate with a strong computational biology background and a keen interest for genome assembly and #3Dgenomics to join our subproject in the exciting EvoREST initiative on genome evolution. @yourUMG @uniGoettingen
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Jonas Paulsen retweeted
5 Jun 2024
Thanks to @Vesselinka, here is a great picture from @NCMMnews scientific retreat with @emma_haapaniemi presenting her group's research! #WomenDoScience #InclusionMatters
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Jonas Paulsen retweeted
23 Feb 2024
We are hiring an #engineer in the field of #molecular_biology to work with #single_cell_RNA_sequencing and #spatial_transcriptomics in the context of #breast_cancer research. Apply here: finn.no/job/fulltime/ad.html…
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Jonas Paulsen retweeted
15 Dec 2023
Last couple of days to apply for this postdoc position to generate deep learning models and expand the great JASPAR and UniBind databases @NCMMnews!
It's a fantastic project in a very supportive group with outstanding collaborators!
10 Nov 2023
🧬Opening for a postdoc in my group @NCMMnews @UniOslo @UniOslo_MED @unioslo_mn to generate deep learning models to enhance JASPAR @jaspar_db & UniBind, boosting gene regulation research. Project in collaboration with @anshulkundaje, @WyWyWa.
Plz share
jobbnorge.no/en/available-jo…
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Jonas Paulsen retweeted
18 Sep 2023
Congratulations to Eivind Hovig! And thanks for great collaboration through more than two decades! You have made invaluable contributions to FUGE, @elixirnorway and Norwegian bioinformatics and cancer research!
18 Sep 2023
🎉 Happy 70th Birthday to Eivind Hovig! 🎂🥳 Your outstanding contributions to #bioinformatics have paved the way for groundbreaking research in Norway and beyond. 🧬🇳🇴 Your dedication and expertise are invaluable to us, @UniOslo, @UiO_LifeSci & @Oslounivsykehus. 🏆🔬
ALT portrait photo Eivind Hovid
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Jonas Paulsen retweeted
24 Aug 2023
Associate professor of Medicine (Biochemistry) position open at Institute of Basic Medical Sciences, University of Oslo!
We are recruiting a new colleague working within the fields of chromatin biology or membrane dynamics!
@UniOslo_MED @WAutophagy
jobbnorge.no/en/available-jo…
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Jonas Paulsen retweeted
13 Jun 2023
Truly amazing to see the @ELIXIREurope crowd gathered for the All Hands Meeting in Dublin taking bioinformatics to new heights!
8 Jun 2023
🎊 2023 ELIXIR All Hands Meeting #ELIXIR23 has come to an end with @NBlomberg’s closing remarks.
👏 Thank you all for joining us in Dublin and we look forward to seeing you again next year in Uppsala, Sweden 🇸🇪 for #ELIXIR24!
@sysbioire #ELIXIR_IE @NBISwe #ELIXIR_SE
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Jonas Paulsen retweeted
2 May 2023
We're excited to share our manuscript describing COBIND, a novel tool for the identification of transcription factor co-binding patterns with non-negative matrix factorization
biorxiv.org/content/10.1101/…
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Jonas Paulsen retweeted
8 Dec 2022
MoDLE, modeling of DNA loop extrusion, from @robomics, @jonnings, simulates DNA contact maps quickly, using low memory. It requires a genome region and the barrier positions in the region eg CTCF binding sites. Predicts effects of deletoins on TADS genomebiology.biomedcentral.…
ALT Comparisoin of MicroC data (top) and MoDLE prediction for a region of Chromosome 2
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Jonas Paulsen retweeted
New publication: "MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions" with Roberto Rossini and Jonas Paulsen @biovitenskap. @jonnings @robomics @GenomeBiology
genomebiology.biomedcentral.…
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Jonas Paulsen retweeted
1 Dec 2022
Great to see the peer-reviewed version of this work now out.
Thanks @jonnings @robomics for having us involved! And congrats again 👏
genomebiology.biomedcentral.…
19 Apr 2022
New preprint out! biorxiv.org/cgi/content/shor…
MoDLE allows simulating HiC-like contacts generated by loop extrusion genome wide in a matter of minutes. Opens up for exploring underlying features of genome structure. Available on the command line. github.com/paulsengroup/modl… @INC_COST
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10 Aug 2022
Haha! Never underestimate a feeling, I guess. Good luck with the replies 😟
10 Aug 2022
second time in my career that a reviewer "feels" the mathematics are wrong, but does not demonstrate why 🤷♀️
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Jonas Paulsen retweeted
8 Jul 2022
Happy to publish our latest work as a preprint in bioRxiv. DNA methylation can predict and explain response to chemotherapy and bevacizumab. biorxiv.org/content/10.1101/…
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Jonas Paulsen retweeted
19 Apr 2022
Very happy to see the peer-reviewed version of this work out at epigeneticsandchromatin.biom…
We performed expression-methylation quantitative trait loci in 19 cancer types and identified 13 TFs likely driving DNA methylation patterns around their TFBS in at least 2 cancer types 1/6
11 May 2021
Our new preprint is out
We found that pioneer TFs are associated with the modulation of DNA methylation patterns around their binding sites in cancer and immune cells across cancers
Led by @RozaBLemma w/ @TF_82 E Martinsen @Vesselinka @ragnhildes1 @oddsgab biorxiv.org/content/10.1101/…
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Jonas Paulsen retweeted
19 Apr 2022
Happy to share our latest work!
A big thanks to @jonnings for his support and supervision.
Many thanks also to our collaborators for their invaluable comments and feedback @torognes, @AMathelier and Vipin Kumar.
19 Apr 2022
New preprint out! biorxiv.org/cgi/content/shor…
MoDLE allows simulating HiC-like contacts generated by loop extrusion genome wide in a matter of minutes. Opens up for exploring underlying features of genome structure. Available on the command line. github.com/paulsengroup/modl… @INC_COST
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