@robomics

Postdoc at UiO developing tools for 3D genomics

 Oslo
Joined May 2020
  • Tweets19
  • Following138
  • Followers49
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.
Jonas Paulsen@jonnings19 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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Roberto Rossini retweeted
Jonas Paulsen@jonnings3 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…

hictk: blazing fast toolkit to work with .hic and .cool files

AbstractMotivation. Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher

academic.oup.com
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Anthony Mathelier@AMathelier2 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/… 1/9

Identification of transcription factor co-binding patterns with non-negative matrix factorization

Transcription factor (TF) binding to DNA is critical to transcription regulation. Although the binding properties of numerous individual TFs are well-documented, a more detailed comprehension of how...

biorxiv.org
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A 4-year PhD fellowship in Informatics/Bioinformatics is available at @unioslo_bioinfo as part of @UiO_LifeSci. The projects will focus on synthetic data generation, applied machine learning and benchmarking within molecular life sciences: jobbnorge.no/en/available-jo…. Please RT.
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With BioNumPy, I claim my postdocs @ivargrytten and Knut Rand have given the entire bioinformatics community a Christmas present🫢☺️. This is the fundamental library for working effectively with sequence data that I have been missing since I entered bioinformatics 17 years ago!
Geir Kjetil Sandve@SandveGeir25 Dec 2022
Replying to @SandveGeir @biorxiv_bioinfo @IvarGrytten @KnutRand
biorxiv.org/content/10.1101/…

BioNumPy: Fast and easy analysis of biological data with Python

Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and...

biorxiv.org
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Anthony Mathelier@AMathelier8 Dec 2022
So happy to finally see the peer-reviewed version of our manuscript "Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers" out. doi.org/10.1093/nar/gkac1143

Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of...

Abstract. Most cancer alterations occur in the noncoding portion of the human genome, where regulatory regions control gene expression. The discovery of no

academic.oup.com
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Genome Biology@GenomeBiology8 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.…
Comparisoin of MicroC data (top) and MoDLE prediction for a region of Chromosome 2

ALT Comparisoin of MicroC data (top) and MoDLE prediction for a region of Chromosome 2

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New publication: "MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions" with Roberto Rossini and Jonas Paulsen @biovitenskap. @jonnings @robomics @GenomeBiology genomebiology.biomedcentral.…

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Genome Biology - DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts...

link.springer.com
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Anthony Mathelier@AMathelier1 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.…

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Genome Biology - DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts...

link.springer.com
Jonas Paulsen@jonnings19 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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Registration is open for the first Oslo Bioinformatics Workshop Week (Dec 7th-13th) at the University of Oslo. Please see the announcement for schedule, program and registration: mn.uio.no/sbi/english/events…. Please RT and circulate to interested. @RSGNorway @unioslo_bioinfo
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(1/n) Excited to share preprint by @ViraatGoel @mileshuseyin We develop Region-Capture Micro-C (RCMC) By focusing on specific regions, we generate the deepest 3D genome maps thus far We see coalescence of enhancer and promoters into “microcompartments” biorxiv.org/content/10.1101/…
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Out now in @GigaScience after substantial improvement since the first version: doi.org/10.1093/gigascience/…. Improvements since the first version are briefly summarised in the 🧵

Profiling the baseline performance and limits of machine learning models for adaptive immune...

AbstractBackground. Machine learning (ML) methodology development for the classification of immune states in adaptive immune receptor repertoires (AIRRs) h

academic.oup.com
Chakravarthi Kanduri@KanduriC24 May 2021
AIRR ML: Did you know that baseline machine learning methods can perform well even when disease-associated signals are present in only 2 out of 100 000 receptors in diseased adaptive immune repertoires? Check our latest preprint: biorxiv.org/content/10.1101/… 1/10
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Anthony Mathelier@AMathelier28 Apr 2022
Very happy to host @renee_beekman @BeekmanLab from @CRGenomica today for our Furberg seminar. Renée will tell us about "Understanding early lymphoma formation from a single-cell epigenomics and 3D chromatin perspective." Oslo tweeps, join us at 14:30 mn.uio.no/sbi/english/furber…
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Anthony Mathelier@AMathelier19 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

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across...

Epigenetics & Chromatin - Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked...

link.springer.com
Anthony Mathelier@AMathelier11 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/…

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across...

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regula...

biorxiv.org
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Mariike Kuijjer@mkuijjer15 Apr 2022
𝗣𝗢𝗥𝗖𝗨𝗣𝗜𝗡𝗘 analyzes complex, genome-wide, patient-specific regulatory networks directly on the network's edge weights. It is our latest addition to the network zoo and now out on @biorxivpreprint doi.org/10.1101/2022.04.13.4…
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Jonas Paulsen@jonnings25 Oct 2021
PhD position in 3D genome bioinformatics. Deadline: 1. Nov. Apply now! Please RT.
Jonas Paulsen@jonnings1 Oct 2021
Fully funded PhD position in bioinformatics available in my group. Exciting project focusing on analyzing in-house Hi-C data to model 3D genome alterations in cancer. Please RT. Read more and apply here: jobbnorge.no/en/available-jo… @biovitenskap @INC_COST
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Jonas Paulsen@jonnings1 Oct 2021
Fully funded PhD position in bioinformatics available in my group. Exciting project focusing on analyzing in-house Hi-C data to model 3D genome alterations in cancer. Please RT. Read more and apply here: jobbnorge.no/en/available-jo… @biovitenskap @INC_COST
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Please RT! Exciting #PhD opportunity to work with @fjruizruano @SimoneFouche @SimoneImmler & me at @biouea in beautiful Norwich, to help understand why songbirds have a germline-restricted chromosome. Feel free to DM me for questions. findaphd.com/phds/project/ex…
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