Roberto Rossini

Postdoc at UiO developing tools for 3D genomics

[Roberto Rossini @robomics]

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 @jonnings]

New preprint out! https://t.co/YRgJZFZOCr

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. https://t.co/K3nQoTUTn6 @INC_COST

[Jonas Paulsen @jonnings]

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 https://t.co/IPD8PctISc

[Anthony Mathelier @AMathelier]

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

https://t.co/uGLl8Maqix

1/9

[Centre for Bioinformatics, University of Oslo @unioslo_bioinfo]

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: https://t.co/wWfoL7d9be. Please RT.

[Roberto Rossini @robomics]

@AMathelier @UniOslo @NCMMnews @UniOslo_MED @unioslo_bioinfo @unioslo_mn @Oslounivsykehus Congrats Anthony!

[Geir Kjetil Sandve @SandveGeir]

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!

[Anthony Mathelier @AMathelier]

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.

https://t.co/ULGgBazFU8

[Genome Biology @GenomeBiology]

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 https://t.co/mYtd52KIum

[Department of Biosciences, University of Oslo @biovitenskap]

New publication: "MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions" with Roberto Rossini and Jonas Paulsen @biovitenskap. @jonnings @robomics @GenomeBiology
https://t.co/RYqHHCVn7v

[Anthony Mathelier @AMathelier]

Great to see the peer-reviewed version of this work now out.
Thanks @jonnings @robomics for having us involved! And congrats again 👏

https://t.co/pYrNRLvUFe

[Centre for Bioinformatics, University of Oslo @unioslo_bioinfo]

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: https://t.co/CF7BZ4sV2x. Please RT and circulate to interested. @RSGNorway @unioslo_bioinfo

[Anders Sejr Hansen @Anders_S_Hansen]

(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”

https://t.co/1Fsd6ixnK9

[Chakravarthi Kanduri @KanduriC]

Out now in @GigaScience after substantial improvement since the first version: https://t.co/aEIZPQE0Cl. Improvements since the first version are briefly summarised in the 🧵

[Anthony Mathelier @AMathelier]

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
https://t.co/iRHk1QyaI5

[Anthony Mathelier @AMathelier]

Very happy to see the peer-reviewed version of this work out at https://t.co/PzsH01N1dd
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

[Mariike Kuijjer @mkuijjer]

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 https://t.co/3IoNHg1ni5

[Jonas Paulsen @jonnings]

PhD position in 3D genome bioinformatics. Deadline: 1. Nov. Apply now! Please RT.

[Jonas Paulsen @jonnings]

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:
https://t.co/Ocsk8lT99R
@biovitenskap
@INC_COST

[Alexander Suh 서상재 @alexander_suh]

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. https://t.co/HCGBa7t9ss