LoopBin – a VaDE-based neural network for chromatin loop classification Classifying chromatin loops from 3D genomics data according to their epigenetic and structural attributes is important for inferring their functional roles. Currently, such classification typically relies on the manual intersection of epigenomic signal peaks and loop anchor locations. To automate this, remove peak-calling biases and include information inherent to 3D genomics signal structure, we developed LoopBin, a framework based on a variational deep embedding (VaDE) neural network. We applied LoopBin to kilobase-resolution Micro-C data and segmented tens of thousands of loops into clusters with distinct features using minimal histone modification and transcription factor-binding data. These features were indicative of apparently distinct biological function by each subgroup of loops. Therefore, LoopBin can provide insights into the dynamic shifts in loop classification that can occur upon perturbation of cell homeostasis or signaling. ### Competing Interest Statement The authors have declared no competing interest.

Preprint alert! 🥸

Yajie Zhu (PhD graduate) and Mariano Barbieri (postdoc, @spp2202.bsky.social Accelerator award) produced a package that will classify loops in your #3Dgenomics data based on (whichever) epigenomic data you have available. Keep reading...

1/n

www.biorxiv.org/content/10.6...

I'll be at #FoG2026 in London, for @dtgenomics.bsky.social . I look forward to seeing many familiar faces there and hope to meet some new ones. Let me know if you are attending and would like to catch up?
#3DGenomics #Epigenomics #StructuralVariants

🎥 Missed our latest “Ask the Experts” webinar? Watch it on demand! 👉 vimeo.com/1139356204

Part II of our 2025 ATE series explores HOW to integrate 3D genomics with other omics datasets — visualize, interpret & unlock deeper biological insights.

#3DGenomics #MultiOmics #Webinar

Doctoral INPhINIT fellowships - Incoming Call 2026 We grant 30 fellowships for researchers of any nationality who wish to pursue a doctorate in a STEM discipline at research centres of excellence in Spain or Portugal.

Interested in #3DGenomics #4Dnucleome? Like #Barcelona? Would like to enjoy doing #science and to have fun during your #PhD?

Apply now to La Caixa Foundation Doctoral #INPhINIT fellowships with us. DM or email in case of interest... 👇🏼👍🏼

lacaixafoundation.org/en/doctoral-...

Please, repost... 🔄🙏🏼

Welcome! You are invited to join a webinar: Sixth Annual Meeting on Advances on Nuclear Topology and 3D Chromatin Architecture in Cancer. After registering, you will receive a confirmation email about joining the webinar. This virtual symposium, supported by the National Cancer Institute (NIH-NCI), will focus on Advances in Nuclear Topology and 3D Chromatin Architecture in Cancer. Hosted jointly by NYU Langone Health and...

⏰ Final call! Our Nuclear Topology & 3D Chromatin Architecture in Cancer conference streams Nov 25.
Free & online → nyulangone.zoom.us/webinar/regi...
#3DGenomics #CancerResearch #SciComm

Postdoctoral Researcher in "Cancer Neuroscience: the impact of neural activity on 3D genome organization and cellular plasticity in glioblastoma”

Excited to share I’ve received a #SSMF #Consolidator grant!

📣 Recruiting a #postdoc to study #cancer #neuroscience #3Dgenomics #multiomics #singlecellomics

🔬How neural inputs shape #3Dgenome and #cellplasticity in #glioblastoma #GBM

Interested? Apply now 👇
rb.gy/m7xz7b

Enhanced Genomics Expands Series A Round to $19M The Cambridge, UK-based multiomics drug discovery company previously raised around $13.6 million in Series A funding in 2022.

Enhanced Genomics Expands Series A Round to $19M #3DGenomics
www.genomeweb.com/business-new...

🧬 Our CSO @dnaturner.bsky.social presents at @agbt.bsky.social Precision Health (Sept 8-10, San Diego) on 3D genomics for personalized medicine.

🎯 Only company with genome-wide causal biology mapping—10× faster GWAS results.

👋 See you there!

#AGBTPH25 #3DGenomics

🔬 Researchers from UWA, AGRF, SCGH & Dovetail team used Micro-C to build the first 3D regulatory atlas of human osteoclasts — linking non-coding GWAS variants to gene targets and opening new paths for understanding bone disease like osteoporosis 🦴
🔗 doi.org/10.1093/jbmr...
#3DGenomics #Multiomics

We’re excited to exhibit at #GSA2025 in Auckland, NZ! Visit our booth to see how LinkPrep™ tech enables same-day, high-res chromatin interaction maps. Connect enhancers, silencers & more to gene targets. Integrates with ATAC-seq, ChIP-seq, RNA-seq & other omics data. #ChromatinTopology #3DGenomics

StripePy: fast and robust characterization of architectural stripes AbstractMotivation. Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair. Despite their importance,

🧬 New in Bioinformatics! We’re excited to share StripePy - a Python application for fast, robust detection of architectural stripes in Hi-C & Micro-C data.
🔗 Read the paper 👉 doi.org/10.1093/bioi...
#3DGenomics #Bioinformatics #HiC #cool #hic @robomics.bsky.social @rea191.bsky.social

Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomics - Genome Biology Advances in the field of three-dimensional (3D) genomics have revealed an ever-expanding array of architectural features that were unknown only a few years ago. Just as ribbon diagrams integrate spati...

Aficionados of #3DGenomics / #4DNucleome, please share this piece with friends 🙏🏼

genomebiology.biomedcentral.com/articles/10....

Great to connect with the epigenetics community at the 5th Meeting of the Melbourne Epigenetics Club! 🤝 Our very own Dr Brent Thomson shared how LinkPrep™ enables rapid, high-res 3D genome mapping. 🧬 Thanks to all who joined the conversation!
#3DGenomics #Epigenetics #LinkPrep #MelbEpigenetics

Stellaromics unlocks deeper insights in neuroscience, oncology, immunology & cell therapy with 3D spatial biology! Explore complex systems like never before. Learn more: stellaromics.com/product/ #SpatialBiology #3DGenomics #Stellaromics

Last “invited speaker at the Statistical Approaches to Modern Biology" workshop! Elisa Salviato on enhancer–target gene regulation and 3D chromatin topology.

#Epigenomics #3DGenomics

Fellowships, grants and career support – Postdoctoral Fellowships – EMBO Supporting internationally mobile postdoctoral researchers in Europe and around the world

If you are interested in #3DGenomics #4DNucleomics and want to help us dig into this fascinating world.... visit our Web site marciuslab.org and drop us an email to apply together for a EMBO postdoc fellowship 👇🏼

www.embo.org/funding/fell...

Unlock richer biological insights with Stellaromics.
Analyze thick tissue samples (20–100+ μm) while preserving native architecture.
Supports short and long RNA, across human, mouse, NHP, and more.
stellaromics.com/product/
#SpatialBiology #3DGenomics #Transcriptomics

Postdoctoral Fellowships The information provided on this page is a summary of the main rules and requirements for Postdoctoral Fellowships (PFs) and who can apply for them.

If you are interested in #3DGenomics #4DNucleomics and want to help us dig into this fascinating world.... visit our Web site marciuslab.org and drop us an email to apply together for a Marie Skłodowska-Curie postdoc fellowship 👇🏼

marie-sklodowska-curie-actions.ec.europa.eu/actions/post...

Our study shows how combining chromatin profiling, CRISPR-based functional assays, and large-scale biobank data can advance our understanding of genetic risk in atrial fibrillation.
#AFib #LMNA #iPSC #Genomics #Preprint #RegulatoryGenomics #3DGenomics #AtrialFibrillation #Cardiogenomics

Years ago, @arnausebe.bsky.social gave talk that prompted us to discuss on #3DGenomics and #Evolution. I offered we could help. Next, @ianakim.bsky.social came to the rescue 😁.

The results are out today at Nature, including support from @encent.bsky.social.

Iana explains what she did here 👇🏻🎉👏🏻 👏🏻👏🏻

Happy to be visiting the lab of Aurora Ruiz-Herrera & learning more about #3Dgenomics from Laia Marin Gual & the group at UAB Barcelona for the next couple of weeks! Thanks to the SNSF SPARK grant awarded to Kay Lucek. Rainy & spring weather in Barcelona reminds me of home (Bengaluru) 🌸

Are you interested in joining #RNGS25 in beautiful Antwerp but lack the funds? Then we have good news for you as we offer 4 travel grants to international junior scientists. Find out more here: vibbio.tech/4f0tG9N
Conference topics: #sequencing #ngs #multiomics #3DGenomics #epigenomics #ML #AI

#IntroWeek 5/7

Enough of papers 😅.

Some keywords that describe the work we do at marciuslab.org

Mainly:
#nucleus
#4DNucleome, #4Dnucleomics
#3Dgenome, #3Dgenomics
#chromatin
#epigenetics,
#generegulation, #geneexpression, #transcription

but also:
#microbiome
#spatialmicrobiome
#biogeography

#IntroWeek 4/7

some key papers at marciuslab.org showing a transition from dry only to wet/dry lab:

My early days on Protein Structure Prediction:
tinyurl.com/ncj3e56a

Our first steps in #3DGenomics:
tinyurl.com/3f3k43j7

Key papers from our ERC-Synergy:
tinyurl.com/ypuucs4f
tinyurl.com/3ajfmpdj

#IntroWeek 2/7

Again, introducing the lab --> marciuslab.org

A few key recent papers on #3DGenomics from the lab:

www.cell.com/cell/fulltex...

www.sciencedirect.com/science/arti...

www.biorxiv.org/content/10.1...

Structural Genomics @ CNAG/CRG [home] Structural Genomics at CNAG · CRG

Let me introduce our work -> marciuslab.org

Some may know what we do, others may not. We contribute to #3DGenomics & #4DNucleome fields. More recently we also work on #SpatialMicrobiomics.

I will post this once a day over a week. Science is here now, I think it is worth 😀. Sorry for the SPAM 😉.