Yang Zhang, a project scientist in the Ray and Stephanie Lane Computational Biology Dept., received a $25,000 grant from the Chan Zuckerberg Initiative Initiative for his project "Napari-Nucleome: Integrative Multi-Omic Exploration of the Cell Nucleus." bit.ly/3VgCPSn

We're excited to introduce GAGE-seq, a single-cell co-assay for 3D genome (#scHiC) & transcriptome (#scRNA). We revealed 3D genome--gene expression interplay in mouse cortex (even integrated w/ #spatialtranscriptome) & during human hematopoiesis. Preprint: biorxiv.org/content/10.110…

In Nature Reviews Genetics today, we discuss recent advances in computational methods for #3Dgenome analysis, pointing to an integrative future. Apologies for any missed refs. Joint w/ @NCITomMisteli Frank Alber Yang Zhang Lorenzo Boninsegna Muyu "Wendy" Yang. 4DNucleome nature.com/articles/s4157…

Computational methods for analysing multiscale 3D genome organization go.nature.com/3Lhb4Xb #Review by Yang Zhang, Lorenzo Boninsegna, Muyu "Wendy" Yang, @NCITomMisteli, Frank Alber & Jian Ma 4DNucleome Ray and Stephanie Lane Computational Biology Dept. CMU School of Computer Science UCLA UCLA QCBio National Cancer Institute

Check out the upcoming Cold Spring Harbor meeting on Genome Organization & Nuclear Function, Apr 20 – May 4, 2024, on advances in spatial and temporal aspects of nuclear structure & function. We look forward to seeing you! Wickstrom-Lab Jane Skok Andrew Belmont CSHL Meetings

Pleased to share our TSA-seq mapping of human genome localization relative to nucleoli and pericentric heterochromatin (PCH) which provides new insights into nuclear genome organization. doi.org/10.1101/2023.1…

Computational genomics Postdoc & PhD openings @ Duke🧑‍💻🧬🥰 Postings: academicjobsonline.org/ajo/jobs/26447 | careers.iscb.org/jobs/view/8654 ; Lab website: yi-zhang-compbio-lab.github.io ; Pls RT🙌

nature.com/articles/s4158… I am very excited to share our recent paper on nature . It is a great collaboration with Dr. Murre and Dr. Fisch at UCSD. We discovered a molecular mechanism to shape nuclear morphology. Cleveland Clinic Lerner Research Institute

Great application of DNA language models to prokaryotic genomes. Excellent impactful application use cases of the model. Congrats to all the authors! But a quick answer to the first question. No - DNA is not all you need. 1/

Thrilled to announce our paper in nature introducing MUSIC! For the first time, MUSIC enables simultaneous mapping of multiplexed chromatin interactions, RNA-chromatin interactions, RNA-RNA interactions & gene transcription at single-cell resolution. doi.org/10.1038/s41586…

scGHOST offers a computational tool to annotate single cell subcompartments from scHi-C or imaging data using graph-based learning. Jian Ma, Kyle Xiong, Ruochi Zhang, Ray and Stephanie Lane Computational Biology Dept., CMU School of Computer Science, Carnegie Mellon University nature.com/articles/s4159…

Excited to share new results from our 4DN collaboration between the Gilbert, Ma, van Steensel, and Belmont research groups. Joint analysis, led by our trainees, compared chromosome positioning relative to multiple nuclear locales across 4 cell types doi.org/10.1101/2024.0…

Our scFoundation has been finally published. It is currently one of the largest cellular models, pretrained on the transcriptomes of 50M single cells. Check out its performance on all the downstream tasks. nature.com/articles/s4159…

Beta-version of the new VISTA Enhancer Browser, 7 years in the making, with support for developmental stages, different species and variant comparison is finally online. Feedback is welcome! vista-enhancer.lbl.gov #enhancers #embryos #evodevo

Very excited to share our primer on LLM for biology Nature Methods! We discuss how to use: ⚡️human & protein LMs (eg #ESM) ⚡️#singlecell & #multimodel LMs ⚡️when to fine-tune, transfer learn etc. Paper nature.com/articles/s4159… Colab tutorial colab.research.google.com/drive/1zIIRGeq… Written for a

Genome-wide analyses correlate nuclear speckle proximity with gene expression. We share our minireview discussing possible functional relationships between nuclear speckles and gene expression in both health and disease: authors.elsevier.com/sd/article/S09…

Proper and meaningful benchmark datasets are crucial for advancing genomic LLMs/FMs, and ML methods for genomics in general. Fantastic collab w/ Lei Li's group. Amazing work led by Wenduo Cheng Zhenqiao Song Yang Zhang

A new benchmarking study assesses methods for comparing chromatin contact maps in 3D genome research. Katie Gjoni, Evonne McArthur, Gladstone Institutes nature.com/articles/s4159…

Final version of our paper eLife - the journal (led by Andrew Belmont): Major nuclear locales define nuclear genome organization and function beyond A and B compartments. elifesciences.org/articles/99116