Yang Zhang

The @ENCODE_NIH Phase 4 Registry of candidate cis regulatory elements (ccREs) (2.37 million human and 967,000 mouse cCREs) is officially out screen.wenglab.org nature.com/articles/s4158… Congrats to @MooreJillE @ZhipingWeng & everyone else. Lots more incoming ...

Happy to share #DNALONGBENCH @NatureComms. We challenge DNA #FoundationModels w/ long-range sequence context and hope this sparks more meaningful ways to evaluate growing AI+BIO models. Kudos to @WenduoC @ZhenqiaoSong @zocean636. Great collab w/ @lileics. nature.com/articles/s4146…

DNALONGBENCH: a benchmark suite for long-range DNA prediction #DNAfoundationmodels #BiotechNatureComms @WenduoC @ZhenqiaoSong @zocean636 @lileics  @jmuiuc   doi.org/10.1038/s41467…

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

A new benchmarking study assesses methods for comparing chromatin contact maps in 3D genome research. @GjoniKatie, @EvonneMcArthur, @GladstoneInst nature.com/articles/s4159…

Proper and meaningful benchmark datasets are crucial for advancing genomic LLMs/FMs, and ML methods for genomics in general. Fantastic collab w/ @lileics's group. Amazing work led by @WenduoC @ZhenqiaoSong @zocean636

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…

Very excited to share our primer on LLM for biology @naturemethods! 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 broad audience. Great job @ElanaPearl @KyleWSwanson!

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

@cliao345 @GeiselMed Congrats! That's amazing news!

Excited to share that I'll start my lab @GeiselMed as an assistant professor in July 2025! We will build a hybrid lab that focuses on microbial metabolism & human gut microbiome. We're hiring at all levels. Especially seeking experimental microbiologists for the wet lab work!

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…

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…

scGHOST offers a computational tool to annotate single cell subcompartments from scHi-C or imaging data using graph-based learning. @jmuiuc, @KyleXiongCMU, @RuochiZhang, @CMUCompBio, @SCSatCMU, @CarnegieMellon nature.com/articles/s4159…

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…

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/

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. @CCLRI

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! @WickstromLab @jane_skok @belmont_andrew @cshlmeetings

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🙌

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…

In @NatureRevGenet today, we discuss recent advances in computational methods for #3Dgenome analysis, pointing to an integrative future. Apologies for any missed refs. Joint w/ @NCITomMisteli @faucla @zocean636 @LoreBonimba @muyu_wendy_yang. @4DNucleome nature.com/articles/s4157…