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My rules for academia: 1. there are many paths to success, look for your own, 2. if the project excites you, do it; if it doesn’t, don’t. 3. let the project change, that’s what it’s supposed to do, 4. review the work of as you’d want to be reviewed, 5. one sentence, one idea.

Happy to share the final version of our #GAGEseq published today Nature Genetics! The single-cell co-assay for #scHiC and #scRNA reveals 3D genome & gene expression interplay in mouse cortex (also integration w/ #MERFISH) and during human hematopoiesis. 1/3 nature.com/articles/s4158…

Zhuang lab reunion at Single-Cell Genomics Gordon Research Conference in beautiful Les Diablerets, Vaud (fr), Switzerland! :-D

How do enhancers work over distances that sometimes exceed megabases? Excited to share our work led by Grace Bower where we uncover a unique sequence signature globally associated with long-range enhancer-promoter interactions in developing limb buds: biorxiv.org/content/10.110… 1/

Our new work utilizing 5hmC to predict gene expression & to prioritize putative enhancers with the help of Hi-C . Joint work of our lab & Rao Lab Made possible by the dedication and hard work of Edahi G.-Avalos, our prev UC San Diego BISB PhD student doi.org/10.1186/s13059…

Tuning cohesin trajectories enables differential readout of the Pcdhα cluster across neurons | Science science.org/doi/10.1126/sc… Super cool new paper on how regulation of loop extrusion affects Protocadherin diversity.

(1/16) Check out our Simon Gaudin paper tiny.cc/icuazz from the Canzio lab out in Science Magazine today on how tuning local cohesin trajectories enables differential readout of the clustered Protocadherin (Pcdh) locus across different types of neurons.

Excited to share our preprint "Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome & epigenome". This work extends single-cell CRISPR screens to simultaneously profile gene expression & chromatin accessibility.

Happy to share our work about DNA supercoiling, an understudied physical feature of the double helix and the chromatin. 1/5 nature.com/articles/s4159…

All compbiologists and wet-lab biologists working with compbio folks should print this & paste it on their doors and monitors. Too many folks think comp analysis is just a way to create pretty figs for a decorative ad for the data. Rigor is paramount. There should no compromise.

Genome-wide Mapping Eukaryotic Open Chromatin Regions with Double-Stranded DNA Deaminase biorxiv.org/cgi/content/sh… #biorxiv_genomic

Congratulations to all (Wenyang DONG @Chloe32896294)! FOODIE has been published in PNAS. A powerful technique for analysing transcription factor binding events and chromatin states. Glad to have contributed to this work! This will open up vew avenues for the epigenomic field.

Starting 2025 with a genome architecture paper about absolute quantification of looped states, lead by James Jusuf!

Thrilled to introduce a new single-cell 3D genome analysis tool to our toolkit! Our high-throughput droplet Hi-C (dscHi-C) and dscHi-C-multiome methods use droplet microfluidics to generate tens of thousands of single-cell Hi-C profiles with high sensitivity in a single batch.

I’m excited to share that our work on the macaque T2T genome and its insights into evolutionary medicine has been published in nature) This study (nature.com/articles/s4158…) focuses on the unique features of macaques and sheds light on how SVs impact brain evolution in primates.

Genomic snowflakes: how the uniqueness of DNA folding allows us to sme... sciencedirect.com/science/articl…

Congrats to Xinyao and Xie Chen! In eukaryotes, multiple transcription factors bind cooperatively to a regulatory region on genomic DNA to control gene expression. In this paper (bit.ly/3GV1BoP), we present an experimental metric for quantifying such cooperativity.

Congrats to Rita, Ji-Xin, Wei and Meng for the special issue of Nature Methods on vibrational imaging (nature.com/nmeth/volumes/…). Happy to share my account for the 25 years of Nonlinear Raman imaging. Thanks to all former group members and collaborators for their contributions.

Our scMicro-C paper is out in Nature Genetics! Huge thanks to the reviewers for their valuable insights, to SunneyXie for unwavering support, and to fantastic collaborators Jiankun Zhang & Longzhi Tan. Thrilled to share this work!

Congratulations to Honggui, Jiankun, and Tan for improving the single-cell 3D genome resolution by a factor of 4 (to 5 Kb). This allowed direct visualization that multiple enhancers cluster to a particular gene promoter at the same time in a single cell. nature.com/articles/s4158…