@yang__wang

Single cell epigenomics & gene regulation

 Cambridge, England
Joined November 2017
  • Tweets180
  • Following280
  • Followers123
Paired-Tag in the Wild! – “Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain” bit.ly/4kbZdK2 A bioRxiv article employs Droplet Paired-Tag from #EpigenomeTech #Epigenetics #PairedTag #Multiomics #SingleCell
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Yang Wang retweeted
Sai Ma@saima_labFeb 3
1/ Exciting news! We just released a preprint on a new single-cell technology, ME-seq, that maps DNA methylation, gene expression & chromatin accessibility—all in the same cell, at scale. And yes, it’s a LOT cheaper 🤑than current methods! 🧬 #SingleCell #Epigenetics
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Now out in the July 10th issue of @CellCellPress LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs: Cell cell.com/cell/fulltext/S0092…
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Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation science.org/doi/10.1126/scie… @ScienceMagazine @JD_Buenrostro @ajaylabade31 @CarolineComenho
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Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex dlvr.it/TKvngd

Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex

Johansen et al. report the results of a community challenge to predict functional enhancers targeting specific brain cell types. By comparing multi-omics machine learning approaches using in vivo...

cell.com
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Absolutely thrilled to share with you the final version of EPIclone, out now (open access) in @Nature. This has been an amazing collaboration with the lab of Lars Velten (@larsplus) at @CRGenomica nature.com/articles/s41586-0…
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Yang Wang retweeted
Hao Yin
@HaoYin204 Apr 2025
Multiomics single-cell optimal transport moscot.spatiotemporal An #OptimalTransport-based common coordinate framework to map & align #SpatialTranscriptomics with single-cell/-nucleus omics data scalable for millions of cells across multiple time points vs Tangram gimVI ▶️pancreatic epsilon cell progenitors, fate & regulons @LickertHeiko @fabian_theis @Nature 2025 nature.com/articles/s41586-0…
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Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day on Friday 4/25. All talks will be live-streamed (no registration required) at satijalab.org/scgd25
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happy to see our cell2fate model out at @naturemethods. It is a completely new take on RNA velocity to disentangle complex cell trajectories from scRNA data & we have some very cool applications coming up! nature.com/articles/s41592-0…

Cell2fate infers RNA velocity modules to improve cell fate prediction

Nature Methods - Cell2fate improves RNA velocity analysis of single-cell and spatial transcriptomics data by module decomposition of realistic biophysical models of transcription dynamics.

nature.com
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📢 CUT&Tag version 3 Sometimes the preprint to paper route can be quite the odyssey. And so in that vein, we are delighted to give you version 3 of our CUT&Tag optimization and benchmarking manuscript: biorxiv.org/content/10.1101/…

CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

Techniques for genome-wide epigenetic profiling have been undergoing accelerated development toward recovery of high-quality data from bulk and single cell samples. DNA-protein interactions have...

biorxiv.org
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dscHi-C allows us to investigate chromatin reorganization during mouse brain aging, while dscHi-C-Multiome reveals the complex relationship between genome structure and gene regulation. Learn more here: nature.com/articles/s41421-0…

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous...

Cell Discovery - Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics

nature.com
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Super excited to share our new study from the @JD_Buenrostro Lab in @Nature! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: nature.com/articles/s41586-0…

Multiscale footprints reveal the organization of cis-regulatory elements

Nature - We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of...

nature.com
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Yang Wang retweeted
Li Li@Li_Li_66616 Jan 2025
We present MethylTree to accurately infer cellular lineages based on DNA methylation epimutations, which really enables noninvasive lineage tracing in humans and non-human primates. Thanks specially to @ShouwenW. nature.com/articles/s41592-0…

High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylat...

Nature Methods - This work presents a computational tool MethylTree to infer cell lineages based on epimutations on DNA methylation.

nature.com
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Modeling early gastrulation in human blastoids with DNA methylation patterns of natural blastocysts: Cell Stem Cell cell.com/cell-stem-cell/full…
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2. learning-bioinformatics-at-home github.com/harvardinformatic… I started this repo 5 years ago at Harvard FAS informatics.

GitHub - harvardinformatics/learning-bioinformatics-at-home: resources for learning bioinformatics

resources for learning bioinformatics. Contribute to harvardinformatics/learning-bioinformatics-at-home development by creating an account on GitHub.

github.com
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VACANCY: Postdoctoral Research Scientist Join the Rugg-Gunn lab as they seek to understand early human development. Deadline: 5th January babrahaminstitute.livevacanc…
The Rugg-Gunn lab are looking for someone to investigate the dynamics and mechanisms of epigenetic programming during post-implantation development of human embryos. Deadline: Sunday 5th January

ALT The Rugg-Gunn lab are looking for someone to investigate the dynamics and mechanisms of epigenetic programming during post-implantation development of human embryos. Deadline: Sunday 5th January

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Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling nature.com/articles/s41587-0…
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Happy to see this was published yesterday! It was great working on this with Shankar and @ShifaanT. And thank you to the great editorial team at @NatRevMCB.
Nature Reviews Molecular Cell Biology@NatRevMCB3 Dec 2024
Now Online: Origin, fate and function of extraembryonic tissues during mammalian development go.nature.com/3OELOeK
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Delighted to share new work from our lab: MultiPerturb-seq 🎛️❌📥📤 Over the last few years, we've been combining CRISPR screens with multimodal readouts of gene expression (RNA) and chromatin accessibility (DNA). In this study, we bring those together within the same cells.
Nature Biotechnology
@NatureBiotech21 Nov 2024
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O
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how does PCA projection work? How do KNN and MNN for label transferring work in Seurat? A blog post on how I attempt to understand it at a low level. #singlecell #bioinformatics RT if you like it! divingintogeneticsandgenomic…
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