William J. Greenleaf
@WJGreenleaf
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Professor, Stanford University, Department of Genetics. Exploring the physical genome
Stanford U, Stanford CA
Joined July 2011
Very happy to share the most recent work from the lab!
1/ 🧵Happy to share our preprint from @WJGreenleaf’s Lab: beCasKAS, our method to directly detect #CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. https://t.co/i7eHqKXrje
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Our preprint describing single-cell multiomic dissection of human lung development is now out on bioRxiv! Congratulations to @bySamHKim and all co-authors!
biorxiv.org
Human lung development is governed by complex gene regulatory networks that orchestrate cellular differentiation and organogenesis. We present a single cell multiomic atlas of human pulmogenesis,...
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Pleased to announce this latest work from the lab!
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human development! https://t.co/zIUjPy6ZLz. Read on for more 🧵 [1/16]
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1/ Have you ever run out of memory while trying to analyze a large scRNA-seq or scATAC-seq dataset? Check out our new preprint from @WJGreenleaf lab about BPCells: an R package for high performance single cell analysis. Read on for more 🧵 https://t.co/QcSMPS0TEp
biorxiv.org
The growth of single-cell datasets to multi-million cell atlases has uncovered major scalability problems for single-cell analysis software. Here, we present BPCells, a package for high-performance...
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Our work using thermodynamic principles to link in vitro TF affinities and kinetics to single-molecule chromatin states in cells is now on bioRxiv! Amazing effort by first author @juliaschaepe in @WJGreenleaf lab: https://t.co/NG2bXd8SfJ
@Stanford @scilifelab @Stockholm_Uni [1/9]
biorxiv.org
The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood – including how sequence context modulates affinity,...
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Noisy neighbor? Clown. Tell them. Save 20% and get free shipping with code SHUTDOWN, but only until the government reopens!
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Huge congrats to Howard! We will sorely miss him here at Stanford, but wish him all the best for this immensely exciting opportunity!
Excited to welcome @HowardYChang to @Amgen as our new SVP for Research & CSO! A pioneering physician-scientist, Howard’s expertise in genetics, oncology, & inflammation will help us push the boundaries of discovery. We’re excited to embark on this journey together to redefine the
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Incredibly excited that our paper linking single molecule states of TF binding to gene expression using quantitative thermodynamic models is out in Nature today. An amazing collaboration with the Bintu Lab. Congrats to Ben, Michaela, and Julia!
nature.com
Nature - A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription...
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Our single-cell, pan-cancer analysis of open chromatin in human cancers, done in collaboration with TCGA and the Chang and Corces labs (among others including Illumina), is out in Science today. Congrats to Laksshman Sundaram and all authors!
science.org
To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin...
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No game this week so we did a inter-squad scrimmage. Our starting D has only given up 20pts all season... so I put up 3 TDs in 3 series! Sorry guys 😎 @QBHitList @quarterbackmag @PrepRedzoneNext @AlPopsFootball @iam_alinedouard @QBUniverseQBU @247recruiting @Rivals @TheUCReport
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The Greenleaf and Gifford Labs are looking for graduate students and postdocs interested in perturbing transcription factors and chromatin remodelers in human heart organoid systems with an aim of quantitatively understanding drivers of normal human development. Email Will!
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The Greenleaf lab is looking to recruit graduate students and postdocs interested in combinatorial cell state engineering. If you are interested combining multiplex perturbations and single cell readouts to "push" cells into target states, email Will!
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The Greenleaf and Pasca Labs are looking for graduate students and postdocs interested in perturbing transcription factors and chromatin remodelers in human brain organoid systems with an aim of quantitatively understanding drivers of normal human development. Email Will!
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Our human multipotent lymphoid progenitor paper is finally out! https://t.co/Spp9GrA3P6 After revision, we added more in vitro validations of the lympho-myeloid potential of this HSPC population. Lots of thanks to @Bendall_Lab & @WJGreenleaf
nature.com
Nature Communications - How lymphoid and myeloid specification occurs in human haematopoietic progenitors is not fully understood. Here the authors perform a proteomic screen on human bone marrow...
Excited to share my preprint with @Bendall_Lab and @WJGreenleaf on novel human lymphoid progenitors! Turns out they had been misidentified as myeloid progenitors thus far. Check out how we revealed their true identity in the tweetorial below 🧵 https://t.co/x7nP81Cr1b
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The Greenleaf and Pasca Labs are looking for graduate students and postdocs interested in perturbing transcription factors and chromatin remodelers in human brain organoid systems with an aim of quantitatively understanding drivers of normal human development. Email Will!
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The Greenleaf lab is looking to recruit graduate students and postdocs interested in combinatorial cell state engineering. If you are interested combining multiplex perturbations and single cell readouts to "push" cells into target states, email Will!
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I'm building my next product in public. It's called LEANSpark. And I'm using it to validate itself. Here's what you need to know 🧵
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The Greenleaf and Gifford Labs are looking for graduate students and postdocs interested in perturbing transcription factors and chromatin remodelers in human heart organoid systems with an aim of quantitatively understanding drivers of normal human development. Email Will!
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The Greenleaf and Pasca Labs are looking for graduate students and postdocs interested in perturbing transcription factors and chromatin remodelers in human brain organoid systems with an aim of quantitatively understanding drivers of normal human development. Email Will!
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Congrats also to @georgimarinov, @abbythurm, @carolina_rios23, @bn_parks, @yxjtan, and @DubocDan. We are excited to see where this system takes us, and we would love to hear your thoughts! Greenleaf Lab is hiring people to work on these types of questions! [10/10]
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Finally, we build thermodynamic and kinetic models to predict TF binding and gene expression, both at steady state and over time, recapitulating the diversity of microstates observed at our enhancer and the temporal delays in the central dogma [9/n]
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We don’t only study a synthetic TF – we also make the same measurements for ISGF3 (involved in type-I interferon response) and show that we can distinguish between a TF monomer that creates accessibility pre-stimulation from the trimer which drives expression after [8/n]
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It turns out that promoter state isn’t completely determined by instantaneous TF occupancy (e.g. molecules with 3 TFs bound out of 3 total sites look different than molecules with 3/6 bound), implying that promoters integrate information from multiple rounds of TF binding [7/n]
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