Lab won a Chan-Zuckerberg grant for exploring the Human Cell Atlas

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Our new paper "Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements" is out

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Our new paper "An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues" is out

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Our new paper "chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data" is out

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New Postdoc in the lab : Georgi K. Marinov

New Postdoc in the lab : Lisa McGinnis

Our new paper using massively parallel method for profiling protein–DNA interactions to quantify nuclease-dead Cas9 (dCas9) binding across thousands of off-target sequences

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The Greenleaf lab and Jarosz Lab new paper "Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genome" is out

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April Fools Day but its not a joke Will got tenure!

The Greenleaf lab is part of ENCODE-funded production center

The Greenleaf lab togther with the Bassik lab won ENCODE functional validation center grant

Will Greenleaf named in first cohort of Chan Zuckerberg Biohub investigators

Jeffrey Granja has joined the lab from the Biophysics program. Welcome Jeffrey!

We've posted two new single cell epigenomics papers on bioRxiv-- one describes our new R package facilitating interpretable analysis of single cell andother sparse epigenomics data, and the other describes single cell mapping of the epigenomic landscape of human hematopoesis. Congrats to Alicia Schep and Jason Buenrostro!

Our paper with the Goronzy Lab on the changes to the chromatin landscape and transcription factor networks in CD8 T cell aging in humans is out in Science Immunology! Our findings implicate shifts in BATF and NRF1 binding activity in the functional decline associated with immune aging. Congrats to David Moskowitz and Dave Zhang!

Our paper on in situ mapping of three-dimensional DNA-DNA contacts at the tri-nucleosome length scale in the chromatin fibers of human fibroblasts has been published in Nature! This paper describes RICC-seq, a new addition to the lab's toolbox of methods that combines spatially correlated cleavage of folded DNA with high-throughput sequencing. Congrats to Viviana Risca and Sarah Denny!

Our paper on HiChIP, a new protein-centric chromatin conformation method, has been published in Nature Methods! HiChIP of cohesin reveals multi-scale genome architecture with greater signal to background than in situ Hi-C. Thus, HiChIP adds to the toolbox of 3D genome structure and regulation for diverse biomedical applications. Congrats to Max Mumbach!

Our paper with the Chang and Majeti labs defining the chromatin landscape of human hematopoiesis and acute myeloid leukemia is out in Nature Genetics. Congratulations to Jason Buenrostro, Ryan Corces, and all the co-authors!

Two new postdocs have joined the lab this summer. Welcome Zohar and Anja!

Our paper with the Winslow and Sage labs on chromatin changes in tumor vs metastasis in SCLC is out in Cell. Congratulations to Sarah Denny and all the co-authors!

Our work describing the recurrent targets of oncogenic mutations as revealed by an analysis of significantly mutated regions (SMRs) in 21 cancer types is now online at Nature Genetics. Congratulations to Carlos Araya and Can Cenik!

Check out Nucleo-ATAC, our new 2D, high-resolution nucleosome caller, now published online at Genome Research. Congratulations to Alicia Schep!

Winston Becker has joined the lab from the MD/PhD program. Welcome Winston!

Ben Ober-Reynolds has joined the lab from the MD/PhD program. Welcome Ben!

Our single-cell ATAC-seq study is now published online at Nature. Congratulations to Jason Buenrostro for all the work!

Lauren Chircus has defended her thesis! Congrats!

Greenleaf lab awarded an Human Frontier Science Program grant for investigation of epigenomics of stem cells!

The Greenleaf lab, along with other labs at Stanford, has been awarded a Center for Excellence in Genomics grant!

The Greenleaf lab, along with other labs at Stanford, has been awarded a Genomics of Gene Regulation grant!

The Greenleaf lab has been awarded an R01 to carry out high-throughtput, quantitative studies on nucleic acid arrays!

Evan Boyle has joined the lab joint with the Pritchard Lab. Welcome to Evan!

Max Mumbach has joined the lab joint with the Chang lab. Welcome Max!

Alex Trevino has joined the lab! Welcome to Alex!

Sandy Klemm has joined the lab as a postdoc! Welcome to Sandy!

Peter Frick has joined the lab as a postdoc! Welcome to Peter!

Our ultra high-throughput RNA-protein interaction study is featured on the cover of this issue of Nature Biotechnology. Thanks to Carlos Araya for the artwork!

Our work on quantitative, high-throughput analysis of RNA-protein interactions is highlighted in Nature Methods!

A paper published in collaboration with Jonathan Weissman's and Bob Landick's labs has been posted to Science Express. The work explores the sequence-dependent base-resolved kinetics of transcription in vivo and in vitro at the single molecule level.

Our MS2 RNA array paper describing how we hacked a genome sequencer to perform 12 Million biochemical assays in parallel is now published online at Nature Biotechnology!

Will has been profiled on GenomeWeb Daily News! Read the feature: "William Greenleaf: The DNA Folding Question".

Welcome Johan Andreasson, a new postdoc in the lab!

Our paper with the Chang lab describing ATAC-seq, a powerful and simple new method for probing open chromatin, nucleosomes, and factor binding in limited numbers of cells, has been published in Nature Methods. Also, see the News and Views feature by Anil Raj and Graham McVicker.

Our paper with the Bustamante and Willerslev labs describing target enrichment methods for ancient DNA sequencing was just published online! Congrats to Jason and Meredith!.

One postdoctoral position available for those interested in integrative epigenomic analysis. See our Join Us page for details.

Congrats to Lauren Chircus for winning best poster at the Chemical Systems Biology retreat!

One joint postdoctoral position (between the Greenleaf and Sherlock labs) is available! See our Join Us page for details.

The lab has received a grant from the Rita Allen Foundation to work on epigenomics of cancer. Read more.

Also welcome Nandita Damaraju as a visiting summer student from IIT.

David Moskowitz (BMI) and Alicia Schep (Genetics) have joined the lab! Welcome!

Congrats for Sarah Denny for being selected for a Bio-X Fellowship! How many fellowships does one need?

Carlos Araya (joint with Michael Snyder) has joined the lab as a new postdoc.

Congrats to Sarah Denny, Jason Buenrostro for both getting NSF Fellowships. Further congrats to rotation students Ian Winters, Alicia Schep, and Zach Zappala for also getting NSF Fellowships. Well done to all!

Congratulations to Viviana Risca; She has been selected as a Berry Fellow!

Welcome Lauren Chircus to the lab. Lauren is a Chemical and Systems Biology Graduate Student.

Congratulations to Curtis Layton. He has been awarded a Dean's Postdoctoral Fellowship!

Welcome Viviana Risca from Dan Fletcher's lab as a new postdoc!

Welcome Vlad Karas from Anne Meyer's lab as a visiting student!

Our paper describing microfluidic digital PCR in microreactors is published.