For mid Nov., I am writing a grant to support improved algorithms and functionality for bedtools. I would be eager to know of desired new functionality, file support, algorithms, or things that you cannot do easily but wish you could. User feedback is incredibly valuable. Pls. RT

Looking forward to co-moderating a great set of talks with the wonderful @mollygasp. Join us and our exciting lineup of speakers: Jesse Engreitz, Wendy Bickmore, F. Hormozdiari, and E. Weeks today (Wed) at 3:30ET for our session on variant-to-function coupling! #ASHG20

First foray into single cell genomics, first postdoc paper, first tweet! Excited to share our human cell atlas of fetal chromatin accessibility, a very fun collaboration with Jay Shendure Andrew J Hill Riza Daza Darren Cusanovich and others. science.sciencemag.org/content/370/65… (1/5)

We are looking for a research assistant to join our lab Columbia BME. Our lab develops and applies single-cell genomic tools to understand how cancer responds to therapy. Join us! To apply: opportunities.columbia.edu/en-us/job/5127…

We’re hiring a molbio RA in Seattle! You'd be the newest member of our bad ass in vitro team nested in CajalNeuro's Functional Genomics group. You'd use your cloning skills for neurodegen high throughput projects (spoiler- largely learning new CRISPR screen skills from me! :).

If you know a terrific RA with a bent for TC interested in a longterm gig in biotech, send em my way! We're still looking for this RA position.

We are recruting postdoctoral fellows to join us in defining responses to exposure using single cell genomics. We will review postdoc applications in January. DM, email ([email protected]) or use the link below to apply!

Well fellas, I tried the 10x Genomics’ RNA Fix solution…and it was a breeze. Not surprising easy to follow protocols, descriptions of what to expect were spot on, and there were zero challenging steps…even when I did use crazy challenging samples! Sequencing will follow 🔜

We wondered what a side-to-side comparison between 3’ v3.1 & RNA Fix solution from 10x Genomics would look like? Well, we have WINNER! I said it two #10Xperiences ago…this kit is by far the best these guys have ever produced yet! Andres F Vallejo 🧬 💻 Jens Durruthy Dr. Jasmine Plummer 👩🏻‍🔬🧬🇨🇦🇺🇸 Geoffrey McDermott

It’s spatial profiling day on bioRxiv! Now 10x Genomics out with a preprint on integrated single cell, spatial and in situ analysis of FFPE tissue. Very excited by the extension of these high dimensional technologies to archival samples! biorxiv.org/content/10.110…

We tested the 10x Fixed RNA Profiling (FRP) kit (green) to see how it stacks up against 10x 3’ (red). We ran the same human PBMCs from our recent Parse experiment, sequenced all libraries and analyzed the data including introns. FRP is about 2x more sensitive than 3’ v3.1 (1/13)

Our lab's latest protocol, more brilliant work from @bethkarenmartin & Chengxiang Qiu We can't send to bioRxiv b/c they desk-reject all protocols ;) Onwards to eLife - the journal where I predict Michael Eisen's assessment will be "delicious" Non-paywalled PDF: tinyurl.com/3zsyabpp

Single cell RNA-seq is more powerful than ever! Chromium Single Cell Gene Expression Flex provides our most sensitive whole transcriptome assay, the ability to store & transport samples without losing data quality, and access to FFPE tissues. Explore now: 10xgen.com/3in2Pgk

These goals, this crew, this city, with the most fun(ctional genomics) tools - thrilled and lucky to do this work!

Excited to share our preprint biorxiv.org/content/10.110… (my first)! This was an amazing collaboration with the incredibly talented and rare gem Jean-Benoît (JB) Lalanne. Also indebted to a rockstar team Silvia Domcke Diego Calderon (diegoisworking@bluesky) @bethkarenmartin Tony Li Chase Suiter Cole Trapnell! 🧵(1/10)

Our latest preprint from brilliant Jean-Benoît (JB) Lalanne & Samuel Gabriel Regalado is new single cell MPRA assay (sQers) with remarkable quantitative range, precision approaching Poisson shot noise. We apply sQers to discover autonomous germ layer-specific enhancers. PDF here: tinyurl.com/ym8r2jat

Excited to share our preprint describing sci-Plex-GxE. A highly multiplexed workflow for combined exposure and genetic molecular screens at single-cell resolution. biorxiv.org/content/10.110…

Absolutely thrilled to share mine and Troy McDiarmid’s work describing the development of a multiplexed, scalable CRISPRa cell type-specific screening framework that is able to identify…(1/n) biorxiv.org/content/10.110…

Thrilled to share my work describing chromatin-context dependent regulation of prime editing and our effort in leveraging this knowledge to modulate prime editing outcomes. biorxiv.org/content/10.110… 1/21

In our latest preprint, the brilliant Xiaoyi Li: 1) discovers massive influence of chromatin on prime editing & 2) shows epigenetic "pre-treatment" of a locus w/ CRISPRa can markedly enhance prime editing efficiency. See thread below & biorxiv.org/content/10.110… for more details!