Excited to announce a new resource for the zebrafish community and fun collaboration with Dylan Farnsworth and Adam Miller University of Oregon - a meticulously annotated scRNA-seq atlas of early larval development. Can't wait to see what new things the community finds in this data!

DONE! I defended in July, today I submitted my #PhD thesis! In Sept I start a #postdoc with Prof Ben Garcia at Penn Epigenetics 👩‍🔬 Would not have been possible without advisers @mjmaccoss and William Stafford Noble, colleagues Brian Searle and Hannah Pliner, and everyone at UW Genome Sciences 🥰

A new study led by Jose L. McFaline-Figueroa is now out in Nature Genetics: nature.com/articles/s4158…. José used single-cell RNA-seq and multiplexed CRISPR screening to dissect the molecular regulation of epithelial-to-mesenchymal transitions.

Happy to share our sci-L3 (previously called sci-LIANTI), which stands for "single-cell combinatorial indexing", "linear amplification" and "3-level barcoding" from the happiest postdoc lab ever: Jay Shendure lab! cell.com/molecular-cell…

Our manuscript on Garnett, which allows you to rapidly annotate cells by type in your scRNA-seq data, is now out in Nature Methods: rdcu.be/bQGtG. In response to reviewer comments, Hannah Pliner made lots of improvements over the pre-print.

News! Garnett and CellAssign are out in Nature Methods . Views! They both look great! Read more here go.nature.com/2lMS89x Jimmy Lee Cole Trapnell Kieran Campbell

How do we grow from a single cell to the trillions of cells that make up an adult body? A new DREAMchallenges Challenge, spearheaded by Jay Shendure & ElowitzLab, is launching to help find answers. alleninstitute.org/what-we-do/fro…

Extremely excited to announce sci-Plex, described in a new paper out today science.sciencemag.org/content/early/…! Joint work with Jay Shendure lab, led by a crack team: Sanjay Srivatsan, Jose L. McFaline-Figueroa, and Vishnu Ram. With sci-Plex, we can profile expression in single cells from thousands of samples.

Sanjay Srivatsan just published his first Ph.D. paper (science.sciencemag.org/content/early/…), a culmination of endless perseverance, incredible mentorship, and collaborative teamwork-congrats all! My Haiku summary of #sciPlex: One experiment Many single cells profiled Future of drug screens

The new paper from Lindsay K Pino - @[email protected] and @MacCossLab has been really impactful on my work. Easily drawing full calibration curves for every peptide in a proteome has completely changed collaborator conversations where they insist proteins are present or absent! pubs.acs.org/doi/10.1021/ac…

The team at the Seattle Flu Alliance have sequenced the genome the #COVID19 community case reported yesterday from Snohomish County, WA, and have posted the sequence publicly to gisaid.org. There are some enormous implications here. 1/9

Thanks to rapid global data sharing of #SARSCoV2 genomic data via gisaid.org, we can reconstruct large and small scale patterns of #COVID19 spread. This is a thread discussing this intersection of large and small. 1/7

Our paper studying how to infer gene regulatory networks based on single-cell RNA-seq data is out today in Cell Systems: cell.com/cell-systems/f…. Led by evo-devo and Arman Rahimzamani from Sreeram Kannan's group. We explore the limits of current tech for network inference.

Thanks to Seattle Flu Alliance and UW Virology, we have new genomic data on the spread of #COVID19 in Washington State with 2 new #SARSCoV2 genomes sequenced today, bringing the total number of WA genomes to five. 1/8

It’s official. Seattle Flu Alliance has shifted focus to supporting public health response to #COVID19 to launch SCAN for home based swab collection. Trevor Bedford Lea Starita Jay Shendure Mike Famulare Debbie Nickerson Jan Englund Michael Boeckh @mjonasrieder UW Medicine

As the molecular team behind the Seattle Flu Alliance, Debbie Nickerson and I are excited to begin COVID-19 community testing in partnership with Public Health - Seattle & King County through #SCANCOVID scanpublichealth.org Resources and thread 1/8

Happy to report that our paper on using UMAP to analyze many mutants is now out in Nature Communications nature.com/articles/s4146…; we used UMAP to group transcriptomes of >1000 single-gene deletions of yeast and were able to group pathways, protein complexes, and interactions.

I am very happy to share the official announcement!!! I look forward to starting my lab Columbia BME.

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)

Four years' work, 178 billion sequencing reads, and nearly 5 million cells went into constructing atlases of gene expression and chromatin accessibility in human development, out now.