Assoc. Prof. of Molecular & Medical Genetics at OHSU. He/Him. General nerd. Runner. All views my own.
Portland, OR
Joined February 2012
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It has been a while since I have tweeted, but I am super excited to announce the release of our single-cell DNA methylation analysis tool, Amethyst. Developed by an extremely talented postdoc, Lauren Rylaarsdam!
biorxiv.org/content/10.1101/…
The major advantage is the robust visualization and data interaction capabilities of Amethyst, making cell type identification and the ability to uncover novel biological insight as smooth as possible.
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Andrew Adey retweeted
We are honored to welcome Dr. Andrew Adey to ScaleBio’s Scientific Advisory Board! His expertise in #singlecell technologies and #epigenetics helps us to bring you innovative approaches through massively parallelized barcoding of single cells. Welcome Andrew! @acadey80
Andrew Adey retweeted
This kidney atlas is an example of team science, with key contributors from six different institutions, significant supports from two NIH consortia (KPMP, HuBMAP). Congratulations to everyone behind this effort (peer review alone took two years)!
nature.com/articles/s41586-0…
New preprint! sciMET-cap, where we use hybrid capture to reduce the sequencing burden of scMethylation and show ~6,000 cell preps are possible using a benchtop sequencer! Led by S. Acharya and @oconnellphds with @DrTedPBraun & @L_Rylaarsdam. biorxiv.org/content/10.1101/…
Great collaboration with @cusanovich !
Hey again, science people! To reiterate, the Cusanovich lab released 2 preprints last week! Worth repeating! Here's a 🧵on txci-ATAC-seq (biorxiv.org/content/10.1101/…), a method for multiplex single-cell ATAC-seq marrying combinatorial indexing and 10x microfluidic barcoding. (1/13)
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#eugenemarathon! 2:54:26 for an 8 min PR, NYC Qual and first sub3! Last 5 were full on pain zone but managed to hang on and hit my goal. strava.app.link/BP8KvWasqzb
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Andrew Adey retweeted
Our work on the mechanism of dual FLT3 and LSD1 inhibition has been released in print by @MCR_AACR! Follow this link to check it out: aacrjournals.org/mcr/article…. #Leukemia #AACR23 #AcademicTwitter
Andrew Adey retweeted
In our latest preprint, the brilliant @XiaoyiLi10: 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/10.1101/… for more details!
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/10.1101/… 1/21
Andrew Adey retweeted
Excited to share our lab's latest preprint, led by @CXchengxiangQIU, @bethkarenmartin & Ian Welsh of @jacksonlab.
We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup.
Preprint: tinyurl.com/2nhe4mm9 1/n
This is super cool! - optimal metabolism in cancer is so important; targeting it like this is super innovative and a really exciting new direction!
Tumors need a lot of nutrients to grow. By engineering and implanting fat cells to outcompete cancers for nutrients we can suppress them. Novel cancer therapy called Adipose Manipulation Transplantation (AMT). AMAZING work by Hai Nguyen and others! biorxiv.org/content/10.1101/…
Andrew Adey retweeted
Single-cell ATAC-seq finds active regulatory elements across cell types, but its resolution can be limited. What if we could identify when and where proteins bind to chromatin?
Introducing PRINT, a new single-cell footprinting tool from @JD_Buenrostro lab
biorxiv.org/content/10.1101/…
Summary of our latest two papers on GenomeWeb! Thanks for the coverage - we are excited about both of these techniques regarding how they can improve the scale of single-cell epigenomic studies; both led by @oconnellphds! @OHSUSOM #singlecell #epigenetics
OHSU Researchers Push Throughput, Accessibility for Single-Cell Epigenetic Assays. An improved sample prep workflow for single-cell methylation analysis offers the prospect of commercialization, which could be readily taken up in cancer genomics. ow.ly/6NBa104wCnV
Andrew Adey retweeted
Thrilled to see our new paper out in @NatureBiotech . Spatial-CITE-seq: spatially resolved co-indexing of transcriptome and epitopes for multi-omics sequencing. Big shoutout to Yang Liu, my former postdoc @YaleBME and now assistant professor of pathology and neurology @YaleMed !
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq go.nature.com/3koGTTC
Andrew Adey retweeted
Excited to share the latest work from our lab, part of a collaboration with Ye Zheng's lab at Salk. We studying 3D genome organization in Tregs and investigated the role for Foxp3 in establishing Treg specific 3D genome interactions.
biorxiv.org/content/10.1101/…