@JakeFreimer
Joined July 2013
  • Tweets63
  • Following358
  • Followers192
I’m hiring a computational scientist 3 at Genentech to analyze cutting-edge single-cell genomics and high-throughput screening data in an extremely collaborative environment focused on finding cures for disease. Please reach out to learn more. careers.gene.com/us/en/job/G…
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We've known for a long time that a large fraction of noncoding GWAS hits are not currently explained by eQTLs. Why?? I'm excited to share our new preprint on this! Take home: GWAS and eQTL assays maximize power for different types of variants. (1/n) biorxiv.org/content/10.1101/…

Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery

Most signals in genome-wide association studies (GWAS) of complex traits point to noncoding genetic variants with putative gene regulatory effects. However, currently identified expression quantita...

biorxiv.org
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Thrilled to share findings published today @Nature from our lab in collaboration with @MarsonLab @GladstoneInst and two labs (Ye Zheng and Ron Evans) @salkinstitute. nature.com/articles/s41586-0…
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Thrilled to have our recent work from the @marsonlab published in @ScienceMagazine science.org/doi/10.1126/scie…. This was the result of an awesome collaboration between myself and fellow Marson Lab postdoc, @R_Schmidt_ (1/12)

CRISPR activation and interference screens decode stimulation responses in primary human T cells

Complementary gain- and loss-of-function CRISPR-based genetic screens reveal tunable regulators of human T cell activity.

science.org
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The @MarsonLab has a position open for a research associate to work on gene regulatory network mapping in human immune cells. Check out this related preprint: biorxiv.org/content/10.1101/… & apply here: bit.ly/3ohe4rM

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture...

Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed it can lead to disease. To understand how gene expression...

biorxiv.org
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Excited to announce that our paper describing NEAT-seq, a method to simultaneously measure transcription factor protein abundance, ATAC-seq, and RNA-seq in single cells, is out on biorxiv! Congrats to Amy and Ben! biorxiv.org/content/10.1101/…

NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene...

Oligonucleotide-conjugated antibodies[1][1] have allowed for joint measurement of surface protein abundance and the transcriptome in single cells using high-throughput sequencing. Extending these...

biorxiv.org
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Excited to share new work w/ co-lead @CamilliaAzimi, @MarsonLab @kickassscience1 @roybal_lab: using a method we call 'CAR Pooling', we tested many CARs in multiplex & found new non-T cell signaling domains which improve CAR-T efficacy. biorxiv.org/cgi/content/shor… 👇🧵 1/10
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Excited to share our recent preprint from the @marsonlab, where we used complementary genome-wide CRISPRa and CRISPRi screens to map regulators of cytokine response in primary human T cells. Terrific collaboration with fellow Marson Lab postdoc, Ralf Schmidt @R_Schmidt_! (1/15)
bioRxiv@biorxivpreprint13 May 2021
CRISPR activation and interference screens in primary human T cells decode cytokine regulation biorxiv.org/cgi/content/shor… #bioRxiv
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How can we systematically measure gene regulatory networks around key disease genes? Excited to share our new work using CRISPR KOs in primary T cells, with @MarsonLab, led by @JakeFreimer and Oren Shaked: biorxiv.org/content/10.1101/…

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture...

Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed it can lead to disease. To understand how gene expression...

biorxiv.org
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Big new serology study from @MarsonLab @pdhsu et al. Lots of really detailed data on 12 different tests (10 lateral flow, 2 ELISAs). A lot of disagreement and specificity issues. Super detailed and important work. covidtestingproject.org/inde…
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Really amazing work co-lead by my student @cody_mowery, the @MarsonLab and @pdhsu to show the performance of serological assays (lateral flow and ELISA) for detecting Sars2-CoV-2 antibodies: covidtestingproject.org.
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Our latest: "GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background": biorxiv.org/content/10.1101/… We use urate, IGF-1, and testosterone as model molecular traits to learn general principles about the architecture of complex traits.

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic...

Genome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. However, for most traits it remains difficult to interpret...

biorxiv.org
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n=1 prelim optimization of CRISPR editing in lung cell lines, >80-95% efficient. An effort from @MarsonLab facilitated by @KroganLab @TheOttLab Greene lab. Hopefully this will accelerate your #coronavirus studies, share widely. We're wrestling with Calu3, plz share culture tips!
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Unveiling SwabSeq. We repurposed a part of @OctantBio's platform to detect #SARSCoV2. We think the method is cheap (~1$), sensitive (1-6 molecules), quantitative (3-4 logs), and scalable (10k/day w/o automation; much more with). Lots of details below, I’ll lead with data [1/14]
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Delighted to share our latest work, on ancient DNA of individuals from in and around Rome, spanning the last 12,000 years. At its peak Rome was the largest city of the ancient world with 1M inhabitants, controlling an empire of 70M people science.sciencemag.org/conte…
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Okay, here's how you do the QR code for feedback: 1. Make a Google Form for your talk feedback. Here's mine: docs.google.com/forms/d/e/1F… What I do is make a pre-filled link (gear top right) where you pre-fill the particulars of that talk. Then…

Feedback on talks by Dr. GoodTalk

A forum for honest (hopefully constructive) feedback on talks that I've given. I will usually send a link with the specific talk pre-filled.

docs.google.com
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ML, functional genomics, RNA-splicing regulation or hi-throughput screens float your ⛵️? I have postdoc positions available in my shiny new lab at @nygenome / @Columbia. Lets chat at #ASHG18 or go to nygenome.org/careers/job-pos… Please RT!
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Ask a scientist: How can we use #CRISPR gene editing tools to hack the human immune system? UCSF's Alex Marson talks DNA editing, immunology and more tomorrow afternoon during an open-ended @reddit #AMA. Mark your calendar for 9/24 at 3pm PST! #science #askscience @MarsonLab
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Check out our preprint about newly generated chromatin accessibility data from 30+ human immune cell types! @misshmash + Anja Mezger (1/n)
bioRxiv@biorxivpreprint6 Sep 2018
Landscape of stimulation-responsive chromatin across diverse human immune cells biorxiv.org/cgi/content/shor… #bioRxiv
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I can't get this map out of my head: when adjusted for cost of living, SF postdocs fare really poorly.... from @SeanCMcConnell @erin_heckler @joepierre3 et al. @biorxivpreprint dx.doi.org/10.1101/355511.
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