@evaubo

Molecular biology researcher @exaibio. Genomics and RNA biology for cancer diagnostics. Previous head of @ucsddasl, @QueerScience_SD. PhD. 🏳️‍🌈

 Palo Alto, CA
queersciencesociety.org/
Joined July 2014
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Now published! 📰 While the paper underwent review we added some cool results showing how Skipper can inform RNA-binding protein studies. cell.com/cell-genomics/fullt… github.com/YeoLab/skipper
Evan Boyle@evaubo10 Oct 2022
Searching for RNA-protein interactions?🔎 We @yeo_lab found more of them! 🎁 In our preprint we report >3x the number of interactions discovered by @EVNmoreRNA's CLIPper. Our new method "Skipper" is available now! 🧵 biorxiv.org/content/10.1101/…

Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in transla...

Technology for crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of...

biorxiv.org
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I had a great conversation that I’m so happy to share! Subscribe to the DASL pod, y’all.
Silvia Vicenzi@VicenziSilvia3 Sep 2024
1/ 🎧 New Episode Alert! The first episode of the DASL Podcast is live! I chat with Dr. Evan Boyle, about his journey in RNA biology and his role in founding the Diversity and Science Lecture Series (DASL). #DASLPodcast @evaubo buzzsprout.com/2398968/15653…
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🔥🔥How does the LINE-1 retrotransposon jump around in the human genome? Super excited to present my postdoctoral work answering this published today @Nature together with twitterless Kathy Collins's lab and @NogalesLab @UCBerkeley nature.com/articles/s41586-0… A 🧵

Template and target-site recognition by human LINE-1 in retrotransposition

Nature - Human LINE-1 ORF2p relies on upstream single-stranded target DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick...

nature.com
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Graduate students are accusing the University of California of wage theft months after signing a contract that ended mass strikes. Some say they've been underpaid by $4k or more. What's going on? Check out my latest for @statnews statnews.com/2023/09/05/univ…

Graduate students accuse University of California of wage theft, just months after strike was...

University of California students expected big pay hikes after an unprecedented strike, but they say it hasn't worked out that way.

statnews.com
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Students and postdocs working at the intersection of RNA and cancer, there is still time to apply for short talks and travel awards #RNACancerSRC
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Our work describing chromatin and gene expression programs in human scalp is now out in Nature Genetics. Congrats to Ben Ober-Reynolds and our other wonderful collaborators! nature.com/articles/s41588-0…

Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulat...

Nature Genetics - Single-cell RNA- and ATAC-seq analysis of human scalp biopsies characterizes the regulatory programs of heterogeneous cell types. Integration with genome-wide association studies...

nature.com
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💛🐧yesterday, palmerpenguins reached 1 million CRAN downloads! The adoption & love this little data package has received over the past 3 years has been truly overwhelming. Here are some of my favorite (and maybe lesser known) moments from palmerpenguins’ history. 🧵1/11
A line chart showing the cumulative downloads of palmerpenguins R package from CRAN, surpassing 1 million on 2023-07-17. The palmerpenguins hex logo is in the top right.

ALT A line chart showing the cumulative downloads of palmerpenguins R package from CRAN, surpassing 1 million on 2023-07-17. The palmerpenguins hex logo is in the top right.

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Fantastic!
Greg Findlay@TheGenomeLab15 Jun 2023
NEW! Our first @biorxivpreprint from @TheCrick, led by @megan_buckley01: biorxiv.org/content/10.1101/… "Saturation Genome Editing Resolves the Functional Spectrum of Pathogenic VHL Alleles" We present a high-quality variant effect map of VHL to advance precision medicine. (1/18)

Saturation Genome Editing Resolves the Functional Spectrum of Pathogenic VHL Alleles

To maximize the impact of precision medicine approaches, it is critical to accurately identify genetic variants in cancer-associated genes with functional consequences. Yet, our knowledge of rare...

biorxiv.org
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A 🧵 on algorithms for predicting regulatory variant effects to help understand complex disease. IMO an extremely challenging problem that's at a glass mostly full / glass mostly empty point right now depending on who you ask.
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Fantastic work! Everything I wanted after browsing gnomAD and seeing genes with few LOF variants with pLI/LOEUF scores I wasn't sure whether to trust.
Tony Zeng@tkyzeng23 May 2023
Measures of gene constraint like pLI and LOEUF have been hugely useful in human genetics, but they lack power to detect constraint in the shortest 25% of genes. Here, we introduce an empirical Bayes framework (GeneBayes) to solve this problem. biorxiv.org/cgi/content/shor… 1/n
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Very cool!
Tineke Lenstra@tinekelenstra16 May 2023
Ever wondered how transient transcription factor DNA binding can robustly activate transcription? In this new preprint, we find support for one of the possible mechanisms: transcription factors exchange. A 🧵 1/9. biorxiv.org/content/10.1101/…

Transcription factor exchange enables prolonged transcriptional bursts

Single-molecule imaging inside living cells has revealed that transcription factors (TFs) bind to DNA transiently, but a long-standing question is how this transient binding is related to transcrip...

biorxiv.org
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Also with @JackNaritomi we profiled binding of dominant negative Diamond-Blackfan anemia mutant RPS19. Surprisingly we saw an increase in CDS binding. Using Skipper's repetitive element output we also saw increased tRNA binding signal.
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We also fixed some bugs in the code so it should be easier than ever to use Skipper to learn about how WT and mutant RBPs regulate genes co- and post-transcriptionally in human health and disease!
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A 🧵 on some of my intuitions/priors about the genetics of complex and molecular traits in humans (i.e. what I think of as typical), largely motivated by GWAS/QTL studies over the past decade [citing papers with nice figures where possible]
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Scaling scRNA-seq data by log(p/s+1) outperforms other approaches, including recent methods with thousands of citations. [Ahlmann-Eltze & Huber, 2023 Nat Methods, nature.com/articles/s41592-0…]
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Great work, Arbel!
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Great progress!
Jon Freeman@freemanjb24 Mar 2023
Update 🎉 NSF is taking a major step toward properly collecting data to improve LGBTQ+ equity in STEM. All PhD students in the US finishing in 2023-24 will be given LGBTQ+ questions in the survey required to graduate. Some concerns but almost there. PDF: bit.ly/3LO5Z9I
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Great article!
Joe Pickrell
@joe_pickrell15 Mar 2023
Interesting piece: "After enduring severe nausea and vomiting in pregnancy, the geneticist Marlena Fejzo made finding the cause of her condition, hyperemesis gravidarum, her life’s work." nytimes.com/2023/03/14/well/… The referenced GWAS: nature.com/articles/s41467-0…
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So you're thinking about doing a #CRISPR screen... @ENCODE_NIH is here to help! The CRISPR group is proud to share: “Multi-center integrated analysis of non-coding CRISPR screens” Lotsa great stuff inside for newbies and experts, here's a quick tour biorxiv.org/content/10.1101/…

Multi-center integrated analysis of non-coding CRISPR screens

The ENCODE Consortium’s efforts to annotate non-coding, cis -regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes which play a major role in health and disease....

biorxiv.org
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