Sign in

Graham McVicker

@grahammcvicker.bsky.social
98 followers 117 following 12 posts

Associate Professor at the Salk Institute

PostsRepliesMedia
Reposted by Graham McVicker
Jacob Schreiber @jmschreiber91.bsky.social · 16/02/2025
Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers www.nature.com/articles/s41...
nature.com
Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers - Nature Communications
The oncogene MYC plays a key role in cancer initiation and progression. Using thousands of CRISPR perturbations, the authors investigate regulators of MYC in six different cancers. These tumor-specifi...
0194
Reposted by Graham McVicker
Hilary Martin @hilarycmartin.bsky.social · 16/02/2025
Our new paper about rare variant contributions to sex differences in autism is out at AJHG, led by Mahmoud Koko with @vw1234.bsky.social and Kyle Satterstrom. Biggest analysis of exome data in autism to date including SPARK and ASC. www.sciencedirect.com/science/arti...
sciencedirect.com
Contribution of autosomal rare and de novo variants to sex differences in autism
Autism is four times more prevalent in males than females. To study whether this reflects a difference in genetic predisposition attributed to autosom…
0145
Reposted by Graham McVicker
Gonzalo Benegas @gonzalobenegas.bsky.social · 13/02/2025
Can DNA sequence models predict mutations affecting human traits? We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ Gökcen Eraslan and @yun-s-song.bsky.social 🧵👇
12815
Graham McVicker @grahammcvicker.bsky.social · 11/02/2025
Excited to announce our preprint describing SUPERB-SEQ 🦸, a new method to measure Cas9 edits and their effects on gene expression in single cells. Led by @micklorenzini.bsky.social and @bradbalderson.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
Joint single-cell profiling of CRISPR-Cas9 edits and transcriptomes reveals widespread off-target events and their effects on gene expression
A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to measure Cas9 edit outcomes and their functional effects at single-cell resolution. Here we present Superb-seq , ...
194
Reposted by Graham McVicker
Molly Przeworski @mollyprz.bsky.social · 02/02/2025
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
biorxiv.org
The distribution of highly deleterious variants across human ancestry groups
A major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry...
113169
Reposted by Graham McVicker
Zixuan (Eleanor) Zhang @elezzx.bsky.social · 27/01/2025
Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵 www.medrxiv.org/content/10.1...
medrxiv.org
Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping
Population-scale single-cell transcriptomic technologies (scRNA-seq) enable characterizing variant effects on gene regulation at the cellular level (e.g., single-cell eQTLs; sc-eQTLs). However, existi...
13911
Reposted by Graham McVicker
David A Knowles @davidaknowles.bsky.social · 09/12/2024
Excited to share our first foray into (noncoding) rare variant association testing: a probabilistic model that learns functional annotation importance and finds associations missed by existing methods. Anjali did a fantastic job with model assessment and scaling! www.medrxiv.org/content/10.1...
medrxiv.org
Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere
The increasing availability of whole-genome sequencing (WGS) has begun to elucidate the contribution of rare variants (RVs), both coding and non-coding, to complex disease. Multiple RV association tes...
13811