Graham McVicker
@grahammcvicker.bsky.social
Associate Professor at the Salk Institute
Reposted by Graham McVicker
This is the preprint write up of my sabbatical work with Dave Kelley’s group at Calico. We tried out several transformer replacements for multi-task learning in functional genomics (i.e. what Borzoi does). Mamba, in particular, seems to outperform a mini version of Borzoi, especially when “striped”.
Selective State Space Models Outperform Transformers at Predicting RNA-Seq Read Coverage https://www.biorxiv.org/content/10.1101/2025.02.13.638190v1
February 18, 2025 at 4:17 AM
This is the preprint write up of my sabbatical work with Dave Kelley’s group at Calico. We tried out several transformer replacements for multi-task learning in functional genomics (i.e. what Borzoi does). Mamba, in particular, seems to outperform a mini version of Borzoi, especially when “striped”.
Reposted by Graham McVicker
Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
February 16, 2025 at 10:34 AM
Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Graham McVicker
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...
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…
www.sciencedirect.com
February 16, 2025 at 12:29 PM
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...
Reposted by Graham McVicker
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 🧵👇
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 🧵👇
February 13, 2025 at 8:57 PM
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 🧵👇
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 🧵👇
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...
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 , ...
www.biorxiv.org
February 11, 2025 at 11:25 PM
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...
Reposted by Graham McVicker
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
February 2, 2025 at 7:00 PM
“The distribution of highly deleterious variants across human ancestry groups”. Preprint with Anastasia Stolyarova and @gcbias.bsky.social: www.biorxiv.org/content/10.1...
Reposted by Graham McVicker
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...
www.medrxiv.org/content/10.1...
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...
www.medrxiv.org
January 27, 2025 at 6:29 PM
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...
www.medrxiv.org/content/10.1...
Reposted by Graham McVicker
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...
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...
www.medrxiv.org
December 9, 2024 at 5:03 PM
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...