PGY-3 @brighamwomens Hospital, Internal Medicine | Cardiovascular Genomics | PhD in Bing Ren Lab @UCSanDiego
Boston, MA
Joined June 2020
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Our latest work in @CellCellPress is a cell atlas of chromatin accessibility in 30 human tissues, integrated with prior data from 15 fetal tissues:
- 222 cell types, ~1.2 million cCREs
- Cell type & adult/fetal-specific elements
- Interpretation of GWAS
cell.com/cell/fulltext/S0092…
James Hocker, MD, PhD retweeted
Great to see @bethanyfixsen and @jamesdhocker featured in the @BrighamMedRes Bulletin! We are sad to see you leave California, but so excited for your new journey in Boston!
bwhbulletin.org/2024/03/21/i…
James Hocker, MD, PhD retweeted
So incredibly grateful to have couples matched in San Diego with my wife @HanaMedDO!!! Our 👶🏻 Grace and 🐶 Ozzy are overjoyed! #Match2024 @UCSDMedSchool @WesternUCOMP @UCSDRadRes @ucsd_mstp @HsiaoMDPhD @albertssong @SanYsidroHealth
Thrilled to have couples matched at @BrighamMedRes with @bethanyfixsen - we are so excited to start!!! Thank you to our family, friends, and mentors Neil Chi, @UCSDGlassLab, & Bing Ren #UCSDMatch2024 @UCSDMedSchool @ucsd_mstp @UCSDBMS
James Hocker, MD, PhD retweeted
Link to paper
nature.com/articles/s41586-0…
James Hocker, MD, PhD retweeted
Single cell sequencing, gene expression, imaging and spatial omics deconvolute the heart's development in exquisite detail @Nature
video: youtu.be/bGOgq7DMTGg
James Hocker, MD, PhD retweeted
What if 1 million scRNA-seq libraries can be prepared within $1k? Here we go 👉 21 million cells from 623 mouse tissues, spanning 5 life stages & 3 genotypes, all in a SINGLE study by ONE remarkable student Zehao @Tommyz626 from our lab @RockefellerUniv! shorturl.at/epsz7
James Hocker, MD, PhD retweeted
1. This validates the observation/hypothesis that causal genes for a disease are connected in gene regulatory networks — and shows that we can find them with systematic Perturb-seq and V2G2P. Here we linked 41 CAD GWAS loci to a single pathway in endothelial cells.
13/
James Hocker, MD, PhD retweeted
Our latest in @Nature:
Convergence of coronary artery disease genes on endothelial cell programs
nature.com/articles/s41586-0…
Incredible work led by Gavin Schnitzler and @kanghelenyihua — a long-standing partnership between our lab and @Dr_RajatGupta
My comments below:
1/
James Hocker, MD, PhD retweeted
Our study is out @Nature. We identify non-lipid risk pathways for coronary artery disease using pooled CRISPR-interference for 2,285 genes at GWAS loci. With an amazing team we identified the genetic risk pathways for CAD that act in endothelial cells.
nature.com/articles/s41586-0…
James Hocker, MD, PhD retweeted
Our work using single-molecule chromatin configurations to link TF binding to gene expression is now out on bioRxiv! Amazing effort from @bgrdoughty, @MichaelaThinks, and @juliaschaepe, and an immensely rewarding collaboration with the @BintuLab: biorxiv.org/content/10.1101/… [1/n]
James Hocker, MD, PhD retweeted
The prevalence of suboptimal affinity binding sites within enhancers creates a vulnerability in genomes whereby single-nucleotide changes that optimize affinity, even slightly, can be pathogenic. doi.org/10.1038/s41586-023-0…
James Hocker, MD, PhD retweeted
Pinpointing causal variants that disrupt development. So proud of the amazing team on this epic enhancer genotype-to-phenotype study. Well Done, Fabian Lim, @JoeSolvason, Genevieve Ryan, Sophia Le, @granton_jindal, Paige Steffen and Simran Jandu!!! doi.org/10.1038/s41586-023-0…
James Hocker, MD, PhD retweeted
SnapATAC2 is a non-linear dimension reduction algorithm tailored for single-cell omics data including scATAC-seq, scRNA-seq, scHi-C, and multiomics datasets. snapATAC is also efficient in runtime and memory usage.
nature.com/articles/s41592-0…
James Hocker, MD, PhD retweeted
Gene expression involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. We developed ChIP-DIP – a method for simultaneous, genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. biorxiv.org/content/10.1101/…
James Hocker, MD, PhD retweeted
Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height biorxiv.org/cgi/content/shor… #bioRxiv
James Hocker, MD, PhD retweeted
I'm delighted to announce that I am joining the talented research community at @BIG_CenterWashU @wusm_pathology. The Han Lab, with a focus on brain #macrophages in neuropathologies, will be open shortly. More info and website coming soon!
James Hocker, MD, PhD retweeted
Excited to share our latest work on bioRxiv!
biorxiv.org/content/10.1101/…
A highly collaborative effort with @ksmualim @karbalayghareh, @mayayayas, @kanishkadey, @evelynjagoda,@WangXijhu, @LarsMSteinmetz, @anshulkundaje, @jengreitz and many others from @ENCODE_NIH!
Thread👇
James Hocker, MD, PhD retweeted
Excited to share our collaboration with ENCODE to map enhancer-gene regulatory interactions across the human genome!
We developed a new model that beats ABC by incorporating additional information on promoter class and enhancer-enhancer interactions.
Thread 👇
Excited to share our latest work on bioRxiv!
biorxiv.org/content/10.1101/…
A highly collaborative effort with @ksmualim @karbalayghareh, @mayayayas, @kanishkadey, @evelynjagoda,@WangXijhu, @LarsMSteinmetz, @anshulkundaje, @jengreitz and many others from @ENCODE_NIH!
Thread👇
James Hocker, MD, PhD retweeted
Proud to join WashU with a dual appointment in
@WashUNeurosurg and @WashUGenetics
@WashuBTC @WUSTLmed @SitemanCenter.
We are recruiting! 🎉🧪🖥️
