Bohan Ni
@bohanni.bsky.social
PhD student in CompSci, Johns Hopkins University. I try to find rare and common variants with impacts on traits/health.
Reposted by Bohan Ni
Really excited to share our new PRS method, developed with @aprilkim.bsky.social and @alexisbattle.bsky.social ! Our approach is to use a lot of recently developed functional annotations to better estimate the weights of the SNPs.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Polygenic prediction of phenotypes with a neural empirical Bayes approach
Polygenic risk scores (PRS) estimate the expected value of a phenotype based on individual genotypes. Although statistical approaches for calculating PRS have advanced considerably in recent years, fe...
www.medrxiv.org
July 22, 2025 at 9:25 PM
Really excited to share our new PRS method, developed with @aprilkim.bsky.social and @alexisbattle.bsky.social ! Our approach is to use a lot of recently developed functional annotations to better estimate the weights of the SNPs.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Check out the amazing work from my colleague and friend!
Our pre-print on investigating variation in South Asian genomes is now out!
Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.
🧵 A thread on the key results and takeaways from our work:
Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.
🧵 A thread on the key results and takeaways from our work:
Assembling unmapped reads reveals hidden variation in South Asian genomes https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1
May 15, 2025 at 3:27 PM
Check out the amazing work from my colleague and friend!
Reposted by Bohan Ni
Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀
May 9, 2025 at 4:26 PM
Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀
Reposted by Bohan Ni
If you are here at #bog25 please check out my poster (number 87) tonight! 😁 Showing our work on common variation associated with aneuploidy in human embryos
May 7, 2025 at 5:26 PM
If you are here at #bog25 please check out my poster (number 87) tonight! 😁 Showing our work on common variation associated with aneuploidy in human embryos
Reposted by Bohan Ni
1/n 🚨Very excited to share our recent work!🚨
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
May 5, 2025 at 7:07 PM
1/n 🚨Very excited to share our recent work!🚨
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro.
www.biorxiv.org/content/10.1...
Reposted by Bohan Ni
Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
March 28, 2025 at 5:23 PM
Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
March 26, 2025 at 2:30 PM
Happy to share our work characterizing functional rare SVs in rare diseases with long-read genome sequencing and transcriptomic outlier data: genome.cshlp.org/content/earl...
Reposted by Bohan Ni
Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.
Mumemto: efficient maximal matching across pangenomes
Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...
www.biorxiv.org
January 6, 2025 at 3:27 PM
Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.
Reposted by Bohan Ni
Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1
January 6, 2025 at 3:46 AM
Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1