Lightnews — Scholar-powered news

Reposted by Bohan Ni

Josh Weinstock @joshweinstock.bsky.social · Jul 22

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...

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

1 10 26

Bohan Ni @bohanni.bsky.social · May 15

Check out the amazing work from my colleague and friend!

Arun Das @arun-das.bsky.social · May 15

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:

bioRxiv Genomics @biorxiv-genomic.bsky.social · May 15

Assembling unmapped reads reveals hidden variation in South Asian genomes https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1

2

Reposted by Bohan Ni

Vikram Shivakumar @vikramshivakumar.bsky.social · May 9

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 👀

14 34

Reposted by Bohan Ni

Sara Carioscia @saracarioscia.bsky.social · May 7

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

7 20

Reposted by Bohan Ni

Mingyuan "Merlin" Li @supmerlin.bsky.social · May 5

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...

3 15 36

Reposted by Bohan Ni

Nature Methods @natmethods.nature.com · Mar 28

Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications.

www.nature.com/articles/s41...

1 26 46

Bohan Ni @bohanni.bsky.social · Mar 26

SV prioritization tools in both prioritizing coding and noncoding variant benchmarks. Finally, we were able to prioritize confident rare disease candidate SVs and genes in the Undiagnosed Disease Network data. To learn more, read our paper here: 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

Bohan Ni @bohanni.bsky.social · Mar 26

After extensive analyses of rare SVs near gene expression outliers using long and short-read sequencing, we developed Watershed-SV, extending Watershed, to prioritize functional rare SVs and genes they impact. Our model significantly improves from a baseline model and state-of-the-art

1

Bohan Ni @bohanni.bsky.social · Mar 26

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

1 7 10

Reposted by Bohan Ni

Vikram Shivakumar @vikramshivakumar.bsky.social · Jan 6

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

1 29 34

Reposted by Bohan Ni

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jan 6

Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1

12 22