Alex Sweeten
@alexsweeten.bsky.social
PhD student at the NHGRI genomeinformatics.github.io & JHU Schatzlab
🛰️ 🧬🇨🇦
🛰️ 🧬🇨🇦
Reposted by Alex Sweeten
Check out the cool work being presented by our students at Genome Informatics! This year’s event was co-organized by @benlangmead.bsky.social, & features talks from @vikramshivakumar.bsky.social & more, plus posters from @alexsweeten.bsky.social, @maojanlin.bsky.social, & @sinamajidian.bsky.social:
Johns Hopkins researchers to present at Genome Informatics 2025
Students from the Department of Computer Science will give talks and present posters on their research in genome informatics.
www.cs.jhu.edu
November 4, 2025 at 5:14 PM
Check out the cool work being presented by our students at Genome Informatics! This year’s event was co-organized by @benlangmead.bsky.social, & features talks from @vikramshivakumar.bsky.social & more, plus posters from @alexsweeten.bsky.social, @maojanlin.bsky.social, & @sinamajidian.bsky.social:
Reposted by Alex Sweeten
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Reposted by Alex Sweeten
Congratulations @benlangmead.bsky.social!
Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬
July 22, 2025 at 7:17 PM
Congratulations @benlangmead.bsky.social!
Reposted by Alex Sweeten
Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...
June 17, 2025 at 1:39 PM
Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...
Reposted by Alex Sweeten
Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social.
Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n
Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n
Partitioned Multi-MUM finding for scalable pangenomics
Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...
www.biorxiv.org
May 27, 2025 at 7:35 PM
Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social.
Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n
Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n
Reposted by Alex Sweeten
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 2:19 PM
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:
Reposted by Alex Sweeten
NIH is allowing us to recruit postbacs and postdocs again. Please reach out if you are interested in working with us! Ad: genomeinformatics.github.io/jobs2025/
We are looking for postbacs and postdocs!
Join our team and contribute to the development of complete, personalized “telomere-to-telomere” (T2T) genome assemblies and the analysis of previously inaccessible regions of the genome! We are curre...
genomeinformatics.github.io
May 12, 2025 at 8:50 PM
NIH is allowing us to recruit postbacs and postdocs again. Please reach out if you are interested in working with us! Ad: genomeinformatics.github.io/jobs2025/
Reposted by Alex Sweeten
Thank you to everyone who attended, and thank you to everyone who got me to this point - I appreciate you all.
I'm on the job market this summer, so please send any interesting opportunities my way 😃
I'm on the job market this summer, so please send any interesting opportunities my way 😃
May 2, 2025 at 2:25 PM
Thank you to everyone who attended, and thank you to everyone who got me to this point - I appreciate you all.
I'm on the job market this summer, so please send any interesting opportunities my way 😃
I'm on the job market this summer, so please send any interesting opportunities my way 😃
Reposted by Alex Sweeten
@alexsweeten.bsky.social (John Hopkins) closes the session with improvements in annotation of satellite DNA in human assemblies
April 24, 2025 at 5:14 AM
@alexsweeten.bsky.social (John Hopkins) closes the session with improvements in annotation of satellite DNA in human assemblies
Reposted by Alex Sweeten
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
April 9, 2025 at 9:31 PM
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
Reposted by Alex Sweeten
We ran Mumemto on 474 human assemblies from @humanpangenome.bsky.social to find syntenic regions using MUMs. Mumemto scales remarkably well to large pangenomes thanks to compressed-space algos! It took under 2 days across 7 nodes (each using ~500 GB memory).
February 26, 2025 at 6:01 PM
We ran Mumemto on 474 human assemblies from @humanpangenome.bsky.social to find syntenic regions using MUMs. Mumemto scales remarkably well to large pangenomes thanks to compressed-space algos! It took under 2 days across 7 nodes (each using ~500 GB memory).
Reposted by Alex Sweeten
ModDotPlot session is happening now:
www.youtube.com/watch?v=fkkJ...
You can learn how to visualizate tandem repeats.
academic.oup.com/bioinformati...
@thebgacademy.bsky.social @alexsweeten.bsky.social
www.youtube.com/watch?v=fkkJ...
You can learn how to visualizate tandem repeats.
academic.oup.com/bioinformati...
@thebgacademy.bsky.social @alexsweeten.bsky.social
October 7, 2024 at 3:25 PM
ModDotPlot session is happening now:
www.youtube.com/watch?v=fkkJ...
You can learn how to visualizate tandem repeats.
academic.oup.com/bioinformati...
@thebgacademy.bsky.social @alexsweeten.bsky.social
www.youtube.com/watch?v=fkkJ...
You can learn how to visualizate tandem repeats.
academic.oup.com/bioinformati...
@thebgacademy.bsky.social @alexsweeten.bsky.social
Reposted by Alex Sweeten
ModDotPlot preprint is now out! Winner of best poster at RECOMB 2023, it can generate either static or interactive dotplots in minutes using hierarchical modimizers. With @alexsweeten.bsky.social and @mikeschatz.bsky.social
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...
Animated GIF - Find & Share on GIPHY
Discover & share this Animated GIF with everyone you know. GIPHY is how you search, share, discover, and create GIFs.
media.giphy.com
April 22, 2024 at 2:53 PM
ModDotPlot preprint is now out! Winner of best poster at RECOMB 2023, it can generate either static or interactive dotplots in minutes using hierarchical modimizers. With @alexsweeten.bsky.social and @mikeschatz.bsky.social
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...