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Alex Sweeten

@alexsweeten.bsky.social
74 followers 73 following 3 posts

PhD student in computational genomics at JHU Phillippy & Schatzlab 🛰️ 🧬🇨🇦

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Reposted by Alex Sweeten
Adam Phillippy @aphillippy.bsky.social · 06/08/2026
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
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JHU Computer Science @jhucompsci.bsky.social · 30/04/2026
Celebrate the last day of finals by joining us for the last CS seminar of the semester @sergek.bsky.social! Learn more here: www.cs.jhu.edu/event/cs-sem...
Computer Science Seminar Series. Genome Assembly: The Long and Short of It. May 12, 2026, 228 Malone Hall. Refreshments available 10:30 a.m. Seminar begins 10:45 a.m. Sergey Koren, National Human Genome Research Institute.
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Adam Phillippy @aphillippy.bsky.social · 30/03/2026
More acrocentric investigations, this one led by @arhie.bsky.social 🕵🏻‍♀️ “Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes” 🧵[1/8] 📄 www.biorxiv.org/content/10.6...
biorxiv.org
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Adam Phillippy @aphillippy.bsky.social · 23/03/2026
Recently amplified gene arrays are a super interesting phenomenon, but many still resist our attempts to assemble them. @dantipov.bsky.social has developed a new method (Trivial Tangle Traverser) that resolves assembly graph tangles caused by such sequences (1/4) www.biorxiv.org/content/10.6...
biorxiv.org
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Matthew Nguyen @mnguyen667.bsky.social · 09/03/2026
1/ Excited to share my first first-author preprint from my PhD! We introduce Perseus, a lineage-aware confidence estimation framework for taxonomic classification in long-read metagenomics. Preprint: www.biorxiv.org/content/10.6... Code: github.com/matnguyen/Pe...
biorxiv.org
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Adam Phillippy @aphillippy.bsky.social · 02/02/2026
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
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Alex Sweeten @alexsweeten.bsky.social · 29/01/2026
Legal disclaimer: We are in no way affiliated with Auntie Anne’s or any other pretzel-based entity 🥨
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Reposted by Alex Sweeten
JHU Computer Science @jhucompsci.bsky.social · 04/11/2025
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:
cs.jhu.edu
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.
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Reposted by Alex Sweeten
Adam Phillippy @aphillippy.bsky.social · 22/09/2025
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]
biorxiv.org
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 ...
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Mike Schatz @mikeschatz.bsky.social · 22/07/2025
Congratulations @benlangmead.bsky.social!
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Adam Phillippy @aphillippy.bsky.social · 17/06/2025
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...
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Vikram Shivakumar @vikramshivakumar.bsky.social · 27/05/2025
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
biorxiv.org
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...
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Arun Das @arun-das.bsky.social · 15/05/2025
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:
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Adam Phillippy @aphillippy.bsky.social · 12/05/2025
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/
genomeinformatics.github.io
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...
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Arun Das @arun-das.bsky.social · 02/05/2025
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 😃
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Camille Marchet ⚡ @camillemrcht.bsky.social · 24/04/2025
@alexsweeten.bsky.social (John Hopkins) closes the session with improvements in annotation of satellite DNA in human assemblies
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Adam Phillippy @aphillippy.bsky.social · 09/04/2025
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...
A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.
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Vikram Shivakumar @vikramshivakumar.bsky.social · 26/02/2025
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).
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Sina Majidian @sinamajidian.bsky.social · 07/10/2024
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
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Adam Phillippy @aphillippy.bsky.social · 22/04/2024
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...
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