Mohsen Zakeri
@mohsenzakeri.bsky.social
Postdoctoral Fellow at Johns Hopkins University, Computational Biology ❤️
www.mohsenzakeri.com
www.mohsenzakeri.com
Reposted by Mohsen Zakeri
Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory.
List of talks and posters: meetings.cshl.edu/abstracts.as...
List of talks and posters: meetings.cshl.edu/abstracts.as...
November 6, 2025 at 12:38 AM
Ben Langmead @benlangmead.bsky.social delivers the official opening for this year's Genome Informatics Conference #GI2025 at Cold Spring Harbor Laboratory.
List of talks and posters: meetings.cshl.edu/abstracts.as...
List of talks and posters: meetings.cshl.edu/abstracts.as...
Reposted by Mohsen Zakeri
As our beloved Genome Informatics 2025 (#gi2025) approaches, I'm moved to share some photos from past years at CSHL. A couple more photos coming in a reply below...
November 3, 2025 at 8:47 PM
As our beloved Genome Informatics 2025 (#gi2025) approaches, I'm moved to share some photos from past years at CSHL. A couple more photos coming in a reply below...
We’re all so proud of Steven Tan! He’s a super talented undergraduate at JHU. Thanks to the incredible support of @benlangmead.bsky.social, I had the opportunity to help guide this work, and I really loved it. Many thanks also to @sinamajidian.bsky.social for his valuable collaboration and input.
Huge congratulations to Steven Tan, a superb undergraduate junior at JHU CS whose first-author paper "Movi Color: fast and accurate taxonomic classification with the move structure" won best paper at ACM-BCB. Please check it out: www.biorxiv.org/content/10.1.... Congrats, Steven!!
November 2, 2025 at 7:27 PM
We’re all so proud of Steven Tan! He’s a super talented undergraduate at JHU. Thanks to the incredible support of @benlangmead.bsky.social, I had the opportunity to help guide this work, and I really loved it. Many thanks also to @sinamajidian.bsky.social for his valuable collaboration and input.
Reposted by Mohsen Zakeri
Very excited about Movi 2! Excellent work by Mohsen here. FYI, I have a series of 5 videos on the move structure starting with this one: youtu.be/REniD2dKf6A?...
October 21, 2025 at 9:39 PM
Very excited about Movi 2! Excellent work by Mohsen here. FYI, I have a series of 5 videos on the move structure starting with this one: youtu.be/REniD2dKf6A?...
Reposted by Mohsen Zakeri
Great work and congrats to all authors! 🥳 Can't wait to read the preprint. Just for reference: a Fulgor index ⚡ on the same HPRC collection takes 8.26 GB (not in its most succinct representation). Fulgor, however, can be regarded as a "lossy" method here since it is based on kmers.
5/6 On the 466 haplotypes from the 2nd release of HPRC, the fastest Movi 2 index is under 50 GB. It can be reduced to 24 GB while remaining over 3x faster than SPUMONI. Movi 2 is smaller and faster than ropebwt3, although it computes PMLs, which are easier to get than the SMEMs found by ropebwt3.
October 22, 2025 at 7:41 AM
Great work and congrats to all authors! 🥳 Can't wait to read the preprint. Just for reference: a Fulgor index ⚡ on the same HPRC collection takes 8.26 GB (not in its most succinct representation). Fulgor, however, can be regarded as a "lossy" method here since it is based on kmers.
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
An awesome opportunity, strongly recommended to anyone looking for a postdoc in algorithms and genomics!
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 9, 2025 at 3:18 PM
An awesome opportunity, strongly recommended to anyone looking for a postdoc in algorithms and genomics!
Reposted by Mohsen Zakeri
EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/...
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
EvANI benchmarking workflow for evolutionary distance estimation
Abstract. Advances in long-read sequencing technology have led to a rapid increase in high-quality genome assemblies. These make it possible to compare gen
academic.oup.com
September 21, 2025 at 3:26 PM
EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/...
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
Reposted by Mohsen Zakeri
Great talk by Vikram @vikramshivakumar.bsky.social on studying pangenomes and synteny visualization in #WABI25
Github: github.com/vikshiv/mume...
First paper: genomebiology.biomedcentral.com/articles/10....
Second: www.biorxiv.org/content/10.1... #WABI2025
Github: github.com/vikshiv/mume...
First paper: genomebiology.biomedcentral.com/articles/10....
Second: www.biorxiv.org/content/10.1... #WABI2025
August 20, 2025 at 3:03 PM
Great talk by Vikram @vikramshivakumar.bsky.social on studying pangenomes and synteny visualization in #WABI25
Github: github.com/vikshiv/mume...
First paper: genomebiology.biomedcentral.com/articles/10....
Second: www.biorxiv.org/content/10.1... #WABI2025
Github: github.com/vikshiv/mume...
First paper: genomebiology.biomedcentral.com/articles/10....
Second: www.biorxiv.org/content/10.1... #WABI2025
Reposted by Mohsen Zakeri
The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!
WABI 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
August 20, 2025 at 2:45 AM
The 25th iteration of the excellent Conference for Algorithms in Bioinformatics (WABI) starts tomorrow at UMD @umdscience.bsky.social at the Brendan Iribe Center. You can find details at the website wabiconf.github.io/2025/. We'll use the tag #WABI25 for the meeting!
Reposted by Mohsen Zakeri
🧬🖥️ In addition to an update to oarfish, a new version (0.14.0) of piscem (zenodo.org/records/1509...) has just been released. This version pulls in some of the latest improvements to sshash by @jermp.bsky.social! 1/2
The piscem index
This manuscript provides a brief overview of the piscem index — a fast and compact index for the compacted, colored, reference (i.e., storing positional information about the input references) de Brui...
zenodo.org
June 30, 2025 at 2:14 PM
🧬🖥️ In addition to an update to oarfish, a new version (0.14.0) of piscem (zenodo.org/records/1509...) has just been released. This version pulls in some of the latest improvements to sshash by @jermp.bsky.social! 1/2
Reposted by Mohsen Zakeri
The second keynote address at WABI '25 will be by Christina Boucher. She will talk about "Recursive Parsing and Grammar Compression in the Era of Pangenomics". PFP (& RPFP) has enabled tremendous advances in representation & indexing; this will be an exciting talk!
wabiconf.github.io/2025/talks/t...
wabiconf.github.io/2025/talks/t...
Recursive Parsing and Grammar Compression in the Era of Pangenomics
Talk by Christina Boucher - WABI 2025
wabiconf.github.io
June 23, 2025 at 6:59 PM
The second keynote address at WABI '25 will be by Christina Boucher. She will talk about "Recursive Parsing and Grammar Compression in the Era of Pangenomics". PFP (& RPFP) has enabled tremendous advances in representation & indexing; this will be an exciting talk!
wabiconf.github.io/2025/talks/t...
wabiconf.github.io/2025/talks/t...
Reposted by Mohsen Zakeri
Reposted by Mohsen Zakeri
Excited to introduce LiftOn – an open-source tool for accurate, scalable liftover of genome annotations (GFF) across assemblies. 🚀
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
June 17, 2025 at 2:21 PM
Excited to introduce LiftOn – an open-source tool for accurate, scalable liftover of genome annotations (GFF) across assemblies. 🚀
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
Reposted by Mohsen Zakeri
Excellent work, Steven & Mohsen! See thread below
1/5 We introduce Movi Color, led by Steven Tan (a brilliant undergrad member of Langmead lab) for taxonomic and multi-class classification. It uses a full-text index based on the move structure and does not rely on predefined values (like k-mer length) for index building.
github.com/mohsenzakeri...
github.com/mohsenzakeri...
May 29, 2025 at 2:56 PM
Excellent work, Steven & Mohsen! See thread below
1/5 We introduce Movi Color, led by Steven Tan (a brilliant undergrad member of Langmead lab) for taxonomic and multi-class classification. It uses a full-text index based on the move structure and does not rely on predefined values (like k-mer length) for index building.
github.com/mohsenzakeri...
github.com/mohsenzakeri...
May 29, 2025 at 2:36 PM
1/5 We introduce Movi Color, led by Steven Tan (a brilliant undergrad member of Langmead lab) for taxonomic and multi-class classification. It uses a full-text index based on the move structure and does not rely on predefined values (like k-mer length) for index building.
github.com/mohsenzakeri...
github.com/mohsenzakeri...
Reposted by Mohsen Zakeri
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 Mohsen Zakeri
The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
WABI 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
May 7, 2025 at 7:14 PM
The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
* abstract deadline: May 12 (AoE)
* paper deadline: May 15 (AoE)
Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!
Reposted by Mohsen Zakeri
I'll also be on the job market this summer, so please reach out if you're interested!
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
Arun Das
arundas.org
April 21, 2025 at 9:24 PM
I'll also be on the job market this summer, so please reach out if you're interested!
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
You can find out more about me at these links:
LinkedIn: www.linkedin.com/in/arun96/
Personal Website: arundas.org
Reposted by Mohsen Zakeri
Next up is Nathaniel Brown from @benlangmead.bsky.social's group presenting col-bwt, a new algorithm for computing chain statistics using multi-maximal unique matches.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 27, 2025 at 2:00 AM
Next up is Nathaniel Brown from @benlangmead.bsky.social's group presenting col-bwt, a new algorithm for computing chain statistics using multi-maximal unique matches.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mohsen Zakeri
Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI
WABI 2025
WABI Conference on Algorithms in Bioinformatics
wabiconf.github.io
April 5, 2025 at 9:05 PM
Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI
Reposted by Mohsen Zakeri
On Thurs, March 13 at 9AM (ET), @noorpratap.bsky.social will be defending his dissertation!
If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in!
Talk link: umd.zoom.us/j/9873133564...
Abstract: talks.cs.umd.edu/talks/4137
If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in!
Talk link: umd.zoom.us/j/9873133564...
Abstract: talks.cs.umd.edu/talks/4137
Talks
talks.cs.umd.edu
March 12, 2025 at 3:17 AM
On Thurs, March 13 at 9AM (ET), @noorpratap.bsky.social will be defending his dissertation!
If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in!
Talk link: umd.zoom.us/j/9873133564...
Abstract: talks.cs.umd.edu/talks/4137
If you want to learn more about tree-based quantification & differential testing, or scATAC-seq preprocessing; tune in!
Talk link: umd.zoom.us/j/9873133564...
Abstract: talks.cs.umd.edu/talks/4137
Reposted by Mohsen Zakeri
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 Mohsen Zakeri
🚨 Keynotes at RECOMB-seq 2025! 🚨
🌟 Alicia Oshlack – computational transcriptomics
@aliciao.bsky.social
🌟 Rayan Chikhi – sequencing data structures
@rayanchikhi.bsky.social
🗓️ Dates: April 24–25, 2025
📍 Seoul, South Korea
recomb-seq.github.io/speakers/
🌟 Alicia Oshlack – computational transcriptomics
@aliciao.bsky.social
🌟 Rayan Chikhi – sequencing data structures
@rayanchikhi.bsky.social
🗓️ Dates: April 24–25, 2025
📍 Seoul, South Korea
recomb-seq.github.io/speakers/
January 24, 2025 at 10:32 AM
🚨 Keynotes at RECOMB-seq 2025! 🚨
🌟 Alicia Oshlack – computational transcriptomics
@aliciao.bsky.social
🌟 Rayan Chikhi – sequencing data structures
@rayanchikhi.bsky.social
🗓️ Dates: April 24–25, 2025
📍 Seoul, South Korea
recomb-seq.github.io/speakers/
🌟 Alicia Oshlack – computational transcriptomics
@aliciao.bsky.social
🌟 Rayan Chikhi – sequencing data structures
@rayanchikhi.bsky.social
🗓️ Dates: April 24–25, 2025
📍 Seoul, South Korea
recomb-seq.github.io/speakers/
Reposted by Mohsen Zakeri
Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.
Movi: A fast and cache-efficient full-text pangenome index
Biocomputational method; Classification of bioinformatical subject; Genomic analysis
www.cell.com
December 11, 2024 at 4:48 PM
Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.