Mohsen Zakeri
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Explore the profile of Mohsen Zakeri including associated specialties, affiliations and a list of published articles.
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11
Citations
147
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Recent Articles
1.
Majidian S, Hwang S, Zakeri M, Langmead B
bioRxiv
. 2025 Mar;
PMID: 40027788
Advances in long-read sequencing technology has led to a rapid increase in high-quality genome assemblies. These make it possible to compare genome sequences across the Tree of Life, deepening our...
2.
Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore G, et al.
Nat Commun
. 2025 Jan;
16(1):825.
PMID: 39827261
As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host...
3.
Zakeri M, Brown N, Ahmed O, Gagie T, Langmead B
iScience
. 2025 Jan;
27(12):111464.
PMID: 39758981
Pangenome indexes are promising tools for many applications, including classification of nanopore sequencing reads. Move structure is a compressed-index data structure based on the Burrows-Wheeler Transform (BWT). It offers simultaneous...
4.
Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore G, et al.
Res Sq
. 2024 Nov;
PMID: 39502785
As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host...
5.
Shivakumar V, Ahmed O, Kovaka S, Zakeri M, Langmead B
Bioinformatics
. 2024 Jun;
40(Suppl 1):i287-i296.
PMID: 38940135
Summary: Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But...
6.
Zakeri M, Brown N, Ahmed O, Gagie T, Langmead B
bioRxiv
. 2023 Nov;
PMID: 37961660
Efficient pangenome indexes are promising tools for many applications, including rapid classification of nanopore sequencing reads. Recently, a compressed-index data structure called the "move structure" was proposed as an alternative...
7.
Shivakumar V, Ahmed O, Kovaka S, Zakeri M, Langmead B
bioRxiv
. 2023 Aug;
PMID: 37645873
Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past...
8.
Wu E, Singh N, Choi K, Zakeri M, Vincent M, Churchill G, et al.
Genome Biol
. 2023 Jul;
24(1):165.
PMID: 37438847
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at...
9.
He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R
Nat Methods
. 2022 Mar;
19(3):316-322.
PMID: 35277707
The rapid growth of high-throughput single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few years. The size, volume and distinctive characteristics...
10.
Skoufos G, Almodaresi F, Zakeri M, Paulson J, Patro R, Hatzigeorgiou A, et al.
Genome Biol
. 2022 Feb;
23(1):39.
PMID: 35101114
We introduce AGAMEMNON ( https://github.com/ivlachos/agamemnon ) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNON delivers accurate abundances at...