Author

Nika Mansouri Ghiasi

ETH ZurichORCID 0000-0002-0833-0042Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Assay:long-read sequencing· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Approach:deep learning· 1

Frequent Co-Authors

Can FırtınaiD· 3 shared Gagandeep SinghiD· 3 shared Onur MutluiD· 3 shared Can AlkaniD· 2 shared Joël LindeggeriD· 2 shared Meryem Banu CavlakiD· 2 shared Mohammed AlseriD· 2 shared André KahlesiD· 1 shared

Activity by Year

2022-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersBioinformatics

Can FırtınaORCID

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4 papers

Recent·Most cited

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Fırtına, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu

TargetCall filters out off-target reads before basecalling to reduce computational waste, improving basecalling performance and efficiency.

Frontiers in Genetics · Oct 28, 2024Peer-reviewedBioinformatics

RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes

Can Fırtına, Nika Mansouri Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu

RawHash enables fast and accurate real-time analysis of nanopore raw signals for large genomes, outperforming existing methods in throughput and accuracy.

Bioinformatics · May 24, 2023Peer-reviewedBioinformatics

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

Can Fırtına, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu

BLEND improves genomic sequence analysis by efficiently finding fuzzy seed matches, enhancing speed, memory use, and accuracy in read overlapping and mapping.

NAR Genomics and Bioinformatics · Jan 10, 2023Peer-reviewedBioinformatics

Label-guided seed-chain-extend alignment on annotated De Bruijn graphs

Harun Mustafa, Mikhail Karasikov, Nika Mansouri Ghiasi, Gunnar Rätsch, André Kahles

This paper introduces a new alignment method for annotated De Bruijn graphs that improves taxonomic classification accuracy and coverage for long reads.

bioRxiv · Nov 4, 2022 · PreprintBioinformatics