Searched for: author%3A%22Ahmed%2C+N.%22
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Diaz, Vitali (author), van Oosterom, P.J.M. (author), Meijers, B.M. (author), Verbree, E. (author), Ahmed, N. (author), Van Lankveld, T. (author)
The advantages of using point clouds for change detection analysis include comprehensive spatial and temporal representation, as well as high precision and accuracy in the calculations. These benefits make point clouds a powerful data type for spatio-temporal analysis. Nevertheless, most current change detection methods have been specifically...
abstract 2024
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Diaz, Vitali (author), van Oosterom, P.J.M. (author), Meijers, B.M. (author), Verbree, E. (author), Ahmed, N. (author), Van Lankveld, T. (author)
Cloud-to-cloud (C2C) distance calculations are frequently performed as an initial stage in change detection and spatiotemporal analysis with point clouds. There are various methods for calculating C2C distance, also called inter-point distance, which refers to the distance between two corresponding point clouds captured at different epochs....
conference paper 2024
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Bdour, Ahmed N. (author), Al-Sadeq, Noor (author), Gharaibeh, Muna (author), Mendoza-Sammet, Angeles (author), Kennedy, M.D. (author), Salinas-Rodriguez, Sergio G. (author)
Jordan was late in adopting seawater and brackish water desalination as a source until the late 1990s and early 2000s. However, ongoing studies are still discussing the technical, economic, and socio-political aspects of brackish water reverse osmosis (BWRO) desalination plants. In this study, the water–energy nexus was considered, in order...
journal article 2022
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Park, Seongyeon (author), Kim, Hajin (author), Ahmad, T. (author), Ahmed, N. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Kim, Youngsok (author), Lee, Jinho (author)
Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...
conference paper 2022
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Ahmed, N. (author)
Recent advances in DNA sequencing technology have opened new doors for scientists to use genomic data analysis in a variety of applications that directly affect human lives. However, the analysis of unprecedented volumes of sequencing data being produced represents a formidable computational challenge. The conventional CPU-only computing...
doctoral thesis 2020
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Ahmad, T. (author), Ahmed, N. (author), Peltenburg, J.W. (author), Al-Ars, Z. (author)
The rapidly growing size of genomics data bases, driven by advances in sequencing technologies, demands fast and cost-effective processing. However, processing this data creates many challenges, particularly in selecting appropriate algorithms and computing platforms. Computing systems need data closer to the processor for fast processing....
conference paper 2020
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Ahmad, T. (author), Ahmed, N. (author), Al-Ars, Z. (author), Hofstee, H.P. (author)
Background: Immense improvements in sequencing technologies enable producing large amounts of high throughput and cost effective next-generation sequencing (NGS) data. This data needs to be processed efficiently for further downstream analyses. Computing systems need this large amounts of data closer to the processor (with low latency) for...
journal article 2020
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
The seeding heuristic is widely used in many DNA analysis applications to speed up the analysis time. In many applications, seeding takes a substantial amount of the total execution time. In this paper, we present an efficient GPU implementation for computing maximal exact matching (MEM) seeds in long DNA reads. We applied various...
conference paper 2020
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Ahmed, N. (author), Qiu, T.D. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
BACKGROUND: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo...
journal article 2020
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Ahmed, N. (author), Lévy, Jonathan (author), Ren, S. (author), Mushtaq, Hamid (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below. The original article [1] has been corrected. [Typesetter, please insert new supplied figure in package].
journal article 2019
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Ahmed, N. (author), Lévy, Jonathan (author), Ren, S. (author), Mushtaq, Hamid (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
BACKGROUND: Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited performance. In this article we present GASAL2, a GPU library for...
journal article 2019
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Ren, S. (author), Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Background: Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far<br/...
journal article 2019
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Mushtaq, H. (author), Ahmed, N. (author), Al-Ars, Z. (author)
Due to the rapid decrease in the cost of NGS (Next Generation Sequencing), interest has increased in using data generated from NGS to diagnose genetic diseases. However, the data generated by NGS technology is usually in the order of hundreds of gigabytes per experiment, thus requiring efficient and scalable programs to perform data analysis...
journal article 2019
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Ren, S. (author), Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
In order to improve the accuracy of indel detection, micro-assembly is used in multiple variant callers, such as the GATK HaplotypeCaller to reassemble reads in a specific region of the genome. Assembly is a computationally intensive process that causes runtime bottlenecks. In this paper, we propose a GPU-based de Bruijn graph construction...
conference paper 2018
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Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
DNA read alignment is a major step in genome analysis. However, as DNA reads continue to become longer, new approaches need to be developed to effectively use these longer reads in the alignment process. Modern aligners commonly use a two-step approach for read alignment: 1. seeding, 2. extension. In this paper, we have investigated various...
conference paper 2016
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Ahmed, N. (author), Hamminga, G. (author), Vogelaar, H. (author), Slotema, W. (author)
report 2000
Searched for: author%3A%22Ahmed%2C+N.%22
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