Zobrazeno 1 - 10
of 482
pro vyhledávání: '"ALKAN, Can"'
Autor:
Alıcıoğlu, Ahmet Cemal, Alkan, Can
Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters that need t
Externí odkaz:
http://arxiv.org/abs/2311.11082
Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed Chaining, and Seq
Externí odkaz:
http://arxiv.org/abs/2309.17063
Autor:
Cavlak, Meryem Banu, Singh, Gagandeep, Alser, Mohammed, Firtina, Can, Lindegger, Joël, Sadrosadati, Mohammad, Ghiasi, Nika Mansouri, Alkan, Can, Mutlu, Onur
Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art basecallers employ complex deep learning models to achieve high basec
Externí odkaz:
http://arxiv.org/abs/2212.04953
Real-time viral genome detection, taxonomic classification and phylogenetic analysis are critical for efficient tracking and control of viral pandemics such as Covid-19. However, the unprecedented and still growing amounts of viral genome data create
Externí odkaz:
http://arxiv.org/abs/2208.05004
Autor:
Cali, Damla Senol, Kanellopoulos, Konstantinos, Lindegger, Joel, Bingöl, Zülal, Kalsi, Gurpreet S., Zuo, Ziyi, Firtina, Can, Cavlak, Meryem Banu, Kim, Jeremie, Ghiasi, Nika Mansouri, Singh, Gagandeep, Gómez-Luna, Juan, Alserr, Nour Almadhoun, Alser, Mohammed, Subramoney, Sreenivas, Alkan, Can, Ghose, Saugata, Mutlu, Onur
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the linear referen
Externí odkaz:
http://arxiv.org/abs/2205.05883
Autor:
Kim, Jeremie S., Firtina, Can, Cavlak, Meryem Banu, Cali, Damla Senol, Alkan, Can, Mutlu, Onur
Publikováno v:
Bioinformatics, Sep 30; 38(19):4633-4635, 2022
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool. With the exp
Externí odkaz:
http://arxiv.org/abs/2201.06255
Autor:
Firtina, Can, Park, Jisung, Alser, Mohammed, Kim, Jeremie S., Cali, Damla Senol, Shahroodi, Taha, Ghiasi, Nika Mansouri, Singh, Gagandeep, Kanellopoulos, Konstantinos, Alkan, Can, Mutlu, Onur
Publikováno v:
NAR Genomics and Bioinformatics, vol. 5, no. 1, p. lqad004, Mar. 2023
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding ex
Externí odkaz:
http://arxiv.org/abs/2112.08687
Publikováno v:
IEEE Transactions on Computers, 73 (5): 1206-1218, 2024
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the similarities
Externí odkaz:
http://arxiv.org/abs/2103.14978
Autor:
Shojaei, Mona, Mohammadvand, Navid, Doğan, Tunca, Alkan, Can, Çetin Atalay, Rengül, Acar, Aybar C.
Publikováno v:
In Computers in Biology and Medicine February 2024 169
Autor:
Cali, Damla Senol, Kalsi, Gurpreet S., Bingöl, Zülal, Firtina, Can, Subramanian, Lavanya, Kim, Jeremie S., Ausavarungnirun, Rachata, Alser, Mohammed, Gomez-Luna, Juan, Boroumand, Amirali, Nori, Anant, Scibisz, Allison, Subramoney, Sreenivas, Alkan, Can, Ghose, Saugata, Mutlu, Onur
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the computational power
Externí odkaz:
http://arxiv.org/abs/2009.07692