Search Results - "Iliopoulos, Costas"

GenMap: ultra-fast computation of genome mappability by Pockrandt, Christopher, Alzamel, Mai, Iliopoulos, Costas S, Reinert, Knut

“…Abstract Motivation Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging…”
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Predicting the functional consequences of non-synonymous DNA sequence variants — evaluation of bioinformatics tools and development of a consensus strategy by Frousios, Kimon, Iliopoulos, Costas S., Schlitt, Thomas, Simpson, Michael A.

“…The study of DNA sequence variation has been transformed by recent advances in DNA sequencing technologies. Determination of the functional consequences of…”
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Efficient pattern matching in elastic-degenerate strings by Iliopoulos, Costas S., Kundu, Ritu, Pissis, Solon P.

“…Motivated by applications in bioinformatics and image searching, in what follows, we study the classic pattern matching problem in the context of…”
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IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences by Alamro, Hayam, Alzamel, Mai, Iliopoulos, Costas S, Pissis, Solon P, Watts, Steven

“…An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both…”
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Efficient Computation of Sequence Mappability by Charalampopoulos, Panagiotis, Iliopoulos, Costas S., Kociumaka, Tomasz, Pissis, Solon P., Radoszewski, Jakub, Straszyński, Juliusz

“…Sequence mappability is an important task in genome resequencing. In the ( k ,  m )-mappability problem, for a given sequence T of length n , the goal is to…”
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Special Issue of Algorithmica for the 28th London Stringology Days & London Algorithmic Workshop (LSD & LAW) by Alzamel, Mai, Iliopoulos, Costas S., Letsios, Dimitrios, Prezza, Nicola

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Covering problems for partial words and for indeterminate strings by Crochemore, Maxime, Iliopoulos, Costas S., Kociumaka, Tomasz, Radoszewski, Jakub, Rytter, Wojciech, Waleń, Tomasz

“…Indeterminate strings are a subclass of non-standard words having non-deterministic nature. In a classic string every position contains exactly one symbol—we…”
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Locating tandem repeats in weighted sequences in proteins by Zhang, Hui, Guo, Qing, Iliopoulos, Costas S

“…A weighted biological sequence is a string in which a set of characters may appear at each position with respective probabilities of occurrence. We attempt to…”
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Order-preserving indexing by Crochemore, Maxime, Iliopoulos, Costas S., Kociumaka, Tomasz, Kubica, Marcin, Langiu, Alessio, Pissis, Solon P., Radoszewski, Jakub, Rytter, Wojciech, Waleń, Tomasz

“…Kubica et al. [33] and Kim et al. [29] introduced order-preserving pattern matching: for a given text the goal is to find its factors having the same 'shape'…”
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Linear-time superbubble identification algorithm for genome assembly by Brankovic, Ljiljana, Iliopoulos, Costas S., Kundu, Ritu, Mohamed, Manal, Pissis, Solon P., Vayani, Fatima

“…DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and…”
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Fast algorithms for approximate circular string matching by Barton, Carl, Iliopoulos, Costas S, Pissis, Solon P

“…Circular string matching is a problem which naturally arises in many biological contexts. It consists in finding all occurrences of the rotations of a pattern…”
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Transcriptome activity of isochores during preimplantation process in human and mouse by Barton, Carl, Iliopoulos, Costas S., Pissis, Solon P., Arhondakis, Stilianos

“…This work investigates the role of isochores during preimplantation process. Using RNA‐seq data from human and mouse preimplantation stages, we created the…”
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Linear algorithm for conservative degenerate pattern matching by Crochemore, Maxime, Iliopoulos, Costas S., Kundu, Ritu, Mohamed, Manal, Vayani, Fatima

“…A degenerate symbolx˜ over an alphabet Σ is a non-empty subset of Σ, and a sequence of such symbols is a degenerate string. A degenerate string is said to be…”
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Hiding patients’ medical reports using an enhanced wavelet steganography algorithm in DICOM images by Ahmad, Mostafa A., Elloumi, Mourad, Samak, Ahmed H., Al-Sharafi, Ali M., Alqazzaz, Ali, Kaid, Monir Abdullah, Iliopoulos, Costas

“…In the latest years, there is an increasing emphasis on DICOM medical images, especially in digital medical images transmission to e-health services. Besides,…”
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On avoided words, absent words, and their application to biological sequence analysis by Almirantis, Yannis, Charalampopoulos, Panagiotis, Gao, Jia, Iliopoulos, Costas S, Mohamed, Manal, Pissis, Solon P, Polychronopoulos, Dimitris

“…The deviation of the observed frequency of a word from its expected frequency in a given sequence is used to determine whether or not the word is . This…”
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Global and local sequence alignment with a bounded number of gaps by Barton, Carl, Flouri, Tomáš, Iliopoulos, Costas S., Pissis, Solon P.

“…Pairwise sequence alignment techniques have gained renewed interest in recent years, primarily due to their applications in re-sequencing—the assembly of a…”
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Abelian borders in binary words by Christodoulakis, Manolis, Christou, Michalis, Crochemore, Maxime, Iliopoulos, Costas S.

“…In this article we study the appearance of abelian borders in binary words, a notion closely related to the abelian period of a word. We show how many binary…”
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Circular sequence comparison: algorithms and applications by Grossi, Roberto, Iliopoulos, Costas S, Mercas, Robert, Pisanti, Nadia, Pissis, Solon P, Retha, Ahmad, Vayani, Fatima

“…Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes…”
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Transcriptome map of mouse isochores by Arhondakis, Stilianos, Frousios, Kimon, Iliopoulos, Costas S, Pissis, Solon P, Tischler, German, Kossida, Sophia

“…The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression…”
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Efficient enumeration of non-equivalent squares in partial words with few holes by Charalampopoulos, Panagiotis, Crochemore, Maxime, Iliopoulos, Costas S., Kociumaka, Tomasz, Pissis, Solon P., Radoszewski, Jakub, Rytter, Wojciech, Waleń, Tomasz

“…A word of the form WW for some word W ∈ Σ ∗ is called a square. A partial word is a word possibly containing holes (also called don’t cares). The hole is a…”
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