Now showing items 1-20 of 21

    • Accelerating genome analysis: a primer on an ongoing journey 

      Alser, M.; Zülal, Bingöl; Cali, D. S.; Kim, J.; Ghose, S.; Alkan, Can; Mutlu, Onur (IEEE, 2020)
      Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the ...
    • Apollo: A sequencing-technology-independent, scalable and accurate assembly polishing algorithm 

      Fırtına, C.; Kim, J. S.; Alser, M.; Şenol Cali, D.; Çiçek, A. Ercüment; Alkan, Can; Mutlu, Onur (Oxford University Press, 2020-03)
      Motivation: Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject’s genome), which is further ...
    • Author correction: a robust benchmark for detection of germline large deletions and insertions (Nature Biotechnology, (2020), 38, 11, (1347-1355) 

      Zook, J. M.; Hansen, N. F.; Olson, N. D.; Chapman, L.; Mullikin, J. C.; Xiao, C.; Sherry, S.; Koren, S.; Phillippy, A. M.; Boutros, P. C.; Sahraeian, S. M. E.; Huang, V.; Rouette, A.; Alexander, N.; Mason, C. E.; Hajirasouliha, I.; Ricketts, C.; Lee, J.; Tearle, R.; Fiddes, I. T.; Barrio, A. M.; Wala, J.; Carroll, A.; Ghaffari, N.; Rodriguez, O. L.; Bashir, A.; Jackman, S.; Farrell, J. J.; Wenger, A. M.; Alkan, Can; Söylev, A.; Schatz, M. C.; Garg, S.; Church, G.; Marschall, T.; Chen, K.; Fan, X.; English, A. C.; Rosenfeld, J. A.; Zhou, w.; Zhou, W.; Mills, R. E.; Sage, J. M.; Davis, J. R.; Kaiser, M. D.; Oliver, J. S.; Catalano, A. P.; Chaisson, M. J. P.; Spies, N.; Sedlazeck, F. J.; Salit, M. (Nature Research, 2020)
    • Automatic characterization of copy number polymorphism using high throughput sequencing 

      Alkan, Can (TÜBİTAK, 2020)
      Genome structural variation, broadly defined as alterations longer than 50 bp, are important sources for genetic variation among humans, including those that cause complex diseases such as autism, developmental delay, and ...
    • Building and improving reference genome assemblies 

      Steinberg, K. M.; Schneider, V. A.; Alkan, Can; Montague, M. J.; Warren, W. C.; Church, D. M.; Wilson, R. K. (IEEE, 2017-01)
      A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism. In the past four decades, there has been a surge of new sequencing ...
    • Can you really anonymize the donors of genomic data in today’s digital world? 

      Alser, Mohammed; Almadhoun, Nour; Nouri, Azita; Alkan, Can; Ayday, Erman (Springer, 2016-09)
      The rapid progress in genome sequencing technologies leads to availability of high amounts of genomic data. Accelerating the pace of biomedical breakthroughs and discoveries necessitates not only collecting millions of ...
    • Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools 

      Demir, Gülfem; Alkan, Can (Scientific and Technical Research Council of Turkey, 2019)
      Microsatellite polymorphism has always been a challenge for genome assembly and sequence alignment due to sequencing errors, short read lengths, and high incidence of polymerase slippage in microsatellite regions. Despite ...
    • Computational pan-genomics: status, promises and challenges 

      The Computational Pan-Genomics Consortium; Alkan, Can (Oxford University Press, 2018-01-01)
      Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of ...
    • Discovery of tandem and interspersed segmental duplications using high-throughput sequencing 

      Söylev, Arda; Le, T. M.; Amini, H.; Alkan, Can; Hormozdiari, F. (Oxford University Press, 2019-04)
      Motivation: Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of ...
    • Evaluation of genome scaffolding tools using pooled clone sequencin 

      Dal, Elif; Alkan, Can (Scientific and Technical Research Council of Turkey, 2018)
      DNA sequencing technologies hold great promise in generating information that will guide scientists to understand how the genome affects human health and organismal evolution. The process of generating raw genome sequence ...
    • Fast characterization of segmental duplications in genome assemblies 

      Numanagić, I.; Gökkaya, Alim S.; Zhang, L.; Berger, B.; Alkan, Can; Hach, F. (Oxford University Press, 2018)
      Motivation Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a ...
    • GenASM: a high-performance, low-power approximate string matching acceleration framework for genome sequence analysis 

      Şenol-Çalı, D.; Kalsi, G. S.; Bingöl, Zülal; Fırtına, C.; Subramanian, L.; Kim, J. S.; Ausavarungnirun, R.; Alser, M.; Gomez-Luna, J.; Boroumand, A.; Norion, A.; Scibisz, A.; Subramoneyon, S.; Alkan, Can; Ghose, S.; Mutlu, Onur (IEEE Computer Society, 2020)
      Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. To perform genome sequencing, devices extract ...
    • Hercules: a profile HMM-based hybrid error correction algorithm for long reads 

      Fırtına, Can; Bar-Joseph, Z.; Alkan, Can; Çicek, A. Ercüment (Oxford University Press, 2018)
      Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several types of studies require long and accurate reads. In such cases researchers often ...
    • Improving genome assemblies using multi-platform sequence data 

      Kavak, P.; Ergüner, B.; Üstek, D.; Yüksel, B.; Saǧıroǧlu, M. Ş.; Güngör, T.; Alkan, Can (Springer, 2015-09)
      Accurate de novo assembly using short reads generated by next generation sequencing technologies is still an open problem. Although there are several assembly algorithms developed for data generated with different sequencing ...
    • Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions 

      Cali, D. S.; Kim, J. S.; Ghose, S.; Alkan, Can; Mutlu, O. (Oxford University Press, 2018-04)
      Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge ...
    • Realizing the potential of blockchain technologies in genomics 

      Özercan, Halil İbrahim; İleri, A. M.; Ayday, Erman; Alkan, Can (Cold Spring Harbor Laboratory Press, 2018)
      Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to ...
    • A robust benchmark for detection of germline large deletions and insertions 

      Zook, J. M.; Hansen, N. F.; Olson, N. D.; Chapman, L.; Mullikin, J. C.; Xiao, C.; Sherry, S.; Koren, S.; Phillippy, A. M.; Boutros, P. C.; Sahraeian, S. M. E.; Huang, V.; Rouette, A.; Alexander, N.; Mason, C. E.; Hajirasouliha, I.; Ricketts, C.; Lee, J.; Tearle, R.; Fiddes, I. T.; Barrio, A. M.; Wala, J.; Carroll, A.; Ghaffari, N.; Rodriguez, O. L.; Bashir, A.; Jackman, S.; Farrell, J. J.; Wenger, A. M.; Alkan, Can; Söylev, A.; Schatz, M. C.; Garg, S.; Church, G.; Marschall, T.; Chen, K.; Fan, X.; English, A. C.; Rosenfeld, J. A.; Zhou, W.; Mills, R. E.; Sage, J. M.; Davis, J. R.; Kaiser, M. D.; Oliver, J. S.; Catalano, A. P.; Chaisson, M. J. P.; Spies, N.; Sedlazeck, F. J.; Salit, M. (Nature Research, 2020)
      New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and ...
    • Shouji: a fast and efficient pre-alignment filter for sequence alignment 

      Alser, Mohammed; Hassan, H.; Kumar, A.; Mutlu, Onur; Alkan, Can (Oxford University Press, 2019)
      The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design ...
    • Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer 

      Saatçi, Özge; Borgoni, S.; Akbulut, Özge; Durmuş, Selvi; Raza, Umar; Eyüpoğlu, Erol; Alkan, Can; Akyol, A.; Kütük, Ö.; Wiemann, S.; Şahin, Özgür (Nature Publishing Group, 2018)
      Trastuzumab-refractory, HER2 (human epidermal growth factor receptor 2)-positive breast cancer is commonly treated with trastuzumab emtansine (T-DM1), an antibody-drug conjugate of trastuzumab and the microtubule-targeting ...
    • VALOR2: characterization of large-scale structural variants using linked-reads 

      Karaoğlanoğlu, Fatih; Ricketts, C.; Ebren, Ezgi; Rasekh, M. E.; Hajirasouliha, I.; Alkan, Can (BioMed Central Ltd., 2020-03)
      Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, ...