Searching journal content for articles similar to Ekim et al. 33 (7): 1188.

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  1. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...similarity are included in the indexed database.Computational requirements comparisonWith the ever-increasing number of s in public databases comes the need for faster and more space-efficient methods to facilitate metagenomic read classification and profiling. Thus, we assessed the computational...
  2. Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
    • Rashid Al-Abri and
    • Gamze Gürsoy
    Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
    .... This is also why it is difficult to assemble repetitive parts of s using short reads (Treangen and Salzberg 2012). ScatTR overcomes this challenge by using Monte Carlo sampling to efficiently find the best alignment to decoy references.Our results show that our approach enables accurate estimation of TR...
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  3. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...precisely genotype these long expansions (Mousavi et al. 2019). In contrast, modern long-read sequencing (LRS) technologies, like Oxford Nanopore Technologies (ONT) nanopore sequencing with newer chemistry or Pacific Biosciences (PacBio) high-fidelity circular consensus sequencing (HiFi), can give accurate...
  4. Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
    • Fan Feng,
    • Sean Moran,
    • Anders S. Hansen,
    • Xiaotian Zhang,
    • and Jie Liu
    Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
    ...is performed with the efficient dynamic programming approach (Fig. 1C, bottom).In the end, the significance (P-value) of the stripe is determined through the calculation(4) Minimizing computational costDuring Quagga's statistical tests, the slowest step is calculating the Poisson P-values. Because...
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  5. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ...consumption, while41 reducing the sensitivity of decomposition results to parameter settings. These improvements enable more robust,42 accurate, and efficient analysis of TR reads and assemblies.43 1 1 1 1 AA A T T A A A Input Output AA A T T A A A Tandem Repeat Sequence: R AA A TT T STRs LTRs Template...
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  6. Method: Efficient minimizer orders for large values of k using minimum decycling sets
    • David Pellow,
    • Lianrong Pu,
    • Bariş Ekim,
    • Lior Kotlar,
    • Bonnie Berger,
    • Ron Shamir,
    • and Yaron Orenstein
    Genome Res. July 2023 33: 1154-1161; Published in Advance August 9, 2023, doi:10.1101/gr.277644.123
    ...sets. In Research in computational molecular biology, pp. 37–53. Springer International Publishing, Cambridge, MA. ↵Ekim B, Berger B, Chikhi R. 2021. Minimizer-space de Bruijn graphs: whole- assembly of long reads in minutes on a personal computer. Cell Syst 12: 958–968.e6. doi:10.1016/j.cels.2021...
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  7. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ...Accurate short-read alignment through r-index-based pan indexing Rahul Varki1,4, Massimiliano Rossi1,4, Eddie Ferro1, Marco Oliva1, Erik Garrison2, Ben Langmead3 and Christina Boucher1 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611...
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  8. Method: Highly accurate assembly polishing with DeepPolisher
    • Mira Mastoras,
    • Mobin Asri,
    • Lucas Brambrink,
    • Prajna Hebbar,
    • Alexey Kolesnikov,
    • Daniel E. Cook,
    • Maria Nattestad,
    • Julian Lucas,
    • Taylor S. Won,
    • Pi-Chuan Chang,
    • Andrew Carroll,
    • Benedict Paten,
    • Kishwar Shafin,
    • and and the Human Pangenome Reference Consortium
    Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
    ...was primarily used during the assembly stage. We plan to expand the DeepPolisher model to work on ONT reads in the future to address this fraction of errors. Around one-third of the residual errors lie in homopolymers and tandem repeats, sequences that are challenging even for highly accurate HiFi reads. We...
  9. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    ...this shortcoming, we developed Allo, a new approach to allocate multimapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multimapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced...
  10. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...help resolve repetitive and complex regions of the , they also highlight the throughput and coverage requirements needed to accurately resolve variant alleles across large populations using these platforms. At the time of this review, whole- long-read sequencing is more expensive than short-read...
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