Reducing storage requirements for biological sequence comparison

Roberts, Michael, Hayes, Wayne, Hunt, Brian R., Mount, Stephen M., Yorke, James A.·2004·Bioinformatics
DOI 10.1093/bioinformatics/bth408

Cited by (490)

Items 201–300 of 490

  1. GPU Acceleration of Advanced k-mer Counting for Computational Genomics
    Huiren Li, Anand Ramachandran, Deming Chen · 2018 · IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP)
  2. smsMap: mapping single molecule sequencing reads by locating the alignment starting positions
    Ze‐Gang Wei, Shao‐Wu Zhang, Fei Liu · 2020 · BMC Bioinformatics
  3. Strobemers: an alternative to k-mers for sequence comparison
    Kristoffer Sahlin · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  4. A survey of mapping algorithms in the long-reads era
    Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  5. LexicHash: sequence similarity estimation via lexicographic comparison of hashes
    Grant Greenberg, Aditya Narayan Ravi, Ilan Shomorony · 2023 · Bioinformatics
  6. The open-closed mod-minimizer algorithm
    Ragnar Groot Koerkamp, Daniel Liu, Giulio Ermanno Pibiri · 2025 · Algorithms for Molecular Biology
  7. Clustering the protein universe of life using DIAMOND DeepClust
    Benjamin Buchfink, Emile Barbe, Haim Ashkenazy, Klaus Reuter, John A. Kennedy, Hajk‐Georg Drost · 2026 · Nature Methods
  8. Multi-Function CIM Array for Genome Alignment Applications built with Fully Digital Flow
    Christian Lanius, Tobias Gemmeke · 2022 · IEEE Nordic Circuits and Systems Conference (NorCAS)
  9. Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data
    Prakash Chourasia, Sarwan Ali, Simone Ciccolella, Gianluca Della Vedova, Murray Patterson · 2022 · Lecture notes in computer science
  10. Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data
    Prakash Chourasia, Sarwan Ali, Simone Ciccolella · 2023 · Journal of Computational Biology
  11. Seeding with minimized subsequence
    Xiang Li, Qian Shi, Ke Chen · 2023 · Bioinformatics
  12. Sequence-Based Nanobody-Antigen Binding Prediction
    Usama Sardar, Sarwan Ali, Muhammad Sohaib Ayub, Muhammad Shoaib, Khurram Bashir, Imdadullah Khan, Murray Patterson · 2023 · Lecture notes in computer science
  13. Internal Pattern Matching Queries in a Text and Applications
    Tomasz Kociumaka, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń · 2024 · SIAM Journal on Computing
  14. Deconvolute individual genomes from metagenome sequences through short read clustering
    Kexue Li, Yakang Lu, Li Deng, Lili Wang, Lizhen Shi, Zhong Wang · 2020 · PeerJ
  15. GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads
    Nauman Ahmed, Tong Dong Qiu, Koen Bertels · 2020 · BMC Bioinformatics
  16. Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases
    Tao Tang, Jinyan Li · 2020 · Journal of Bioinformatics and Computational Biology
  17. Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
    Hongyu Zheng, Carl Kingsford, Guillaume Marçais · 2020 · Lecture notes in computer science
  18. Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach
    Arash Bayat, Nandan Deshpande, Marc Ronald Wilkins, Sri Parameswaran · 2018 · IEEE Transactions on Computational Biology and Bioinformatics
  19. An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees
    Fatemeh Almodaresi, Jamshed Khan, Sergey Madaminov · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  20. Genome assembly in the telomere-to-telomere era
    Heng Li, Richard Michael Durbin · 2023 · PubMed
  21. Locityper: targeted genotyping of complex polymorphic genes
    Timofey Prodanov, Elizabeth G. Plender, Guiscard Seebohm, Sven Guenther Meuth, Evan E. Eichler, Tobias Marschall · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  22. Taming large-scale genomic analyses via sparsified genomics
    Mohammed Alser, Julien Eudine, Onur Mutlu · 2025 · Nature Communications
  23. Benchmarking fungal species classification using Oxford Nanopore Technologies long-read ITS metabarcodes
    Abigail Graetz, Jinghang Feng, Alex Ringeri, Austin Bird, Duong Vu, Camille Truong, Benjamin Schwessinger · 2025 · Fungal Genetics and Biology
  24. kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes
    Giuseppe Defazio, Marco Antonio Tangaro, Graziano Pesole, Bruno Fosso · 2024 · Briefings in Bioinformatics
  25. Locality-sensitive bucketing functions for the edit distance
    Ke Chen, Mingfu Shao · 2023 · Algorithms for Molecular Biology
  26. Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs
    Ghanshyam Chandra, Chirag Jain · 2023 · Journal of Computational Biology
  27. WENGAN: Efficient and high quality hybrid de novo assembly of human genomes
    Alex Di Genova, Elena Buena‐Atienza, Stephan Ossowski, Marie‐France Sagot · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  28. Comprehensive benchmarking of metagenomic classification tools for long-read sequencing data
    Josip Marić, Krešimir Križanović, Sylvain Riondet, Niranjan Nagarajan, Mile Šikić · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  29. LJA: Assembling Long and Accurate Reads Using Multiplex de Bruijn Graphs
    Anton Bankevich, Andrey V. Bzikadze, Mikhail Kolmogorov, Dmitry Antipov, Pavel A. Pevzner · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  30. Accelerating long-read analysis on modern CPUs
    Saurabh Kalikar, Chirag Jain, Vasimuddin Md, Sanchit Misra · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  31. Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    Dmitry Antipov, Mikko Rautiainen, Sergey Nurk, Brian P. Walenz, Steven J. Solar, Adam M. Phillippy, Sergey Koren · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  32. HIV-1 M group subtype classification using deep learning approach
    Sihua Peng · 2024 · Computers in Biology and Medicine
  33. FastGA: fast genome alignment
    Eugene Wimberly Myers, Richard Michael Durbin, Chenxi Zhou · 2024 · Bioinformatics Advances
  34. GEM: Ultra-Efficient Near-Memory Reconfigurable Acceleration for Read Mapping by Dividing and Predictive Scattering
    Longlong Chen, Jianfeng Zhu, Guiqiang Peng, Mingxu Liu, Shaojun Wei, Leibo Liu · 2023 · IEEE Transactions on Parallel and Distributed Systems
  35. k -nonical space: sketching with reverse complements
    Guillaume Marçais, C.S. Elder, Carl Kingsford · 2024 · Bioinformatics
  36. Parallel Approach to Sliding Window Sums
    Roman Snytsar, Yatish Turakhia · 2020 · Lecture notes in computer science
  37. NvWa: Enhancing Sequence Alignment Accelerator Throughput via Hardware Scheduling
    Yewen Li, Xueqi Li, Ruihao Gao, Wanqi Liu, Guangming Tan · 2023 · IEEE International Symposium on High-Performance Computer Architecture (HPCA)
  38. ViralVectors: compact and scalable alignment-free virome feature generation
    Sarwan Ali, Prakash Chourasia, Zahra Tayebi, Babatunde Bello, Murray Patterson · 2023 · Medical & Biological Engineering & Computing
  39. PanPA : generation and alignment of panproteome graphs
    Fawaz Dabbaghie, Sanjay Kumar Srikakulam, Tobias Marschall, Olga V. Kalinina · 2023 · Bioinformatics Advances
  40. K-mer Counting: memory-efficient strategy, parallel computing and field of application for Bioinformatics
    Ming Xiao, Jiakun Li, Song Ki Hong · 2018 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  41. DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes
    Minh Hoang, Hongyu Zheng, Carl Kingsford · 2022 · Lecture notes in computer science
  42. Indexation de graphe de De Bruijn basee sur les minimisers
    Camille Marchet, Maël Kerbiriou, Antoine Limasset · 2019 · HAL
  43. SimdMinimizers: Computing random minimizers, fast
    Ragnar Groot Koerkamp, Igor Martayan · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  44. Fully Digital, Standard-Cell-Based Multifunction Compute-in-Memory Arrays for Genome Sequencing
    Christian Lanius, Tobias Gemmeke · 2023 · IEEE Transactions on Very Large Scale Integration (VLSI) Systems
  45. MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification
    Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar et al. · 2024 · Bioinformatics
  46. K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets
    Léa Vandamme, Bastien Cazaux, Antoine Limasset · 2024 · Bioinformatics Advances
  47. VACmap: an accurate long-read aligner for unraveling complex genomic rearrangements
    Hongyu Ding, Fritz Joachim Sedlazeck, Christos Proukakis, Caoimhe Morley, Marco Toffoli, Anthony H.V. Schapira, Zhirui Liao, Lianrong Pu, Shanfeng Zhu · 2026 · Nature Communications
  48. Data Set-Adaptive Minimizer Order Reduces Memory Usage in k -Mer Counting
    Dan Flomin, David Pellow, Ron Shamir A · 2022 · Journal of Computational Biology
  49. Efficient homology‐based annotation of transposable elements using minimizers
    Laura Natalia González-García, Daniela Lozano‐Arce, Juan Pablo Londoño, Romain Guyot, Jorge Duitama · 2023 · Applications in Plant Sciences
  50. ESKEMAP: exact sketch-based read mapping
    Tizian Schulz, Paul Medvedev · 2024 · Algorithms for Molecular Biology
  51. Parallelizing Big De Bruijn Graph Construction on Heterogeneous Processors
    Shuang Qiu, Qiong Luo · 2017 · IEEE International Conference on Distributed Computing Systems (ICDCS)
  52. A simple refined DNA minimizer operator enables 2-fold faster computation
    Chenxu Pan, Knut Reinert · 2024 · Bioinformatics
  53. A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome
    Zhong Wang, Harrison Ho, Rob S Egan et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  54. Efficient exact associative structure for sequencing data
    Camille Marchet, Maël Kerbiriou, Antoine Limasset · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Minimizer-space de Bruijn graphs
    Barış Ekim, Bonnie Berger, Rayan Chikhi · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Flexible seed size enables ultra-fast and accurate read alignment
    Kristoffer Sahlin · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Hepatic lipids in Reye-Johnson syndrome and in acute encephalopathy without fatty liver.
    Enrique Chaves Carballo, Ralph D. Ellefson, Manuel R. Gómez · 1976 · PubMed
  58. Matchtigs: minimum plain text representation of kmer sets
    Sebastian Schmidt, Shahbaz Khan, Jarno Alanko · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Efficient reconciliation of genomic datasets of high similarity
    Yoshihiro Shibuya, Djamal Belazzougui, Grégory Kucherov · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  60. Entropy predicts sensitivity of pseudorandom seeds
    Benjamin Dominik Maier, Kristoffer Sahlin · 2023 · Genome Research
  61. Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index
    Jens Zentgraf, Johanna Elena Schmitz, Sven Rahmann · 2025 · Bioinformatics
  62. Efficient seeding for error-prone sequences with SubseqHash2
    Xiang Li, Ke Chen, Mingfu Shao · 2025 · Bioinformatics
  63. Optimizing the Accuracy of Randomized Embedding for Sequence Alignment
    Yiqing Yan, Nimisha Chaturvedi, Raja Appuswamy · 2022 · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum
  64. Sketching and sampling approaches for fast and accurate long read classification
    Arun Das, Michael C. Schatz · 2022 · BMC Bioinformatics
  65. Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow
    Steven A. Eschrich, Xiaoqing Yu, Jamie K. Teer · 2023 · BMC Bioinformatics
  66. Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme
    Minh Hoang, Guillaume Marçais, Carl Kingsford · 2023 · Journal of Computational Biology
  67. Physlr: Next-Generation Physical Maps
    Amirhossein Afshinfard, Shaun D. Jackman, Johnathan Wong, Lauren Coombe, Justin Chu, Vladimir Nikolić, Gokce Dilek, Yaman Malkoç, René L. Warren, İnanç Birol · 2022 · DNA
  68. MiniScrub: de novo long read scrubbing using approximate alignment and deep learning
    Nathan LaPierre, Rob S Egan, Wei Wang, Zhong Wang · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  69. Haplotype-aware sequence alignment to pangenome graphs
    Ghanshyam Chandra, Daniel Gibney, Chirag Jain · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  70. OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier
    Simone Marini, Alexander Davis Barquero, Anisha Ashok Wadhwani, Jiang Bian, Jaime Ruiz, Christina A. Boucher, Mattia Prosperi · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  71. The mod-minimizer: a simple and efficient sampling algorithm for long k -mers
    Ragnar Groot Koerkamp, Giulio Ermanno Pibiri · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Accurate short-read alignment throughr-index-based pangenome indexing
    Rahul Varki, Massimiliano Rossi, Eddie Ferro, Marco Oliva, Erik P. Garrison, Ben Langmead, Christina A. Boucher · 2025 · Genome Research
  73. Accelerating RNA-Seq Quantification on a Real Processing-in-Memory System
    Liang-Chi Chen, Chien-Chung Ho, Yuan-Hao Chang · 2025 · IEEE Transactions on Computers
  74. Precise and scalable metagenomic profiling with sample-tailored minimizer libraries
    Johan Nyström-Persson, Nishad Bapatdhar, Samik Ghosh · 2025 · NAR Genomics and Bioinformatics
  75. On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis
    Yun William Yu · 2024 · Journal of Computational Biology
  76. Survey of Hardware Acceleration of Genomic Analysis
    Zhuren Liu, Shouzhe Zhang, Hui Zhao · 2024 · IEEE International Symposium on Embedded Multicore/Many-core Systems-on-Chip (MCSoC)
  77. Fractional hitting sets for efficient multiset sketching
    Timothé Rouzé, Igor Martayan, Camille Marchet · 2025 · Algorithms for Molecular Biology
  78. G^3SA: A GPU-Accelerated Gold Standard Genomics Library for End-to-End Sequence Alignment
    Yeejoo Han, Sunwoo Kim, Seongyeon Park, Jinho Lee · 2025 · International Conference on Supercomputing
  79. An Efficient Parallel Sketch-based Algorithm for Mapping Long Reads to Contigs
    Tazin Rahman, Oieswarya Bhowmik, Ananth Kalyanaraman · 2023 · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum
  80. PDB2Vec: Using 3D Structural Information for Improved Protein Analysis
    Sarwan Ali, Prakash Chourasia, Murray Patterson · 2023 · Lecture notes in computer science
  81. Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets
    Guillaume Marçais, Dan DeBlasio, Carl Kingsford · 2024 · Journal of Computational Biology
  82. Space-Efficient Indexes for Uncertain Strings
    Estéban Gabory, Chang Liu, Grigorios Loukides · 2024 · IEEE International Conference on Data Engineering (ICDE)
  83. Maptcha: an efficient parallel workflow for hybrid genome scaffolding
    Oieswarya Bhowmik, Tazin Rahman, Ananth Kalyanaraman · 2024 · BMC Bioinformatics
  84. Improving the efficiency of de Bruijn graph construction using compact universal hitting sets
    Yael Ben-Ari, Dan Flomin, Lianrong Pu · 2021 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  85. Memory Efficient De Bruijn Graph Construction
    Yang Li, Pegah Kamousi, Fangqiu Han · 2012 · arXiv (Cornell University)
  86. Construction of Sparse Suffix Trees and LCE Indexes in Optimal Time and Space
    Dmitry Kosolobov, Nikita Sivukhin · 2021 · arXiv (Cornell University)
  87. On Weighted K-Mer Dictionaries
    Giulio Ermanno Pibiri · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  88. Sequence aligners can guarantee accuracy in almost O ( m log n ) time: a rigorous average-case analysis of the seed-chain-extend heuristic
    Jim Shaw, Yun William Yu · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  89. Masked Minimizers: Unifying sequence sketching methods
    Minh Hoang, Guillaume Marçais, Carl Kingsford · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  90. mapquik: Efficient low-divergence mapping of long reads in minimizer space
    Barış Ekim, Kristoffer Sahlin, Paul Medvedev · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  91. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
    Timothé Rouzé, Igor Martayan, Camille Marchet, Antoine Limasset · 2023 · bioRxiv
  92. Memory-bound k -mer selection for large and evolutionarily diverse reference libraries
    Ali Osman Berk Şapcı, Siavash Mirarab · 2024 · Genome Research
  93. Hyper- k -mers: efficient streaming k -mers representation
    Igor Martayan, Lucas Robidou, Yoshihiro Shibuya · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  94. Finimizers: Variable-Length Bounded-Frequency Minimizers for $k$-mer Sets
    Jarno Alanko, Elena Biagi, Simon J. Puglisi · 2025 · IEEE Transactions on Computational Biology and Bioinformatics
  95. A 28-nm 239-bp/μJ Agile Pangenome Analysis Accelerator for Multi-Scheme Read Mapping
    Yichi Zhang, Jianfeng Zhu, Liangwei Li, Gang Zeng, Dibei Chen, Tairan Zhang, Yeyang Deng, Zhicheng Gong, Aoyang Zhang, Yang Liu et al. · 2025 · IEEE Journal of Solid-State Circuits
  96. Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data
    Jorge Díaz-Riaño, Jorge Duitama · 2025 · Methods in molecular biology
  97. CADM: Content addressable commodity off-the-shelf DRAM-based genome classifier
    Esteban Garzón, Alexander Fish, Leonid Yavits · 2026 · Journal of Systems Architecture
  98. Multi-context seeds enable fast and high-accuracy read mapping
    Ivan Tolstoganov, Marcel Martin, Nicolas Buchin, Kristoffer Sahlin · 2026 · Genome biology
  99. MSV: a modular structural variant caller that reveals nested and complex rearrangements by unifying breakends inferred directly from reads
    Markus R. Schmidt, Arne Kutzner · 2023 · Genome biology
  100. Seedability: optimizing alignment parameters for sensitive sequence comparison
    Lorraine A. K. Ayad, Rayan Chikhi, Solon P. Pissis · 2023 · Bioinformatics Advances