A survey of k-mer methods and applications in bioinformatics

Cites (290)

Items 201–281 of 281

1. Redkmer: An Assembly-Free Pipeline for the Identification of Abundant and Specific X-Chromosome Target Sequences for X-Shredding by CRISPR Endonucleases
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2. YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample
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3. Persistent minimal sequences of SARS-CoV-2
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4. Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes
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5. Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures
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6. Minimal Absent Words in Four Human Genome Assemblies
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7. Compact and evenly distributed k-mer binning for genomic sequences
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8. RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly
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9. Utilizing nullomers in cell-free RNA for early cancer detection
   Austin Montgomery, Georgios Christos Tsiatsianis, Ioannis Mouratidis, Candace S. Y. Chan, Μαρία Αθανασίου, Anastasios D. Papanastasiou, Verena Kantere, Nikos Syrigos, Ioannis Athanasios Vathiotis, Konstantinos Syrigos et al. · 2024 · Cancer Gene Therapy
10. Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis
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11. Targeted variant detection using unaligned RNA-Seq reads
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12. SEK: sparsity exploiting k-mer-based estimation of bacterial community composition
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13. A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes
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14. Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data.
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15. Computational Performance Assessment of k-mer Counting Algorithms
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16. Codon number shapes peptide redundancy in the universal proteome composition.
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17. Theoretical Computer Science
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18. iMOKA: k-mer based software to analyze large collections of sequencing data
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19. In the search of potential epitopes for Wuhan seafood market pneumonia virus using high order nullomers
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20. GECKO is a genetic algorithm to classify and explore high throughput sequencing data
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21. Quasi-prime peptides: identification of the shortest peptide sequences unique to a species
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22. Leveraging sequences missing from the human genome to diagnose cancer
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23. Kmerator Suite: design of specific k -mer signatures and automatic metadata discovery in large RNA-seq datasets
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24. Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter
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25. Reference-free transcriptome signatures for prostate cancer prognosis
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26. CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies
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27. Potential implications of availability of short amino acid sequences in proteins: an old and new approach to protein decoding and design.
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28. Molecular phylogenetics before sequences
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29. TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats
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30. Global pentapeptide statistics are far away from expected distributions
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31. CNEFinder: finding conserved non-coding elements in genomes
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32. Comparative analysis of de novo assemblers for variation discovery in personal genomes
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33. MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants
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34. CARE 2.0: reducing false-positive sequencing error corrections using machine learning
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35. Draft genome of the medicinal tea tree Melaleuca alternifolia
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36. A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome
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37. Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations
    Hojoon Lee, Ahmed Shuaibi, J. Bell, Dmitri S. Pavlichin, Hanlee P. Ji · 2020 · bioRxiv
38. KCOSS: an ultra-fast k-mer counter for assembled genome analysis
    Deyou Tang, Yucheng Li, Daqiang Tan, Juan Fu, Ye‐Lei Tang, Jiabin Lin, Rong Zhao, Hongli Du, Zhongming Zhao · 2021 · Bioinformatics
39. BinDash 2.0: New MinHash Scheme Allows Ultra-fast and Accurate Genome Search and Comparisons
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40. Peptide absent sequences emerging in human cancers.
    Georgios Christos Tsiatsianis, Candace S. Y. Chan, I. Mouratidis, Nikol Chantzi, Anna Maria Tsiatsiani, Nelson S. Yee, A. Zaravinos, Verena Kantere, I. Georgakopoulos-Soares · 2023 · European Journal of Cancer
41. Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history
    Ariane Bize, C. Midoux, M. Mariadassou, S. Schbath, P. Forterre, Violette Da Cunha · 2021 · BMC Genomics
42. Optimizing k-mer size using a variant grid search to enhance de novo genome assembly
    So-Young Cha, D. Bird · 2016 · Bioinformation
43. MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
    I. Georgakopoulos-Soares, Naman Jain, Jesse M. Gray, M. Hemberg · 2015 · bioRxiv
44. ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition
    David Koslicki, Saikat Chatterjee, Damon Shahrivar, A. Walker, S. Francis, L. Fraser, Mikko Vehkaperä, Y. Lan, J. Corander · 2015 · PLoS ONE
45. Identifying genetic variants associated with amphotericin B (AMB) resistance in Aspergillus fumigatus via k-mer-based GWAS
    Meng Chen, Guohui Shi, Yi Dai, Wenjing Fang, Qi Wu · 2023 · Frontiers in Genetics
46. The farther the better: Investigating how distance from human self affects the propensity of a peptide to be presented on cell surface by MHC class I molecules, the case of Trypanosoma cruzi
    D. Vergni, R. Gaudio, D. Santoni · 2020 · PLoS ONE
47. Embedded-AMP: A Multi-Thread Computational Method for the Systematic Identification of Antimicrobial Peptides Embedded in Proteome Sequences
    Germán Meléndrez Carballo, Karen Guerrero Vázquez, Luis A. García-González, G. Del Río, Carlos A. Brizuela · 2023 · Antibiotics
48. Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions
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49. Counting Kmers for Biological Sequences at Large Scale
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50. Denoising of Aligned Genomic Data
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51. keeSeek: searching distant non-existing words in genomes for PCR-based applications
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52. Improving CRISPR-Cas9 mediated genome integration in interspecific hybrid yeasts.
    N. Bennis, M. Kostanjšek, M. A. van den Broek, J. Daran · 2023 · New Biotechnology
53. Toward optimal fingerprint indexing for large scale genomics
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54. Mining K-mers of Various Lengths in Biological Sequences
    Jingsong Zhang, Jianmei Guo, Xiaoqing Yu, Xiang-Tian Yu, Weifeng Guo, Tao Zeng, Luo-Nan Chen · 2017 · International Symposium on Bioinformatics Research and Applications
55. Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches
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56. Illumina reads correction: evaluation and improvements
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57. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
    Timothé Rouzé, Igor Martayan, Camille Marchet, Antoine Limasset · 2023 · bioRxiv
58. Ultrafast prediction of somatic structural variations by filtering out reads matched to pan-genome k-mer sets
    Jang-il Sohn, Min-Hak Choi, Dohun Yi, A Vipin Menon, Yeon Jeong Kim, Junehawk Lee, Jung Woo Park, Sungkyu Kyung, Seung‐Ho Shin, Byunggook Na et al. · 2022 · Nature Biomedical Engineering
59. A high-quality genome assembly of Lactarius hatsudake strain JH5
    Ai-Rong Shen, Chen Luo, Yun Tan, Baoming Shen, Li-Na Liu, Ji-Lie Li, Zhu-Ming Tan, Liang-Bin Zeng · 2022 · G3
60. Taxonomic analysis of metagenomic data with kASA
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61. JACKIE: Fast Enumeration of Genome-Wide Single- and Multicopy CRISPR Target Sites and Their Off-Target Numbers
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62. kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species
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63. Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing
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64. Sequence-dependent DNA helical rise and nucleosome stability
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65. Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and Gnetum Species
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66. Mapping antibody binding using multiplexed epitope substitution analysis.
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67. The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure.
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68. KmerKeys: a web resource for searching indexed genome assemblies and variants
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69. Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment
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70. Preferential Nucleosome Occupancy at High Values of DNA Helical Rise
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71. Immunogenically optimized peptides derived from natural mutants of HIV CTL epitopes and peptide combinatorial libraries
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72. A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
    Andrew J. Annalora, Shawn T. O’Neil, Jeremy D. Bushman, James E. Summerton, Craig B. Marcus, Patrick L. Iversen · 2018 · Oncotarget
73. Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
    Giulia Guidi, Gabriel Raulet, Daniel S. Rokhsar, Leonid Oliker, Katherine Yelick, Aydın Buluç · 2022 · Proceedings of the International Conference on Parallel Processing
74. Nucleic Quasi-Primes: Identification of the Shortest Unique Oligonucleotide Sequences in a Species
    I. Mouratidis, Maxwell A. Konnaris, Nikol Chantzi, Candace S. Y. Chan, Austin Montgomery, Fotis A. Baltoumas, Michail Patsakis, M. Mareboina, Georgios A. Pavlopoulos, D. Chartoumpekis et al. · 2023 · bioRxiv
75. The determinants of the rarity of nucleic and peptide short sequences in nature
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76. Unique peptide signatures of SARS-CοV-2 virus against human proteome reveal variants’ immune escape and infectiveness
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77. Automated download and clean-up of family-specific databases for kmer-based virus identification
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78. Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis
    I. Mouratidis, Nikol Chantzi, U. Khan, Maxwell A. Konnaris, Candace S. Y. Chan, M. Mareboina, Camille Moeckel, I. Georgakopoulos-Soares · 2023 · BMC Genomics
79. Nullomer peptide increases immune cell infiltration and reduces tumor metabolism in triple negative breast cancer mouse model
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80. Uniquome: Construction and decoding of a novel proteomic atlas that contains new peptide entities
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81. Negative information for building phylogenies.
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