A survey of k-mer methods and applications in bioinformatics

Moeckel, Camille, Mareboina, Manvita, Konnaris, Maxwell A., Chan, Candace S.Y., Mouratidis, Ioannis, Montgomery, Austin, Chantzi, Nikol, Pavlopoulos, Georgios A., Georgakopoulos-Soares, Ilias·2024·Computational and Structural Biotechnology Journal

Cited by (139)

Items 101–139 of 139

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  5. R-loop Prediction Reveals Generalization Limits of DNA Foundation Models Beyond Regulatory Genomics
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  6. Unconditional de novo generation and functional validation of synthetic promoters with a diffusion model
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  7. KmerSignificance Score: A discriminative and biologically-informed framework for viral k-mer prioritization
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  10. Mining Negative Sequential Patterns to Improve Viral Genomic Feature Representation and Classification
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    Zijie Gu, Gang-Ao Wang, Ziyan Feng, Changzhi Sun, Shiliang Li, Kai Zhang, Honglin Li · 2026 · Molecular Pharmaceutics
  12. Bio-Cybersecurity Threat Detection: Identifying Trojan Payloads in DNA Sequences Using Optimized SVM Models
    D. Shankar, A. S. Azhakath, Sajeev J, Mahalakshmi T · 2026 · Results in Engineering
  13. Fast Iteration of Spaced k-mers
    L. Czech · 2026 · arXiv.org
  14. Composition and higher-order structure in nucleic acids sequenced from a chondrite
    Carmel Farage, George McDonald Church, Ido Bachelet · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  15. MetaBolt: A computationally efficient pipeline for the rapid recovery of metagenome-assembled genomes
    Muhammad Muneeb Nasir, Hajra Qayyum, Shu-Hui Song, Amjad Ali, Masood ur Rehman Kayani · 2026 · Comput. Biol. Chem.
  16. A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data
    Reza Khakvar, Girish Pulinkala, Maya Baghdy Sar, Jan Komorowski · 2025 · Physiological and Molecular Plant Pathology
  17. Prediction of gene expression levels in Saccharomyces cerevisiae based on chromatin accessibility using multiple machine learning models
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  18. Regions Enriched with Reverse Complement Triplets in Bacterial Genomes
    Eugene V. Korotkov · 2026 · International Journal of Molecular Sciences
  19. Transforming DNA Sequences into Musical Patterns Via A 3-mer Classification
    Abel Prayoga, E. Khatizah · 2026 · JURNAL Al-AZHAR INDONESIA SERI SAINS DAN TEKNOLOGI
  20. Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection
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  21. Integrated BSI bacteria identifier-on-chip using approximate k-mer matching
    Esteban Garzón, Victor Galindo, Yuval Harary, Adam Teman, L. Yavits · 2026 · Scientific Reports
  22. Quantum implementation of multi-pattern string matching for k-mer detection
    Christos Papalitsas, I. Mouratidis, Michail Patsakis, Evangelos Stogiannos, I. Georgakopoulos-Soares, G. Koulouras · 2025 · bioRxiv
  23. Predicting Enhancer DNA Utilizing $k$-mer Features and Multi-Headed CNN
    P. Barua, Faisal Ahmed, M. Azim, Mohammad Khairul Islam · 2025 · 2025 28th International Conference on Computer and Information Technology (ICCIT)
  24. A Machine Learning Framework for DNA Sequence–Based Disease Classification: Integrating Computational Genomics with Predictive Modeling in Healthcare
    Busani Sravani, Aragidda Srivalli, Boi Jahnavi, C. Meghana, B. Rajasri, Baddam Pranathi Reddy · 2025 · 2025 2nd International Conference on Artificial Intelligence for Innovations in Healthcare Industries (ICAIIHI)
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  26. SeqEmbedX: Combining LSTM and Transfer Learning for Cross-Domain Sequence Classification with K-mer and Word2vec
    Nishat Taaha, Sheikh Md. Rabiul Islam · 2025 · 2025 IEEE International Conference on Signal Processing, Information, Communication and Systems (SPICSCON)
  27. Evaluating machine learning approaches for host prediction using H3 influenza genomic data
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  28. Solving the gene classification problem with a novel Gene Space approach
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  29. Understanding the Impact of Individual Nucleotide on Oxford Nanopore Current Signals With Interpretable Prediction Models
    Yenan Wang, Zhixing Wu, Jia Meng · 2025 · Bioinformatics and Biology Insights
  30. Longitudinal TCR repertoires in ulcerative colitis patients show features distinguishing disease states
    Sabahat Rahman, M. Farah, Amanda Kwok, Jacob Varghese, Bei-Ya Xu, A. Daraie, Joseph L. Greenstein, Casey Overby Taylor, Nidhi Soley, A. Yan et al. · 2025 · bioRxiv
  31. ProGenFixer: an ultra-fast and accurate tool for correcting prokaryotic genome sequences using a mapping-free algorithm
    Lifu Song, Mei Wang, Xiao-Ping Liao, Zhen-Kun Shi, Ruo-Yu Wang, Hao-Ran Li, Lulu Liu, Bo-Tao He, Xiaomeng Ni, Jin-Shan Li et al. · 2025 · bioRxiv
  32. A comprehensive review on RNA subcellular localization prediction
    Ce-Ce Zhang, Xue-Huan Zhu, Nick B. Peterson, Jie-Qiong Wang, Shi-Biao Wan · 2025 · Briefings in Functional Genomics
  33. GCBLANE: A graph-enhanced convolutional BiLSTM attention network for improved transcription factor binding site prediction
    Jonas Chris Ferrao, Dickson Dias, Sweta Morajkar, Manisha Gokuldas Fal Dessai · 2025 · arXiv.org
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    Love Fadia, Vatsal Shah, Mohammad Hassanzadeh, Majid Ahmadi, Jonathan Wu · 2025 · International Conference on Bioinformatics & Computational Biology
  35. Cellular Activity of CQWW Nullomer-Derived Peptides
    S. Shave, Rebecka Isaksson, N. Phạm, Richard J. R. Elliott, John C. Dawson, Julius Soudant, N. Carragher, Manfred Auer · 2025 · ACS Omega
  36. A Novel Feature Fusion Method Based on RSCU and K-mer to Classify the SARS-Cov-2
    Fuqiang Ye, Jianhua Zhou, Hao Zhang, Lili Wang · 2024 · Academic Journal of Science and Technology
  37. PARMIK: PArtial Read Matching with Inexpensive K-mers
    Morteza Baradaran, Ryan M. Layer, Kevin Skadron · 2024 · bioRxiv
  38. Meta-Learning for Predictive Modeling of Antimicrobial Resistance in Dynamic Healthcare Environments
    Matsiko Ian Sezi, Carlos Mark Kasozi, Lusiba Mark Collins, Bizimaana Gad William, Josephine Nabukenya, Irene Arinaitwe, Agnes Rwashana Semwanga, Ggaliwango Marvin · 2026 · IEEE Access
  39. PyScale: A Curated Nucleotide Propensity-Scale Resource With Reproducible Profile Analysis and a Robust Profile-Level Divergence Index
    A. Chattopadhyay, Yeganeh Abdollahinejad, D. Flower · 2026 · IEEE Access