Research map: Meta-PseU: A Meta-Classifier for Robust Prediction of RNA Pseudouridine Modification Sites from Long Sequences

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  1. CD-HIT Suite: a web server for clustering and comparing biological sequences · Ying Huang · 2010 · 2788 citations · Cited by this paper
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  5. Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA · Schraga Schwartz · 2014 · 1060 citations · Cited by this paper
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  7. MODOMICS: a database of RNA modification pathways. 2021 update · Pietro Boccaletto · 2021 · 856 citations · Cited by this paper
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  11. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome · Xiaoyu Li · 2015 · 591 citations · Cited by this paper
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  13. pLogo: a probabilistic approach to visualizing sequence motifs · Joseph P. O’Shea · 2013 · 543 citations · Cited by this paper
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  15. RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data · Jiajia Xuan · 2017 · 470 citations · Cited by this paper
  16. Information bottleneck-driven Gaussian PID enables modality-level interpretability in multimodal survival prediction · 2026 · Related
  17. PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition · Wei Chen · 2014 · 439 citations · Cited by this paper
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  19. Stabilization of RNA stacking by pseudouridine · Darrell R. Davis · 1995 · 416 citations · Cited by this paper
  20. AI agents in drug discovery: A review of evolution, applications, and future directions · 2026 · Related
  21. RNA modifications in physiology and disease: towards clinical applications · Sylvain Delaunay · 2023 · 352 citations · Cited by this paper
  22. iRNA-PseU: Identifying RNA pseudouridine sites · Wei Chen · 2016 · 298 citations · Cited by this paper
  23. iLearnPlus:a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization · Zhen Chen · 2021 · 297 citations · Cited by this paper
  24. Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution · Vahid Khoddami · 2019 · 295 citations · Cited by this paper
  25. RNAcentral: a comprehensive database of non-coding RNA sequences · Anton I. Petrov · 2016 · 278 citations · Cited by this paper
  26. Regulation and Function of RNA Pseudouridylation in Human Cells · Erin K. Borchardt · 2020 · 260 citations · Cited by this paper
  27. iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition · Wang‐Ren Qiu · 2017 · 216 citations · Cited by this paper
  28. Pseudouridine: Still mysterious, but never a fake (uridine)! · Felix Spenkuch · 2014 · 211 citations · Cited by this paper
  29. Decoding pseudouridine: an emerging target for therapeutic development · Jonas Cerneckis · 2022 · 160 citations · Cited by this paper
  30. Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences · Zhen Chen · 2019 · 154 citations · Cited by this paper
  31. repRNA: a web server for generating various feature vectors of RNA sequences · Bin Liu · 2015 · 153 citations · Cited by this paper
  32. PseUI: Pseudouridine sites identification based on RNA sequence information · Jingjing He · 2018 · 125 citations · Cited by this paper
  33. Machine learning in bioinformatics: A brief survey and recommendations for practitioners · Harish Bhaskar · 2005 · 111 citations · Cited by this paper
  34. BERMP: a cross-species classifier for predicting m6A sites by integrating a deep learning algorithm and a random forest approach · Yu Huang · 2018 · 105 citations · Cited by this paper
  35. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications · Jiajia Xuan · 2023 · 105 citations · Cited by this paper
  36. DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology · Yuxin Zhang · 2022 · 98 citations · Cited by this paper
  37. RF-PseU: A Random Forest Predictor for RNA Pseudouridine Sites · Zhibin Lv · 2020 · 96 citations · Cited by this paper
  38. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications · Viktoriia A. Arzumanian · 2022 · 92 citations · Cited by this paper
  39. Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing · You Wu · 2024 · 92 citations · Cited by this paper

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