Journal article

  • “RNAelem: An Algorithm for Discovering Sequence-Structure Motifs in RNA Bound by RNA-Binding Proteins.” Miyake H, Kawaguchi RK, Kiryu H. Bioinformatics Advances, vbae144, 2024. [link]

  • “The transcriptional legacy of developmental stochasticity.” Ballouz S†, Kawaguchi RK†, Pena MT, Fischer S, Crow M, French L, Knight FM, Adams LB, Gillis J. Nature Communications, 14, 7226, 2023. [link] [bioRxiv]

  • “Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication.” Takizawa N*, Kawaguchi RK. Computational and Structural Biotechnology Journal, 21:5259-72, 2023. [link][bioRxiv]

  • “Learning single-cell chromatin accessibility profiles using meta-analytic marker genes.” Kawaguchi RK, Tang Z, Fischer S, Rajesh C, Tripathy R, Koo PK, Gillis J. Briefings in Bioinformatics, bbac541, 2022. [link] [bioRxiv]

  • “Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters.” Sheu YJ, Kawaguchi RK, Gillis J, Stillman B. eLife, 11:e84320, 2022. [link] [bioRxiv]

  • The list of older papers is available here.

Review

  • Kawaguchi RK and Kiryu H. RNA Secondary Structure Alteration Caused by Single Nucleotide Variants. In: RNA Structure Prediction. Methods in Molecular Biology, vol 2586. Humana, New York, 2023. [link]
  • Kawaguchi RK and Kiryu H. Genome-Wide RNA Secondary Structure Prediction. In: RNA Structure Prediction. Methods in Molecular Biology, vol 2586. Humana, New York, 2023. [link]

Book

  • RNA structure prediction Edited by Kawaguchi RK and Iwakiri J. Methods in molecular biology, Humana New York, 2023. [link]
  • The list goes on [here].

Presentation

  • List of presentations is available here