Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

Cited by (400)

Items 201–300 of 400

1. TCF3 mutually exclusive alternative splicing is controlled by long-range cooperative actions between hnRNPH1 and PTBP1
   Takashi Yamazaki, Lizhi Liu, James L. Manley · 2019 · RNA
2. Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial–Mesenchymal Transition
   Liang Fang, Li Zhang, Mengran Wang, Yuhao He, Jiao Yang, Zengjin Huang, Ying Tan, Ke Fang, Jun Li, Zhiyuan Sun et al. · 2024 · Cancer Research
3. GraphProt2: A graph neural network-based method for predicting binding sites of RNA-binding proteins
   Michael Uhl, Van Dinh Tran, Florian Heyl, Rolf Backofen · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
4. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing
   Jess Floro, Anqi Dai, Abigail Metzger, Alexandra Mora-Martin, Neil J. Ganem, Daniel Cifuentes, Ching-Shyi Peter Wu, Jasbir Singh Dalal, Shawn M. Lyons, Adam Thomas Labadorf et al. · 2021 · Nucleic Acids Research
5. Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis
   Florian Krach, Emily C. Wheeler, Martin Regensburger, Tom Boerstler, Holger Wend, Anthony Q. Vu, Ruth Wang, Stephanie Reischl, Karsten Boldt, Ranjan Batra et al. · 2022 · Acta Neuropathologica
6. Activation-Dependent TRAF3 Exon 8 Alternative Splicing Is Controlled by CELF2 and hnRNP C Binding to an Upstream Intronic Element
   Astrid-Solveig Schultz, Marco Preußner, Mario Bunse, Rotem Karni, Florian Heyd · 2016 · Molecular and Cellular Biology
7. Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control
   Marina Danilenko, Caroline Dalgliesh, Vittoria Pagliarini, Chiara Naro, Ingrid E. Ehrmann, Mikaël Feracci, Mahsa Kheirollahi Chadegani, Alison Jane Tyson-Capper, Gavin John Clowry, Philippe Fort et al. · 2016 · Nucleic Acids Research
8. Emerging roles of RNA – RNA interactions in transcriptional regulation
   Di Wang, Rong Ye, Zhaokui Cai, Yuanchao Xue · 2022 · Wiley Interdisciplinary Reviews - RNA
9. Widespread autogenous mRNA–protein interactions detected by CLIP-seq
   Thomas H Kapral, Fiona Farnhammer, Weihao Zhao, Zhi John Lu, Bojan Žagrović · 2022 · Nucleic Acids Research
10. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
    Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Andreas Grüning, Rolf Backofen · 2019 · GigaScience
11. MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer
    Maciej Bąk, Erik van Nimwegen, Ivan U. Kouzel, Tamer Gür, Ralf L. J. Schmidt, Mihaela Zavolan, Andreas J Gruber · 2024 · Nature Communications
12. An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons
    Timofei M. Ivanov, Dmitri Davidovich Pervouchine · 2018 · Genes
13. Transcription factor-like 5 is a potential DNA- and RNA-binding protein essential for maintaining male fertility in mice
    Weiya Xu, Yiyun Zhang, Dongdong Qin, Yiqian Gui, Shu Wang, Guihua Du, Fan Yang, Lufan Li, Shuiqiao Yuan, Mei Wang et al. · 2021 · Journal of Cell Science
14. Cell-Specific RNA Binding Protein Rbfox2 Regulates Ca_V2.2 mRNA Exon Composition and Ca_V2.2 Current Size
    Allen, Summer E., Toro, Cecilia P., Andrade, Arturo, López-Soto, Eduardo J., Denome, Sylvia, Lipscombe, Diane · 2017 · eneuro
15. Aberrant alternative splicing in cancer: Splicing events and their regulatory mechanisms (Review)
    Yaxuan Sun, Xiaohui Hu · 2024 · International Journal of Oncology
16. Alternative splicing of PBRM1 mediates resistance to PD-1 blockade therapy in renal cancer
    Namjoon Cho, Seung-Yeon Kim, Sung‐Gwon Lee, Chungoo Park, Sunkyung Choi, Eun-Mi Kim, Kee Kwang Kim · 2024 · The EMBO Journal
17. Genomewide m6A Mapping Uncovers Dynamic Changes in the m6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells
    Azime Akçaöz-Alasar, Özge Tüncel, Ayşe Bengisu Gelmez, Buket Sağlam, İpek Erdoğan, Bünyamin Akgül · 2022 · Cells
18. Epitranscriptomic technologies and analyses
    Xiaoyu Li, Liang‐Hu Qu, Jinran Lin, Jinying Peng, Jianhua Yang, Chengqi Yi, Yang Yu, Qiangfeng Cliff Zhang, Keren Zhou · 2020 · Science China Life Sciences
19. IRBIS: a systematic search for conserved complementarity
    Dmitri Davidovich Pervouchine · 2014 · RNA
20. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays
    Li, Bo, Tambe, Akshay, Aviran, Sharon, Pachter, Lior · 2017 · Cell Systems
21. How does precursor RNA structure influence RNA processing and gene expression?
    Austin Herbert, Abigail Hatfield, Lela Lackey · 2023 · Bioscience Reports
22. A network of DZF proteins controls alternative splicing regulation and fidelity
    Nazmul Haque, Alexander Will, Atlanta G. Cook, J. Robert Hogg · 2023 · Nucleic Acids Research
23. Unveiling the regulatory role of GRP7 in ABA signal-mediated mRNA translation efficiency regulation
    Jing Zhang, Wenna Shao, Yongxin Xu, Fa’an Tian, Jinchao Chen, Dongzhi Wang, Xuelei Lin, Chongsheng He, Xiaofei Yang, Dorothee Staiger et al. · 2025 · Nature Communications
24. Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts
    Marilyn Parra, Weiguo Zhang, Jonathan T. Vu, Mark A. DeWitt, John G. Conboy · 2020 · RNA
25. Global analysis of RNA-binding proteins identifies a positive feedback loop between LARP1 and MYC that promotes tumorigenesis
    Ng Desi, Qing Yun Tong, Velda Teh, Jia Jia Chan, Bin Zhang, Hossein Tabatabaeian, Hui Qing Tan, Katannya Kapeli, Wenhao Jin, Chun You Lim et al. · 2022 · Cellular and Molecular Life Sciences
26. Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder
    Calvin S. Leung, Shoshana J. Rosenzweig, Brian Yoon, Nicholas A. Marinelli, Ethan W. Hollingsworth, Abbie M. Maguire, Mara H. Cowen, Michael Schmidt, Jaime Imitola, Ece Dilber Gamsiz Uzun et al. · 2023 · Human Molecular Genetics
27. An encyclopedic regulatory and functional atlas of RNA interactomes
    Keren Zhou, Junhong Huang, Shurong Liu, Wujian Zheng, Shun Liu, Yinghao Xing, Yinan Cao, Yibo Chen, Xinping Hu, Li Cai et al. · 2026 · Nature Methods
28. CLIP-related methodologies and their application to retrovirology
    Paul D. Bieniasz, Sebla B. Kutluay · 2018 · Retrovirology
29. Role of pre-mRNA secondary structures in the regulation of alternative splicing
    П. М. Рубцов · 2016 · Molecular Biology
30. Hypoplastic Left Heart Syndrome: Signaling & Molecular Perspectives, and the Road Ahead
    Sayantap Datta, Wangjia Cao, Mikayla Skillman, Mingfu Wu · 2023 · International Journal of Molecular Sciences
31. Splicing regulation of GFPT1 muscle-specific isoform and its roles in glucose metabolisms and neuromuscular junction
    Paniz Farshadyeganeh, Mohammad Nazim, Ruchen Zhang, Bisei Ohkawara, Kazuki Nakajima, Mohammad Alinoor Rahman, Farhana Nasrin, Mikako Ito, Jun‐ichi Takeda, Kenji Ohe et al. · 2023 · iScience
32. Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP
    Zhuoyi Song, Bongmin Bae, S. Schnabl, Fei Yuan, Thareendra De Zoysa, Maureen V. Akinyi, Charlotte A. Le Roux, Karine Choquet, Amanda J. Whipple, Eric L. Van Nostrand · 2025 · Genome biology
33. The global Protein-RNA interaction map of ESRP1 defines a post-transcriptional program that is essential for epithelial cell function
    Natoya J. Peart, Jae Yeon Hwang, Mathieu Quesnel-Vallières, Matthew J. Sears, Yuequin Yang, Peter Stoilov, Yoseph Barash, Juw Won Park, Kristen W. Lynch, Russ P. Carstens · 2022 · iScience
34. CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals
    Sihyung Park, Seung Hyun Ahn, Eun Sol Cho, You Kyung Cho, Eun-Sook Jang, Sung Wook Chi · 2018 · Nucleic Acids Research
35. Decoding Abnormal Splicing Code in Human Diseases
    Kinji Ohno · 2015 · Journal of Investigative Genomics
36. Aberrant splicing in Huntington’s disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification
    Nguyen, Thai B., Miramontes, Ricardo, Chillon-Marinas, Carlos, Maimon, Roy, Vazquez-Sanchez, Sonia, Lau, Alice L., McClure, Nicolette R., England, Whitney E., Singha, Monika, Stocksdale, Jennifer T. et al. · 2023
37. Dual modes of ZFC3H1 confer selectivity in nuclear RNA sorting
    Jing Fan, Yimin Wang, Miaomiao Wen, Tong Deng, Kai Wu, Kunming Yan, Peixuan Jia, Yi Nian Zhu, Qinyu Liu, Hecun Zou et al. · 2024 · Molecular Cell
38. Computational approaches for the discovery of splicing regulatory RNA structures
    Ryan J. Andrews, Walter N. Moss · 2019 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
39. Post-transcriptional regulation of the transcriptional apparatus in neuronal development
    Mohammad Nazim · 2024 · Frontiers in Molecular Neuroscience
40. MicroRNA mechanisms instructing Purkinje cell specification
    Norjin Zolboot, Yao Xiao, Jessica X Du, Marwan M. Ghanem, Su Yeun Choi, Miranda J. Junn, Federico Zampa, Zeyi Huang, Ian J. MacRae, Giordano Lippi · 2023 · Neuron
41. Systematic identification of NF90 target RNAs by iCLIP analysis
    V. Lodde, M. Floris, R. Munk, J. Martindale, D. Piredda, C. M. Napodano, F. Cucca, S. Uzzau, K. Abdelmohsen, M. Gorospe et al. · 2022 · Scientific Reports
42. Mapping transcriptome‐wide protein‐RNA interactions to elucidate RNA regulatory programs
    Molly M. Hannigan, Leah L. Zagore, Donny D. Licatalosi · 2018 · Quantitative Biology
43. CLIP and complementary methods
    2021 · Nature Reviews Methods Primers
44. Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential
    Pengfei Bao, Taiwei Wang, Xiaofan Liu, Shaozhen Xing, Hanjin Ruan, Hongli Ma, Yuhuan Tao, Qing Zhan, Efres Belmonte‐Reche, Lizheng Qin et al. · 2025 · Genome biology
45. Bioinformatic tools for analysis of CLIP ribonucleoprotein data
    Supriyo De, Myriam Gorospe · 2016 · Wiley Interdisciplinary Reviews - RNA
46. Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis
    Florian Heyl, Daniel Maticzka, Michaël Uhl, Rolf Backofen · 2020 · GigaScience
47. KHSRP combines transcriptional and posttranscriptional mechanisms to regulate monocytic differentiation
    Jiayue Xu, Dongsheng Wang, Hongliu Ma, Xueying Zhai, Yue Huo, Yue Ren, Weiqian Li, Le Chang, Dongxu Lu, Yuehong Guo et al. · 2022 · Blood Science
48. Роль вторичных структур пре-мРНК в регуляции альтернативного сплайсинга
    П. М. Рубцов · 2016 · Molecular Biology
49. Molecular mechanisms of Eda‐mediated adaptation to freshwater in threespine stickleback
    Carlos E. Rodríguez‐Ramírez, Melanie Hiltbrunner, Verena Saladin, Stephanie Walker, Araxi O. Urrutia, Catherine L. Peichel · 2023 · Molecular Ecology
50. Unannotated splicing regulatory elements in deep intron space
    John G. Conboy · 2021 · Wiley Interdisciplinary Reviews - RNA
51. The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multipart RNA regulatory modules
    Parham Peyda, Chia-Ho Lin, Kelechi Onwuzurike, Douglas L. Black · 2025 · Genes & Development
52. Plasma Circular RNAs as Biomarkers for Breast Cancer
    Domenico Tierno, Gabriele Grassi, Fabrizio Zanconati, Barbara Dapas, Bruna Scaggiante · 2024 · Biomedicines
53. Improving CLIP-seq data analysis by incorporating transcript information
    Michaël Uhl, Van Dinh Tran, Rolf Backofen · 2020 · BMC Genomics
54. Spatial Correlation Statistics Enable Transcriptome-Wide Characterization of RNA Structure Binding
    Veronica F. Busa, Alexander V. Favorov, Elana Judith Fertig, Anthony K. L. Leung · 2020 · Cell Reports Methods
55. Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma
    Kameda-Smith, Michelle M., Zhu, Helen, Luo, En-Ching, Suk, Yujin, Xella, Agata, Yee, Brian, Chokshi, Chirayu, Xing, Sansi, Tan, Frederick, Fox, Raymond G. et al. · 2022 · Nature Communications
56. AVJ16 inhibits lung carcinoma by targeting IGF2BP1
    Nadav Wallis, Tehila Gershon, Sojod Shaaby, Froma Oberman, Myriam Grunewald, Deborah Duran, Amandeep Singh, Gilad Wolf Vainer, Vladimir S. Spiegelman, Arun Kumar Sharma et al. · 2025 · Oncogene
57. Transcriptome regulation by PARP13 in basal and antiviral states in human cells
    Veronica F. Busa, Yoshinari Ando, Stefan Aigner, Brian A. Yee, Gene Wei-Ming Yeo, Anthony K. L. Leung · 2024 · iScience
58. Alternative Splicing of the Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT) Is Regulated by RBFOX2 in Lymphoid Malignancies
    Amy M. Cooper, Curtis A. Nutter, Muge N. Kuyumcu‐Martinez, Casey W. Wright · 2022 · Molecular and Cellular Biology
59. PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks
    Jianan Lin, Yuping Zhang, Wayne N. Frankel, Zhengqing Ouyang · 2019 · PLoS Computational Biology
60. Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    Karine Choquet, Louis-Philippe Chaumont, Simon Bache, Autum R. Baxter‐Koenigs, L. Stirling Churchman · 2025 · Genome Research
61. An imbalance between proliferation and differentiation underlies the development of microRNA-defective pineoblastoma
    Claudette R. Fraire, Kavita K. Desai, Indumathy Jagadeeswaran, Uma A Obalapuram, Lindsay K. Mendyka, Veena Rajaram, Teja Sebastian, Yemin Wang, Kenan Onel, Jeon Lee et al. · 2025 · Genes & Development
62. ePRINT: exonuclease assisted mapping of protein-RNA interactions
    Sophie Hawkins, Alexandre Mondaini, Seema Chandramohan Namboori, Grady G. Nguyen, Gene Wei-Ming Yeo, Asif Javed, Akshay Bhinge · 2024 · Genome biology
63. RNA binding proteins in cardiovascular development and disease
    Sunil Kumar Verma, Muge N. Kuyumcu‐Martinez · 2024 · Current topics in developmental biology/Current Topics in Developmental Biology
64. A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration
    Dawei Meng, Qian Sheng Zheng, Xue Zhang, Xuejiao Piao, Li Luo, Yichang Jia · 2022 · Protein & Cell
65. PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data
    Sabrina Krakau, Hugues Richard, Annalisa Marsico · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
66. The RNA-binding Selectivity of the RGG/RG Motifs of hnRNP U is Abolished by Elements Within the C-terminal Intrinsically Disordered Region
    Otto A. Kletzien, Deborah S. Wuttke, Robert Batey · 2024 · Journal of Molecular Biology
67. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders
    Mei Yuan, Maya L. Gosztyla, Xinzhu Tan, Lara E. Dozier, Brent Wilkinson, Justin McKetney, John J. Y. Lee, Michael Chen, D. S. Tsai, Hema Kopalle et al. · 2025 · Cell Systems
68. PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy
    Yao Wei Lu, Zhuomin Liang, Kerry Dorr, Samantha Ruiz, Xiaoran Huang, Denise Fangnibo Hanvi, Sheri M. Juntilla, Gisela Beutner, Shuhan Lyu, Haipeng Guo et al. · 2026 · Nature Cardiovascular Research
69. Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP
    Christina Ernst, Julien Duc, Didier Trono · 2023 · Nucleic Acids Research
70. Cooperation and Competition of RNA Secondary Structure and RNA–Protein Interactions in the Regulation of Alternative Splicing
    Margarita A. Vorobeva, Dmitry Aleksandrovich Skvortsov, Dmitri Davidovich Pervouchine · 2024 · Acta Naturae
71. Identification of splice regulators of fibronectin-EIIIA and EIIIB by direct measurement of exon usage in a flow-cytometry based CRISPR screen
    Jessica A. Hensel, Brent D. Heineman, Amy L. Kimble, Evan R. Jellison, Bo Reese, Patrick A. Murphy · 2021 · Scientific Reports
72. Expression of RNA-binding protein Rbfox1l demarcates a restricted population of dorsal telencephalic neurons within the adult zebrafish brain
    Fengjun Ma, Zhiqiang Dong, Michael A. Berberoglu · 2019 · Gene Expression Patterns
73. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions
    Gene Wei-Ming Yeo, Joy S. Xiang, Jasmine Mueller, En‐Ching Luo, Brian Yee, Danielle Schafer, Jonathan Schmok, Frederick Tan, Katherine Rothamel, Rachael N. McVicar et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
74. Transcriptome and translatome profiling of Col-0 and grp7grp8 under ABA treatment in Arabidopsis
    Jing Zhang, Yongxin Xu, Jun Ying Xiao · 2024 · Scientific Data
75. An ALS-associated TARDBP mutation drives cryptic exon inclusion and RNA dysregulation
    Qi Zhang, Meng Liu, Xiaojuan Fan, N.Y. Chin, Yue Xu, Jessica Suh, Soukaina Amniouel, James Virga, Brothely Jones, Kaari L. Linask et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
76. NAT10 maintains stem cell homeostasis by mitigating mRNA decay through an ac4C-independent mechanism
    Weiqian Li, Yue Huo, Zhaoru Zhang, Yiyang Liu, Xinyue Qian, Jia Ouyang, Rao Gu, Chenxi Han, Shuo Li, Rui Su et al. · 2026 · Nature Cell Biology
77. Modular RNA interactions shape FXR1 condensates involved in mRNA localization and translation
    Jiabin Yang, Zhongyang Chen, Jiayin He, Binbin Zou, Yanmin Si, Yanni Ma, Jia Yu · 2025 · Nature Communications
78. Novel Rbfox2 isoforms associated with alternative exon usage in rat cortex and suprachiasmatic nucleus
    Lucy Partridge, David Carter · 2017 · Scientific Reports
79. Position-dependent effects of hnRNP A1/A2 in SMN1/2 exon7 splicing
    Jiaying Qiu, Ruobing Qu, Mengsi Lin, Jian Xu, Qingwen Zhu, Zhenyu Zhang, Junjie Sun · 2022 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
80. Differential microRNA editing may drive target pathway switching in human temporal lobe epilepsy
    Kelvin Lau, Thanh Ngoc Nguyen, Jaideep Kesavan, Elena Langa, Kevin Fanning, Gary P. Brennan, Amaya Sanz‐Rodriguez, Javier Villegas-Salmerón, Yan Yan, Morten Trillingsgaard Venø et al. · 2023 · Brain Communications
81. Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks
    Peter K. Koo, Matthew Ploenzke, P. Anand, Steffan B Paul, Antonio Majdandzic · 2020 · bioRxiv
82. Global changes in patterning, splicing and primate specific lncRNAs in autism brain
    Neelroop Parikshak, Vivek Swarup, T. Grant Belgard, Michael J. Gandal, Manuel Irimia, Virpi Leppä, Jennifer K. Lowe, Robert Johnson, Benjamin J. Blencowe, Steve Horvath et al. · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
83. RBFOX2: An RNA-binding protein with alternative splicing and non-alternative splicing regulatory functions
    Wei Wang, Yang Zhang, Siyi Liu, Shan Liao, Junyu He, Gengqiu Luo, Qian He, Yanhong Zhou · 2025 · Experimental and Molecular Pathology
84. TheThermus thermophilusDEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism
    Pascal Donsbach, Brian A. Yee, Dione L. Sánchez‐Hevia, José Berenguer, Stefan Aigner, Gene Wei-Ming Yeo, Dagmar Klostermeier · 2020 · RNA
85. Mouse nuclear RNAi-defective 2 promotes splicing of weak 5′ splice sites
    Matyáš Flemr, Michaela Schwaiger, Daniel Heß, Vytautas Iešmantavičius, Josip Ahel, Alex Tuck, Fabio Mohn, Marc Bühler · 2023 · RNA
86. Comparative RNA Genomics
    Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, Peter Florian Stadler · 2024 · Methods in molecular biology
87. RBFOX1 Regulates Calcium Signaling and Enhances SERCA2 Translation
    Sadiq Umar, Wuqiang Zhu, Fernando Souza-Neto, Ingrid K. Bender, Steven C. Wu, Chastity L. Healy, Timothy D. O’Connell, Jop H. van Berlo · 2025 · Cells
88. RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis
    Hyun Young Kim, Orel Mizrahi, Wonseok Lee, Sara Brin Rosenthal, Cuijuan Han, Brian A. Yee, Steven M. Blue, Jesiel Diaz, Jyotiprakash Jonnalagadda, Lena Annika Street et al. · 2026 · Journal of Clinical Investigation
89. Engineered RNA‐Binding Proteins: Studying and Controlling RNA Regulation
    Riley W. Sinnott, Yang Cao, Bryan C. Dickinson · 2024 · Israel Journal of Chemistry
90. A novel RNA-binding activity of ECD contributes to U5 snRNP stability and pre-mRNA splicing
    Mohsin Raza, Asher Rajkumar Rajan, Achyuth Kalluchi, Bhopal Mohapatra, Irfana Saleem, Benjamin B. Kennedy, Kishor K. Bhakat, Hamid Band, M. Jordan Rowley, Vimla Band · 2026 · Nucleic Acids Research
91. Peakhood: individual site context extraction for CLIP-seq peak regions
    Michaël Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen · 2021 · Bioinformatics
92. Full-Length Transcriptome Construction and Systematic Characterization of Virulence Factor-Associated Isoforms in Vairimorpha (Nosema) Ceranae
    Sijia Guo, He Zang, Xiaoyu Liu, Xin Jing, Zhitan Liu, Wende Zhang, Mengyi Wang, Yidi Zheng, Zhengyuan Li, Jianfeng Qiu et al. · 2024 · Genes
93. Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression
    Alessandro Quattrone, Erik Dassi · 2015 · Methods in molecular biology
94. GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins
    Wandi S. Zhu, Adam J. Litterman, Harshaan Sekhon, Robin Kageyama, Maya M. Arce, Kimberly E. Taylor, Wenxue Zhao, Lindsey A. Criswell, Noah Zaitlen, David J. Erle et al. · 2023 · Genome biology
95. omniCLIP: Bayesian identification of protein-RNA interactions from CLIP-Seq data
    Philipp Drewe-Boß, Hans‐Hermann Wessels, Uwe Ohler · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
96. Data Science Issues in Understanding Protein-RNA Interactions
    Anob M. Chakrabarti, Nejc Haberman, Arne Praznik, Nicholas M. Luscombe, Jernej Ule · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
97. Pyruvate Kinase M Links Glucose Availability to Protein Synthesis
    Nevraj S. Kejiou, Lena Ilan, Stefan Aigner, En‐Ching Luo, Ines Rabano, Nishani Rajakulendran, Hamed Shateri Najafabadi, Stéphane Angers, Gene Wei-Ming Yeo, Alexander F. Palazzo · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
98. Splicing factor SRSF1 expands the regulatory logic of microRNA expression
    Marija Dargyte, Julia Philipp, Christina Palka, Michael D. Stone, Jeremy R. Sanford · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
99. The YTHDF proteins shape the brain gene signatures of Alzheimer’s disease
    Shinya Tasaki, Denis R. Avey, Nicola A. Kearns, Chunjiang Yu, Sashini L De Tissera, Himanshu Vyas, Lin Cheng, Jishu Xu, Artemis Iatrou, Daniel J. Flood et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
100. Sequence based prediction of cell type specific microRNA binding and mRNA degradation for therapeutic discovery
     Bhargav Kanuparthi, Sara E. Pour, Scott D. Findlay, Omar Wagih, Jahir M. Gutierrez, Rory Gao, Jeff A. Wintersinger, Jiun-Nong Lin, Martino Gabra, Emma Bohn et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)