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A large-scale binding and functional map of human RNA-binding proteins
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- Salim Megat & Natalia Mora & Jason Sanogo & Olga Roman & Alberto Catanese & Najwa Ouali Alami & Axel Freischmidt & Xhuljana Mingaj & Hortense Calbiac & François Muratet & Sylvie Dirrig-Grosch & Stépha, 2023. "Integrative genetic analysis illuminates ALS heritability and identifies risk genes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Yichi Niu & Jiayi Luo & Chenghang Zong, 2024. "Single-cell total-RNA profiling unveils regulatory hubs of transcription factors," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Hannah E. Salapa & Patricia A. Thibault & Cole D. Libner & Yulian Ding & Joseph-Patrick W. E. Clarke & Connor Denomy & Catherine Hutchinson & Hashim M. Abidullah & S. Austin Hammond & Landon Pastushok, 2024. "hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS)," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Miquel Anglada-Girotto & Ludovica Ciampi & Sophie Bonnal & Sarah A. Head & Samuel Miravet-Verde & Luis Serrano, 2024. "In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Florian Krach & Judith Stemick & Tom Boerstler & Alexander Weiss & Ioannis Lingos & Stephanie Reischl & Holger Meixner & Sonja Ploetz & Michaela Farrell & Ute Hehr & Zacharias Kohl & Beate Winner & Ju, 2022. "An alternative splicing modulator decreases mutant HTT and improves the molecular fingerprint in Huntington’s disease patient neurons," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Zili Song & Shuang Zhou & Hongjiao Zhang & Nancy P. Keller & Berl R. Oakley & Xiao Liu & Wen-Bing Yin, 2023. "Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Wei Hu & Yangjun Wu & Qili Shi & Jingni Wu & Deping Kong & Xiaohua Wu & Xianghuo He & Teng Liu & Shengli Li, 2022. "Systematic characterization of cancer transcriptome at transcript resolution," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Aditya Kshirsagar & Svetlana Maslov Doroshev & Anna Gorelik & Tsviya Olender & Tamar Sapir & Daisuke Tsuboi & Irit Rosenhek-Goldian & Sergey Malitsky & Maxim Itkin & Amir Argoetti & Yael Mandel-Gutfre, 2023. "LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
- Michelle M. Kameda-Smith & Helen Zhu & En-Ching Luo & Yujin Suk & Agata Xella & Brian Yee & Chirayu Chokshi & Sansi Xing & Frederick Tan & Raymond G. Fox & Ashley A. Adile & David Bakhshinyan & Kevin , 2022. "Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Ziqi Ren & Wei Tang & Luxin Peng & Peng Zou, 2023. "Profiling stress-triggered RNA condensation with photocatalytic proximity labeling," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Xiangbin Ruan & Kaining Hu & Xiaochang Zhang, 2023. "PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Matvei Khoroshkin & Andrey Buyan & Martin Dodel & Albertas Navickas & Johnny Yu & Fathima Trejo & Anthony Doty & Rithvik Baratam & Shaopu Zhou & Sean B. Lee & Tanvi Joshi & Kristle Garcia & Benedict C, 2024. "Systematic identification of post-transcriptional regulatory modules," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Haofan Sun & Bin Fu & Xiaohong Qian & Ping Xu & Weijie Qin, 2024. "Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- David Wang & Mathieu Quesnel-Vallieres & San Jewell & Moein Elzubeir & Kristen Lynch & Andrei Thomas-Tikhonenko & Yoseph Barash, 2023. "A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Johanna Luige & Alexandros Armaos & Gian Gaetano Tartaglia & Ulf Andersson Vang Ørom, 2024. "Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Xianjun Dong & Yunfei Bai & Zhixiang Liao & David Gritsch & Xiaoli Liu & Tao Wang & Rebeca Borges-Monroy & Alyssa Ehrlich & Geidy E. Serrano & Mel B. Feany & Thomas G. Beach & Clemens R. Scherzer, 2023. "Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- JohnCarlo Kristofich & Christopher V. Nicchitta, 2023. "Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- Jorge Vaquero-Garcia & Joseph K. Aicher & San Jewell & Matthew R. Gazzara & Caleb M. Radens & Anupama Jha & Scott S. Norton & Nicholas F. Lahens & Gregory R. Grant & Yoseph Barash, 2023. "RNA splicing analysis using heterogeneous and large RNA-seq datasets," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- Sarah E. Harris & Maria S. Alexis & Gilbert Giri & Francisco F. Cavazos & Yue Hu & Jernej Murn & Maria M. Aleman & Christopher B. Burge & Daniel Dominguez, 2024. "Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Qiong Guo & Shidong Zhao & Rosario Francisco-Velilla & Jiahai Zhang & Azman Embarc-Buh & Salvador Abellan & Mengqi Lv & Peiping Tang & Qingguo Gong & Huaizong Shen & Linfeng Sun & Xuebiao Yao & Jinron, 2022. "Structural basis for Gemin5 decamer-mediated mRNA binding," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
- Timofey A. Karginov & Antoine Ménoret & Anthony T. Vella, 2022. "Optimal CD8+ T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Hisakatsu Sone & Tae Jin Lee & Byung Rho Lee & Dan Heo & Sekyung Oh & Sang-Ho Kwon, 2023. "MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Xinzhi Li & Kaixin Ding & Xueying Li & Bingchuan Yuan & Yuqin Wang & Zhicheng Yao & Shuaikang Wang & He Huang & Bolin Xu & Liwei Xie & Tuo Deng & Xiao-wei Chen & Zheng Chen, 2022. "Deficiency of WTAP in hepatocytes induces lipoatrophy and non-alcoholic steatohepatitis (NASH)," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Charles Limouse & Owen K. Smith & David Jukam & Kelsey A. Fryer & William J. Greenleaf & Aaron F. Straight, 2023. "Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
- Anna Knörlein & Chris P. Sarnowski & Tebbe Vries & Moritz Stoltz & Michael Götze & Ruedi Aebersold & Frédéric H.-T. Allain & Alexander Leitner & Jonathan Hall, 2022. "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Arashdeep Singh & Arati Rajeevan & Vishaka Gopalan & Piyush Agrawal & Chi-Ping Day & Sridhar Hannenhalli, 2022. "Broad misappropriation of developmental splicing profile by cancer in multiple organs," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Tamar Sapir & Aditya Kshirsagar & Anna Gorelik & Tsviya Olender & Ziv Porat & Ingrid E. Scheffer & David B. Goldstein & Orrin Devinsky & Orly Reiner, 2022. "Heterogeneous nuclear ribonucleoprotein U (HNRNPU) safeguards the developing mouse cortex," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Erika Schaudy & Kathrin Hölz & Jory Lietard & Mark M. Somoza, 2022. "Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
- Haoran Zhu & Yuning Yang & Yunhe Wang & Fuzhou Wang & Yujian Huang & Yi Chang & Ka-chun Wong & Xiangtao Li, 2023. "Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
- Ting Fu & Kofi Amoah & Tracey W. Chan & Jae Hoon Bahn & Jae-Hyung Lee & Sari Terrazas & Rockie Chong & Sriram Kosuri & Xinshu Xiao, 2024. "Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- Mariela Cortés-López & Laura Schulz & Mihaela Enculescu & Claudia Paret & Bea Spiekermann & Mathieu Quesnel-Vallières & Manuel Torres-Diz & Sebastian Unic & Anke Busch & Anna Orekhova & Monika Kuban &, 2022. "High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Jian Han & Omer An & Xi Ren & Yangyang Song & Sze Jing Tang & Haoqing Shen & Xinyu Ke & Vanessa Hui En Ng & Daryl Jin Tai Tay & Hui Qing Tan & Dennis Kappei & Henry Yang & Leilei Chen, 2022. "Multilayered control of splicing regulatory networks by DAP3 leads to widespread alternative splicing changes in cancer," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Scott D. Findlay & Lindsay Romo & Christopher B. Burge, 2024. "Quantifying negative selection in human 3ʹ UTRs uncovers constrained targets of RNA-binding proteins," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Luke Buerer & Nathaniel E. Clark & Anastasia Welch & Chaorui Duan & Allison J. Taggart & Brittany A. Townley & Jing Wang & Rachel Soemedi & Stephen Rong & Chien-Ling Lin & Yi Zeng & Adam Katolik & Jon, 2024. "The debranching enzyme Dbr1 regulates lariat turnover and intron splicing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Denis Torre & Nancy J. Francoeur & Yael Kalma & Ilana Gross Carmel & Betsaida S. Melo & Gintaras Deikus & Kimaada Allette & Ron Flohr & Maya Fridrikh & Konstantinos Vlachos & Kent Madrid & Hardik Shah, 2023. "Isoform-resolved transcriptome of the human preimplantation embryo," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
- Elsa Zacco & Owen Kantelberg & Edoardo Milanetti & Alexandros Armaos & Francesco Paolo Panei & Jenna Gregory & Kiani Jeacock & David J. Clarke & Siddharthan Chandran & Giancarlo Ruocco & Stefano Gusti, 2022. "Probing TDP-43 condensation using an in silico designed aptamer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Maya Ron & Igor Ulitsky, 2022. "Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Maciej Bak & Erik Nimwegen & Ian U. Kouzel & Tamer Gur & Ralf Schmidt & Mihaela Zavolan & Andreas J. Gruber, 2024. "MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Michelle Maurin & Mohammadreza Ranjouri & Cristina Megino-Luque & Justin Y. Newberg & Dongliang Du & Katelyn Martin & Robert E. Miner & Mollie S. Prater & Dave Keng Boon Wee & Barbara Centeno & Shondr, 2023. "RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Yocelyn Recinos & Dmytro Ustianenko & Yow-Tyng Yeh & Xiaojian Wang & Martin Jacko & Lekha V. Yesantharao & Qiyang Wu & Chaolin Zhang, 2024. "CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements," Nature Communications, Nature, vol. 15(1), pages 1-15, December.