CAPRI enables comparison of evolutionarily conserved RNA interacting regions
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
CAPRI enables comparison of evolutionarily conserved RNA interacting regions
Authors
Keywords
-
Journal
Nature Communications
Volume 10, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-06-18
DOI
10.1038/s41467-019-10585-3
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)
- (2019) Rayner M. L. Queiroz et al. NATURE BIOTECHNOLOGY
- Purification of cross-linked RNA-protein complexes by phenol-toluol extraction
- (2019) Erika C. Urdaneta et al. Nature Communications
- Methods to study RNA–protein interactions
- (2019) Muthukumar Ramanathan et al. NATURE METHODS
- A brave new world of RNA-binding proteins
- (2018) Matthias W. Hentze et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins
- (2018) Daniel Maticzka et al. Nature Communications
- RKIP: A Key Regulator in Tumor Metastasis Initiation and Resistance to Apoptosis: Therapeutic Targeting and Impact
- (2018) Apostolos Zaravinos et al. Cancers
- The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest
- (2018) Jakob Trendel et al. CELL
- Structures of the human pre-catalytic spliceosome and its precursor spliceosome
- (2018) Xiechao Zhan et al. CELL RESEARCH
- Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification
- (2017) Meeli Mullari et al. JOURNAL OF PROTEOME RESEARCH
- Comprehensive Proteomic Investigation of Ebf1 Heterozygosity in Pro-B Lymphocytes Utilizing Data Independent Acquisition
- (2017) Yaarub R. Musa et al. JOURNAL OF PROTEOME RESEARCH
- MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
- (2017) Andy T Kong et al. NATURE METHODS
- Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap
- (2017) Alfredo Castello et al. Nature Protocols
- Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding
- (2017) Bagdeser A. Ozdilek et al. NUCLEIC ACIDS RESEARCH
- La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs
- (2017) Roni M Lahr et al. eLife
- The new (dis)order in RNA regulation
- (2016) Aino I. Järvelin et al. Cell Communication and Signaling
- The mRNA-bound proteome of the early fly embryo
- (2016) Hans-Hermann Wessels et al. GENOME RESEARCH
- LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein–RNA Cross-Linking Integrated into Proteome Discoverer
- (2016) Johannes Veit et al. JOURNAL OF PROTEOME RESEARCH
- High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells
- (2016) Chongsheng He et al. MOLECULAR CELL
- Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations
- (2016) Constantin Cretu et al. MOLECULAR CELL
- Comprehensive Identification of RNA-Binding Domains in Human Cells
- (2016) Alfredo Castello et al. MOLECULAR CELL
- Six alternative proteases for mass spectrometry–based proteomics beyond trypsin
- (2016) Piero Giansanti et al. Nature Protocols
- Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage
- (2016) Samar Alsafadi et al. Nature Communications
- Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila
- (2016) Vasiliy O. Sysoev et al. Nature Communications
- Serial interactome capture of the human cell nucleus
- (2016) Thomas Conrad et al. Nature Communications
- The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease
- (2016) Yalin Liao et al. Cell Reports
- Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights
- (2016) Amitha Sampath Kumar et al. PLoS One
- Systematic Discovery of Xist RNA Binding Proteins
- (2015) Ci Chu et al. CELL
- RNA Controls PolyQ Protein Phase Transitions
- (2015) Huaiying Zhang et al. MOLECULAR CELL
- Conserved mRNA-binding proteomes in eukaryotic organisms
- (2015) Ana M Matia-González et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- KEGG as a reference resource for gene and protein annotation
- (2015) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins
- (2015) Alfredo Castello et al. TRENDS IN ENDOCRINOLOGY AND METABOLISM
- The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs
- (2015) Benedikt M. Beckmann et al. Nature Communications
- Conserved mRNA-binding proteomes in eukaryotic organisms
- (2015) Ana M Matia-González et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
- (2014) Jürgen Cox et al. MOLECULAR & CELLULAR PROTEOMICS
- Biological functions of casein kinase 1 isoforms and putative roles in tumorigenesis
- (2014) Birgit Schittek et al. Molecular Cancer
- Ultrasensitive proteome analysis using paramagnetic bead technology
- (2014) C. S. Hughes et al. Molecular Systems Biology
- Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
- (2014) Katharina Kramer et al. NATURE METHODS
- A census of human RNA-binding proteins
- (2014) Stefanie Gerstberger et al. NATURE REVIEWS GENETICS
- MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins
- (2014) Emilio Potenza et al. NUCLEIC ACIDS RESEARCH
- The InterPro protein families database: the classification resource after 15 years
- (2014) Alex Mitchell et al. NUCLEIC ACIDS RESEARCH
- Methods for comprehensive experimental identification of RNA-protein interactions
- (2014) Colleen A McHugh et al. GENOME BIOLOGY
- iCLIP: Protein–RNA interactions at nucleotide resolution
- (2013) Ina Huppertz et al. METHODS
- Defining the RGG/RG Motif
- (2013) Palaniraja Thandapani et al. MOLECULAR CELL
- A compendium of RNA-binding motifs for decoding gene regulation
- (2013) Debashish Ray et al. NATURE
- Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS
- (2013) Hong Joo Kim et al. NATURE
- Structure and assembly of the NOT module of the human CCR4–NOT complex
- (2013) Andreas Boland et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Structure and RNA-binding properties of the Not1–Not2–Not5 module of the yeast Ccr4–Not complex
- (2013) Varun Bhaskar et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Pfam: the protein families database
- (2013) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Protein Complex-Based Analysis Framework for High-Throughput Data Sets
- (2013) A. Vinayagam et al. Science Signaling
- Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
- (2012) Masato Kato et al. CELL
- Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
- (2012) Alfredo Castello et al. CELL
- Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer
- (2012) Christian D. Kelstrup et al. JOURNAL OF PROTEOME RESEARCH
- Investigation of protein–RNA interactions by mass spectrometry—Techniques and applications
- (2012) Carla Schmidt et al. Journal of Proteomics
- The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts
- (2012) Alexander G. Baltz et al. MOLECULAR CELL
- An integrative approach to ortholog prediction for disease-focused and other functional studies
- (2011) Yanhui Hu et al. BMC BIOINFORMATICS
- De NovoSequencing and Homology Searching
- (2011) Bin Ma et al. MOLECULAR & CELLULAR PROTEOMICS
- PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification
- (2011) Jing Zhang et al. MOLECULAR & CELLULAR PROTEOMICS
- Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction
- (2011) Anh Tuân Phan et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold
- (2010) K. K. Singh et al. RNA
- Enrichment of protein-RNA crosslinks from crude UV-irradiated mixtures for MS analysis by on-line chromatography using titanium dioxide columns
- (2009) Florian Martin Richter et al. BIOPOLYMERS
- Universal sample preparation method for proteome analysis
- (2009) Jacek R Wiśniewski et al. NATURE METHODS
- Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
- (2009) Da Wei Huang et al. Nature Protocols
- MEME SUITE: tools for motif discovery and searching
- (2009) T. L. Bailey et al. NUCLEIC ACIDS RESEARCH
- Utility of formaldehyde cross-linking and mass spectrometry in the study of protein–protein interactions
- (2008) Brent W. Sutherland et al. JOURNAL OF MASS SPECTROMETRY
- MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
- (2008) Jürgen Cox et al. NATURE BIOTECHNOLOGY
- Dissecting protein–RNA recognition sites
- (2008) Ranjit Prasad Bahadur et al. NUCLEIC ACIDS RESEARCH
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now