GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
出版年份 2019 全文链接
标题
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
作者
关键词
-
出版物
GigaScience
Volume 8, Issue 12, Pages -
出版商
Oxford University Press (OUP)
发表日期
2019-12-06
DOI
10.1093/gigascience/giz150
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
- (2019) Milad Miladi et al. GigaScience
- CMV: visualization for RNA and protein family models and their comparisons
- (2018) Florian Eggenhofer et al. BIOINFORMATICS
- RNA secondary structure profiling in zebrafish reveals unique regulatory features
- (2018) Kriti Kaushik et al. BMC GENOMICS
- Bioconda: sustainable and comprehensive software distribution for the life sciences
- (2018) Björn Grüning et al. NATURE METHODS
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
- (2018) Enis Afgan et al. NUCLEIC ACIDS RESEARCH
- Practical Computational Reproducibility in the Life Sciences
- (2018) Björn Grüning et al. Cell Systems
- High-throughput determination of RNA structures
- (2018) Eric J. Strobel et al. NATURE REVIEWS GENETICS
- Integration of accessibility data from structure probing into RNA-RNA interaction prediction
- (2018) Milad Miladi et al. BIOINFORMATICS
- The identification and functional annotation of RNA structures conserved in vertebrates
- (2017) Stefan E. Seemann et al. GENOME RESEARCH
- IL4 and IL21 cooperate to induce the high Bcl6 protein level required for germinal center formation
- (2017) Stéphane Chevrier et al. IMMUNOLOGY AND CELL BIOLOGY
- Regulation of mRNA stability by CCCH-type zinc-finger proteins in immune cells
- (2017) Kazuhiko Maeda et al. INTERNATIONAL IMMUNOLOGY
- The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
- (2017) Björn A. Grüning et al. NUCLEIC ACIDS RESEARCH
- Ensembl 2018
- (2017) Daniel R Zerbino et al. NUCLEIC ACIDS RESEARCH
- Modeling RNA secondary structure folding ensembles using SHAPE mapping data
- (2017) Aleksandar Spasic et al. NUCLEIC ACIDS RESEARCH
- Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions
- (2017) Zasha Weinberg et al. NUCLEIC ACIDS RESEARCH
- Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
- (2017) Ioanna Kalvari et al. NUCLEIC ACIDS RESEARCH
- Identification and Characterization of a Class of MALAT1 -like Genomic Loci
- (2017) Bin Zhang et al. Cell Reports
- Advances and challenges in the detection of transcriptome-wide protein-RNA interactions
- (2017) Emily C. Wheeler et al. Wiley Interdisciplinary Reviews-RNA
- A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs
- (2016) Elena Rivas et al. NATURE METHODS
- Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
- (2016) Eric L Van Nostrand et al. NATURE METHODS
- Evolution to the rescue: using comparative genomics to understand long non-coding RNAs
- (2016) Igor Ulitsky NATURE REVIEWS GENETICS
- SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells
- (2016) Matthew J. Smola et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- ncRNA orthologies in the vertebrate lineage
- (2016) Miguel Pignatelli et al. Database-The Journal of Biological Databases and Curation
- RNA recognition by Roquin in posttranscriptional gene regulation
- (2016) Andreas Schlundt et al. Wiley Interdisciplinary Reviews-RNA
- Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution
- (2016) Katrina M. Kutchko et al. Wiley Interdisciplinary Reviews-RNA
- StructureFold: genome-wide RNA secondary structure mapping and reconstructionin vivo
- (2015) Yin Tang et al. BIOINFORMATICS
- SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
- (2015) Sebastian Will et al. BIOINFORMATICS
- Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams
- (2015) Peter Kerpedjiev et al. BIOINFORMATICS
- Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq
- (2015) Yiliang Ding et al. Nature Protocols
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway
- (2015) Yasuhiro Murakawa et al. Nature Communications
- Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species
- (2015) Hadas Hezroni et al. Cell Reports
- The potential of the riboSNitch in personalized medicine
- (2015) Amanda C. Solem et al. Wiley Interdisciplinary Reviews-RNA
- Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes
- (2014) Sean R. Eddy Annual Review of Biophysics
- ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search
- (2014) Ping Ge et al. BMC BIOINFORMATICS
- The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA
- (2014) Dazhi Tan et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Dynalign II: common secondary structure prediction for RNA homologs with domain insertions
- (2014) Yinghan Fu et al. NUCLEIC ACIDS RESEARCH
- NoFold: RNA structure clustering without folding or alignment
- (2014) Sarah A. Middleton et al. RNA
- Dissemination of scientific software with Galaxy ToolShed
- (2014) Daniel Blankenberg et al. GENOME BIOLOGY
- LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
- (2013) Sebastian Will et al. Algorithms for Molecular Biology
- Infernal 1.1: 100-fold faster RNA homology searches
- (2013) E. P. Nawrocki et al. BIOINFORMATICS
- Roquin Promotes Constitutive mRNA Decay via a Conserved Class of Stem-Loop Recognition Motifs
- (2013) Kathrin Leppek et al. CELL
- Structure-based whole-genome realignment reveals many novel noncoding RNAs
- (2013) S. Will et al. GENOME RESEARCH
- In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
- (2013) Yiliang Ding et al. NATURE
- Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
- (2013) Michael T Lovci et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions
- (2013) Zsuzsanna Sükösd et al. NUCLEIC ACIDS RESEARCH
- Widespread purifying selection on RNA structure in mammals
- (2013) Martin A. Smith et al. NUCLEIC ACIDS RESEARCH
- Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
- (2013) C. E. Hajdin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- GraphClust: alignment-free structural clustering of local RNA secondary structures
- (2012) Steffen Heyne et al. BIOINFORMATICS
- The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells
- (2012) T. Gutschner et al. CANCER RESEARCH
- GENCODE: The reference human genome annotation for The ENCODE Project
- (2012) J. Harrow et al. GENOME RESEARCH
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Global or local? Predicting secondary structure and accessibility in mRNAs
- (2012) Sita J. Lange et al. NUCLEIC ACIDS RESEARCH
- R- chie : a web server and R package for visualizing RNA secondary structures
- (2012) Daniel Lai et al. NUCLEIC ACIDS RESEARCH
- Making whole genome multiple alignments usable for biologists
- (2011) Daniel Blankenberg et al. BIOINFORMATICS
- R2R - software to speed the depiction of aesthetic consensus RNA secondary structures
- (2011) Zasha Weinberg et al. BMC BIOINFORMATICS
- Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
- (2010) Zasha Weinberg et al. GENOME BIOLOGY
- Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies
- (2009) Parvez Anandam et al. BIOINFORMATICS
- Bcl6 Mediates the Development of T Follicular Helper Cells
- (2009) R. I. Nurieva et al. SCIENCE
- RNAalifold: improved consensus structure prediction for RNA alignments
- (2008) Stephan H Bernhart et al. BMC BIOINFORMATICS
- Accurate SHAPE-directed RNA structure determination
- (2008) K. E. Deigan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
- (2007) E. Torarinsson et al. GENOME RESEARCH
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now