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Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists

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Accurate splice site prediction using support vector machines

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A survey of best practices for RNA-seq data analysis

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Assessment of transcript reconstruction methods for RNA-seq

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Multiple reference genomes and transcriptomes for Arabidopsis thaliana

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RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

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Systematic evaluation of spliced alignment programs for RNA-seq data

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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

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Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome

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SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

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RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma

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Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis

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Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

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Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

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Methods to Study Splicing from High-Throughput RNA Sequencing Data

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Extensive cis -Regulatory Variation Robust to Environmental Perturbation in Arabidopsis

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Rail-RNA: scalable analysis of RNA-seq splicing and coverage

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FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

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MMR: a tool for read multi-mapper resolution

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Accurate detection of differential RNA processing

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Current methods for automated annotation of protein-coding genes

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DART: a fast and accurate RNA-seq mapper with a partitioning strategy

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Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays

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Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma

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Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes

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Next-Generation Sequencing (NGS) Tools and Impact in Plant Breeding

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RNA sequencing in post‐mortem human brains of neuropsychiatric disorders

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AStarix: Fast and Optimal Sequence-to-Graph Alignment

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Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

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Computational challenges, tools, and resources for analyzing co‐ and post‐transcriptional events in high throughput

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Detecting and visualizing gene fusions

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Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis

Sreedharan, V. T., Schultheiß, S. J., Jean, G., Kahles, A., Bohnert, R., Drewe, P., Mudrakarta, P. K., Görnitz, N., Zeller, G., & Rätsch, G. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt731 · Cited by 14 · see citing works

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

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Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana

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EpiMINE, a computational program for mining epigenomic data

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DNA methylation variation in Arabidopsis has a genetic basis and shows evidence of local adaptationPreprint

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RNA sequencing

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RNA Sequencing and its Applications in Cancer Diagnosis and Targeted Therapy

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CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data

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SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data

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The Analyses of Global Gene Expression and Transcription Factor Regulation

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Transcriptomics and proteomics in stem cell research

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AStarix: Fast and Optimal Sequence-to-Graph AlignmentPreprint

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mTim: Rapid and accurate transcript reconstruction from RNA-Seq dataPreprint

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Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data

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An SVM-based approach for discovering splicing junctions with RNA-Seq

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Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes

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Omics Era in Stem Cell Research: Data Integration of Multi-regulatory Layers

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Next‐Generation Sequencing in Cancer: Tools for Fusion Gene Detection

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Linear Programming and Integer Linear Programming in Bioinformatics

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High‐Performance Computing In High‐Throughput Sequencing

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Fast and Accurate Mapping of Next Generation Sequencing Data

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De novo RNA-seq-based Genome Annotation

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Fully Automated Genome Annotation with Deep RNA Sequencing

Miescher, F. (2010)

alternative splicing events from RNA-Seq data

Ong, C. S., & Rätsch, G. (2015)

Analysis of expression profile and gene variation via development of methods for Next Generation Sequencing data

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An Integrated Data Analysis Suite and Programming Framework for High-Throughput DNA Sequencing

Ott, F. (2013) · Max Planck Institute for Plasma Physics

Rätsch G: Optimal spliced alignments of short sequence reads

Bona, F. D., Ossowski, S., Schneeberger, K., & Rätsch, G. (2015)

Optimal spliced alignments of short sequence reads

Bona, F. D., Ossowski, S., Schneeberger, K., & Rätsch, G. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn300 · Cited by 90 · see citing works

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

Grant, G. R., Farkas, M. H., Pizarro, A., Lahens, N. F., Schug, J., Brunk, B. P., Stoeckert, C. J., Hogenesch, J. B., & Pierce, E. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr427 · Cited by 336 · see citing works

SpliceTAPyR — An Efficient Method for Transcriptome Alignment

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Dobin, E., Davis, C. A., Schlesinger, F. J., Drenkow, J., Zaleski, C., Jha, S., Chaisson, M., & Gingeras, T. (2012)