Effective stratification of cancer patients on the basis of their molecular make-up is a key open challenge. Given the altered and heterogenous nature of cancer metabolism, we here propose to use the overall...
Read More »A comprehensive simulation study on classification of RNA-Seq data
RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as ...
Read More »tcgsaseq – variance component score test for time-course gene set analysis of longitudinal RNA-seq data
As gene expression measurement technology is shifting from microarrays to sequencing, the statistical tools available for their analysis must be adapted since RNA-seq data are measured as counts. It has been proposed to model RNA-seq counts as continuous variables using ...
Read More »The Lair – A resource for exploratory analysis of published RNA-Seq data
Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is typically not easily usable ...
Read More »Bringing RNA-Seq into Undergraduate Education
Virtual Workshop, June 2016 Cold Spring Harbor Laboratory’s DNA Learning Center (DNALC) invites you to apply to participate in a free 2-week online workshop for our NSF funded project, Infrastructure and Training to Bring Next-generation Sequence (NGS) Analysis Into Undergraduate ...
Read More »Predicting Protein Functions at the Isoform Level
Integrate isoform co-expression networks for protein isoform function prediction. Propose a novel hybrid method of multiple-instance and semi-supervised graph learning. Predict isoform-isoform interactions and discover isoform functional modules. Over the past few decades, many computational methods have been developed to ...
Read More »Quantitative analysis of bacterial transcriptomes with RNA-seq
RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features ...
Read More »A Comparison of Next Generation Sequencing Technologies for Transcriptome Assembly
De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental ...
Read More »IUTA – a tool for effectively detecting differential isoform usage from RNA-Seq data
Most genes in mammals generate several transcript isoforms that differ in stability and translational efficiency through alternative splicing. Such alternative splicing can be tissue- and developmental stage-specific, and such specificity is sometimes associated with disease. Thus, detecting differential isoform usage ...
Read More »SAT-Assembler – A Scalable and Accurate Targeted Gene Assembly Tool for Next-Generation Sequencing Data
Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, ...
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