Annotation

Proteomics Informed by Transcriptomics

rna-seq

With the recent advent of RNA-seq technology the proteomics community has begun to generate sample-specific protein databases for peptide and protein identification, an approach we call proteomics informed by transcriptomics (PIT). This approach has gained a lot of interest, particularly ...

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ROTS – reproducible RNA-Seq biomarker detector

rna-seq

Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between sample groups, however, still lacks well-defined best practices. Although a number of advanced statistical methods have ...

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PathwaySeq – Pathway analysis for RNA-Seq data

rna-seq

A variety of pathway/gene-set approaches have been proposed to provide evidence of higher-level biological phenomena in the association of expression with experimental condition or clinical outcome. Among these approaches, it has been repeatedly shown that resampling methods are far preferable ...

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Predicting Protein Functions at the Isoform Level

rna-seq

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 ...

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