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Revision as of 09:06, 3 October 2011

Citation Data

This page provides data on how frequently MolMovDB-related work by the Gerstein lab has been cited in the literature. Note that it was last updated in June 2011.

Paper Title	Year Published	No. Times Cited (as of 6/2011)
3V: cavity, channel and cleft volume calculator and extractor	2011	The aggregation and correlation toolbox (ACT) is an aggregation and correlation toolbox for analyses of genome tracks.
FusionSeq	2010	A computational framework for detecting chimeric transcripts from paired-end RNA-seq experiments. It includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and provides a ranked list of fusion-transcript candidates that can be further evaluated via experimental methods. FusionSeq also contains a module to identify exact sequences at breakpoint junctions.
IQseq	2010	A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
RSEQtools	2010	A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.