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Existing bioinformatics tools for the quantitation of post-translational modifications
(Springer, 2012-01)
Mass spectrometry (MS)-based proteomics, by itself, is a vast and complex area encompassing various mass spectrometers, different spectra, and search result representations. When the aim is quantitation performed in different ...
Systematic computational analysis of potential rnai regulation in toxoplasma gondii
(IEEE, 2010)
RNA interference (RNAi) is the mechanism through which RNA interferes with the production of other RNAs in a sequence specific manner. Micro RNA (miRNA) is a type of RNA which is transcribed as pri-miRNAs and processed to ...
Relative protein quantitation with post translational modifications in mass spectrometry based proteomics
(IEEE, 2010)
Mass spectrometry has become the tool of choice for most investigations in proteomics. Identification of proteins from complex mixtures has long been achieved and is now routinely used in countless high throughput studies. ...
Feature selection for microRNA target prediction comparison of one-class feature selection methodologies
(SciTePress, 2016)
Traditionally, machine learning algorithms build classification models from positive and negative examples. Recently, one-class classification (OCC) receives increasing attention in machine learning for problems where the ...
De novo markup language, a standard to represent de novo sequencing results from MS/MS data
(IEEE, 2012)
Proteomics is the study of the proteins that can be derived from a genome. For the identification and sequencing of proteins, mass spectrometry has become the tool of choice. Within mass spectrometry-based proteomics, ...
Comparison of four Ab initio MicroRNA prediction tools
(SciTePress, 2013)
MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by ...
Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches
(IEEE, 2013)
Proteomics is currently driven by mass spectrometry. For the analysis of tandem mass spectra many computational algorithms have been proposed. There are two approaches, one which assigns a peptide sequence to a tandem mass ...
Removing contamination from genomic sequences based on vector reference libraries
(IEEE, 2012)
DNA is often sequenced after being cloned into a vector since this provides the possibility for using standard primers and removes the need to develop custom primers. In this way a certain amount of vector is sequenced ...
Data mining for microrna gene prediction: On the impact of class imbalance and feature number for microrna gene prediction
(IEEE, 2013)
MicroRNAs (miRNAs) are small, non-coding RNAs which are involved in the posttranscriptional modulation of gene expression. Their short (18-24) single stranded mature sequences are involved in targeting specific genes. It ...
Distinguishing between microRNA targets from diverse species using sequence motifs and K-mers
(SciTePress, 2017-02)
A disease phenotype is often due to dysregulation of gene expression. Post-translational regulation of protein abundance by microRNAs (miRNAs) is, therefore, of high importance in, for example, cancer studies. MicroRNAs ...
