Monther Alhamdoosh

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Negative correlation learning (NCL) aims to produce ensembles with sound generalization capability through controlling the disagreement among base learners’ outputs. Such a learning scheme is usually implemented by using feed-forward neural networks with error back-propagation algorithms (BPNNs). However, it suffers from slow convergence, local minima(More)
MOTIVATION Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and(More)
Ensemble learning aims to improve the generalization power and the reliability of learner models through sampling and optimization techniques. It has been shown that an ensemble constructed by a selective collection of base learners outperforms favorably. However, effective implementation of such an ensemble from a given learner pool is still an open(More)
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best(More)
The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential expression testing and pathway analysis with the results obtained informing future experiments and validation(More)
Transcriptional regulation mainly controls how genes are expressed and how cells behave based on the transcription factor (TF) proteins that bind upstream of the transcription start sites (TSSs) of genes. These TF DNA binding sites (TFBSs) are usually short (5-15 base pairs) and degenerate (some positions can have multiple possible alternatives).(More)
Our paper emphasizes the relevance of Extreme Learning Machine (ELM) in Bioinformatics applications by addressing the problem of predicting the disulfide connectivity from protein sequences. We test different activation functions of the hidden neurons and we show that for the task at hand the Radial Basis Functions are the best performing. We also show that(More)
Motivation Gene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE(More)
U nderstanding protein-DNA binding affinity is still a mystery for many transcription factors (TFs). Although several approaches have been proposed in the literature to model the DNA-binding specificity of TFs, they still have some limitations. Most of the methods require a cut-off threshold in order to classify a K-mer as a binding site (BS) and finding(More)
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