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Regulation of dual specificity phosphatases in breast cancer during initial t...
Background 25% of breast cancer patients suffer from aggressive HER2-positive tumours that are characterised by overexpression of the HER2 protein or by its increased tyrosine... -
Pipeline design to identify key features and classify the chemotherapy respon...
Background: During the last decade, the interest to apply machine learning algorithms to genomic data has increased in many bioinformatics applications. Analyzing this type of... -
Significance evaluation in factor graphs
Background Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of... -
On the global CRISPR array behavior in class I systems.
Background Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial... -
Inferring miRNA sponge co-regulation of protein-protein interactions in human...
Background Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers. However, the co-regulation roles of miRNA... -
SCNS: a graphical tool for reconstructing executable regulatory networks from...
Background Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease... -
phylotree.js - a JavaScript library for application development and interacti...
Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks... -
Roles of alternative splicing in modulating transcriptional regulation
Background The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene... -
MultiDCoX: Multi-factor analysis of differential co-expression.
Background Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify... -
A systematic survey of centrality measures for protein-protein interaction ne...
AbstractBackgroundNumerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking... -
Data-driven human transcriptomic modules determined by independent component ...
Abstract Background Analyzing the human transcriptome is crucial in advancing precision medicine, and the plethora of over half a million human microarray samples in the Gene... -
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
Background Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research,... -
GTZ: a fast compression and cloud transmission tool optimized for FASTQ files
Background The dramatic development of DNA sequencing technology is generating real big data, craving for more storage and bandwidth. To speed up data sharing and bring data to... -
Updated and standardized genome-scale reconstruction of <i>Mycobacterium tube...
Background The efficacy of antibiotics against M. tuberculosis has been shown to be influenced by experimental media conditions. Investigations of M. tuberculosis growth in... -
Nanog induced intermediate state in regulating stem cell differentiation and ...
Background Heterogeneous gene expressions of cells are widely observed in self-renewing pluripotent stem cells, suggesting possible coexistence of multiple cellular states with... -
Canary: an atomic pipeline for clinical amplicon assays
Background High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report.... -
Systems healthcare: a holistic paradigm for tomorrow
Systems healthcare is a holistic approach to health premised on systems biology and medicine. The approach integrates data from molecules, cells, organs, the individual,... -
Visualizing histopathologic deep learning classification and anomaly detectio...
Background There is growing interest in utilizing artificial intelligence, and particularly deep learning, for computer vision in histopathology. While accumulating studies... -
A powerful parent-of-origin effects test for qualitative traits on X chromoso...
Background Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting... -
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular i...
[Background]: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively...
