BMC Bioinformatics
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Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks
BMC Bioinformatics - Tập 21 - Trang 1-17 - 2020
Protein phosphorylation networks play an important role in cell signaling. In these networks, phosphorylation of a protein kinase usually leads to its activation, which in turn will phosphorylate its downstream target proteins. A phosphorylation network is essentially a causal network, which can be learned by causal inference algorithms. Prior efforts have applied such algorithms to data measuring...... hiện toàn bộ
On the contributions of topological features to transcriptional regulatory network robustness
BMC Bioinformatics - Tập 13 - Trang 1-12 - 2012
Because biological networks exhibit a high-degree of robustness, a systemic understanding of their architecture and function requires an appraisal of the network design principles that confer robustness. In this project, we conduct a computational study of the contribution of three degree-based topological properties (transcription factor-target ratio, degree distribution, cross-talk suppression) ...... hiện toàn bộ
Glycosylator: a Python framework for the rapid modeling of glycans
BMC Bioinformatics - Tập 20 - Trang 1-7 - 2019
Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiology of many living organisms. Most software for glycan modeling on a personal desktop compute...... hiện toàn bộ
Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features
BMC Bioinformatics - - 2014
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases
BMC Bioinformatics - Tập 6 Số 1
repo: an R package for data-centered management of bioinformatic pipelines
BMC Bioinformatics - Tập 18 - Trang 1-9 - 2017
Reproducibility in Data Analysis research has long been a significant concern, particularly in the areas of Bioinformatics and Computational Biology. Towards the aim of developing reproducible and reusable processes, Data Analysis management tools can help giving structure and coherence to complex data flows. Nonetheless, improved software quality comes at the cost of additional design and plannin...... hiện toàn bộ
CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments
BMC Bioinformatics - Tập 16 - Trang 1-8 - 2015
Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention. Herein, we present a bioinformatics tool, CompGO, for identifying Differentially Enriched Gene Ontologies, called...... hiện toàn bộ
Scaffold filling, contig fusion and comparative gene order inference
BMC Bioinformatics - Tập 11 - Trang 1-15 - 2010
There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to ...... hiện toàn bộ
Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences
BMC Bioinformatics - Tập 17 - Trang 1-16 - 2016
Recognizing the different functional parts of genes, such as promoters, translation initiation sites, donors, acceptors and stop codons, is a fundamental task of many current studies in Bioinformatics. Currently, the most successful methods use powerful classifiers, such as support vector machines with various string kernels. However, with the rapid evolution of our ability to collect genomic info...... hiện toàn bộ
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