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Saccharomyces cerevisiae Proteins

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[Enhancement of Coprinus cinereus peroxidase in Pichia pastoris by co-expression chaperone PDI and Ero1].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
The 1,095 bp gene encoding peroxidase from Coprinus cinereus was synthesized and integrated into the genome of Pichia pastoris with a highly inducible alcohol oxidase. The recombinant CiP (rCiP) fused with the a-mating factor per-pro leader sequence ...

Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks.

BMC bioinformatics
BACKGROUND: The identification of protein functional modules would be a great aid in furthering our knowledge of the principles of cellular organization. Most existing algorithms for identifying protein functional modules have a common defect -- once...

Protein complex detection in PPI networks based on data integration and supervised learning method.

BMC bioinformatics
BACKGROUND: Revealing protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, which makes it possible to predict...

Exploiting ontology graph for predicting sparsely annotated gene function.

Bioinformatics (Oxford, England)
MOTIVATION: Systematically predicting gene (or protein) function based on molecular interaction networks has become an important tool in refining and enhancing the existing annotation catalogs, such as the Gene Ontology (GO) database. However, functi...

Semi-supervised prediction of gene regulatory networks using machine learning algorithms.

Journal of biosciences
Use of computational methods to predict gene regulatory networks (GRNs) from gene expression data is a challenging task. Many studies have been conducted using unsupervised methods to fulfill the task; however, such methods usually yield low predicti...

Genome-Wide Detection and Analysis of Multifunctional Genes.

PLoS computational biology
Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular...

Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences.

BioMed research international
We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein s...

Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.

BMC bioinformatics
BACKGROUND: A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly con...

Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast.

Nucleic acids research
Understanding telomere length maintenance mechanisms is central in cancer biology as their dysregulation is one of the hallmarks for immortalization of cancer cells. Important for this well-balanced control is the transcriptional regulation of the te...

Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus.

Traffic (Copenhagen, Denmark)
The peroxisomal targeting signal type 1 (PTS1) is a seemingly simple peptide sequence at the C-terminal end of most peroxisomal matrix proteins. PTS1 can be described as a tripeptide with the consensus motif [S/A/C] [K/R/H] L. However, this descripti...