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Neoplasm Proteins

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Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks.

Analytical biochemistry
Deep learning has been increasingly used to solve a number of problems with state-of-the-art performance in a wide variety of fields. In biology, deep learning can be applied to reduce feature extraction time and achieve high levels of performance. I...

Integrative Gene Selection on Gene Expression Data: Providing Biological Context to Traditional Approaches.

Journal of integrative bioinformatics
The advance of high-throughput RNA-Sequencing techniques enables researchers to analyze the complete gene activity in particular cells. From the insights of such analyses, researchers can identify disease-specific expression profiles, thus understand...

Multilayer network analysis of miRNA and protein expression profiles in breast cancer patients.

PloS one
MiRNAs and proteins play important roles in different stages of breast tumor development and serve as biomarkers for the early diagnosis of breast cancer. A new algorithm that combines machine learning algorithms and multilayer complex network analys...

A parsimonious 3-gene signature predicts clinical outcomes in an acute myeloid leukemia multicohort study.

Blood advances
Acute myeloid leukemia (AML) is a genetically heterogeneous hematological malignancy with variable responses to chemotherapy. Although recurring cytogenetic abnormalities and gene mutations are important predictors of outcome, 50% to 70% of AMLs harb...

Screening of disorders associated with osteosarcoma by integrated network analysis.

Bioscience reports
Osteosarcoma is a common malignant bone tumor in children and adolescents under the age of 20. However, research on the pathogenesis and treatment of osteosarcoma is still insufficient. In the present study, based on gene-phenotype correlation networ...

DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies.

Nucleic acids research
Although rapid progress has been made in computational approaches for prioritizing cancer driver genes, research is far from achieving the ultimate goal of discovering a complete catalog of genes truly associated with cancer. Driver gene lists predic...

System-level responses to cisplatin in pro-apoptotic stages of breast cancer MCF-7 cell line.

Computational biology and chemistry
Cisplatin ceases cell division and induces apoptosis in cancer cell lines. It is well established that cisplatin alters the expression of many genes involved in several cellular processes and pathways including transcription, p53 signaling pathway, a...

Identifying Cancer-Specific circRNA-RBP Binding Sites Based on Deep Learning.

Molecules (Basel, Switzerland)
Circular RNAs (circRNAs) are extensively expressed in cells and tissues, and play crucial roles in human diseases and biological processes. Recent studies have reported that circRNAs could function as RNA binding protein (RBP) sponges, meanwhile RBPs...