Genetics

Aneuploidy of chromosome 8 in circulating tumor cells correlates with prognosis in patients with advanced gastric cancer.

OBJECTIVE: Previous work indicated that aneuploidy of chromosome 8 in circulating tumor cells (CTCs) correlated with therapeutic efficacy for advanced gastric cancer (AGC) patients. In this follow-up study performed on the same population of AGC patients, we investigated whether and how aneuploidy of chromosome 8 in CTCs correlates with patients' clinical prognosis.

Marsdeniae tenacissimae extract (MTE) suppresses cell proliferation by attenuating VEGF/VEGFR2 interactions and promotes apoptosis through regulating PKC pathway in human umbilical vein endothelial cells.

Marsdeniae tenacissimae extract (MTE), commonly known as Xiao-Ai-Ping in China, is a traditional Chinese herb medicine capable of inhibiting proliferation and metastasis and boosting apoptosis in various cancer cells. However, little is known about the contribution of MTE towards tumor angiogenesis and the underlying mechanism. The present study aimed to evaluate the effects of MTE on the prolifer...

Identifying RNA 5-methylcytosine sites via pseudo nucleotide compositions.

RNA 5-methylcytosine (mC) plays an important role in numerous biological processes. Accurate identification of the mC site is helpful for a better und...

The effectiveness of argumentation in tutorial dialogues with an Intelligent Tutoring System for genetic risk of breast cancer.

BRCA Gist is an Intelligent Tutoring System that helps women understand issues related to genetic testing and breast cancer risk. In two laboratory ex...

Higher order methylation features for clustering and prediction in epigenomic studies.

MOTIVATION: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively as...

Complementary feature selection from alternative splicing events and gene expression for phenotype prediction.

MOTIVATION: A central task of bioinformatics is to develop sensitive and specific means of providing medical prognoses from biomarker patterns. Common...

A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions.

MOTIVATION: Gene-gene interaction (GGI) is one of the most popular approaches for finding and explaining the missing heritability of common complex tr...

DeepChrome: deep-learning for predicting gene expression from histone modifications.

MOTIVATION: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expressio...

Association of ATP-Binding Cassette Transporter (ABC) Gene Polymorphisms with Viral Load in Patients with Genotype 1 Hepatitis C Virus Infection.

BACKGROUND: ATP-binding cassette transporters (ABC) gene polymorphisms are associated with various biological functions, including hepatitis C virus (...

Protective effect of Yiguanjian decoction against DNA damage on concanavalin A-induced liver injury mice model.

OBJECTIVE: To investigate the inhibitory effect of Yiguanjian decoction (YD) on DNA damage in Concanavalin A (Con A)-induced liver injury mice model a...

Genotoxicity in lead treated human lymphocytes evaluated by micronucleus and comet assays.

Lead (Pb) which plays a significant role in modern industry is related to a broad range of physiological, biochemical, behavioural and genetical dysfu...

Generalized Multifactor Dimensionality Reduction (GMDR) Analysis of Drug-Metabolizing Enzyme-Encoding Gene Polymorphisms may Predict Treatment Outcomes in Indian Breast Cancer Patients.

BACKGROUND: Prediction of response and toxicity of chemotherapy can help personalize the treatment and choose effective yet non-toxic treatment regime...

Challenges and Opportunities for Increasing the Knowledge Base Related to Drug Biotransformation and Pharmacokinetics during Growth and Development.

It is generally acknowledged that there is a need and role for informative pharmacokinetic models to improve predictions and simulation as well as ind...

Convolutional neural network architectures for predicting DNA-protein binding.

MOTIVATION: Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. Ye...

What is information?

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotid...

GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.

Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial ge...

Using Semantic Similarities and csbl.go for Analyzing Microarray Data.

Cellular phenotypes result from the combined effect of multiple genes, and high-throughput techniques such as DNA microarrays and deep sequencing allo...

KNOWLEDGE-ASSISTED APPROACH TO IDENTIFY PATHWAYS WITH DIFFERENTIAL DEPENDENCIES.

We have previously developed a statistical method to identify gene sets enriched with condition-specific genetic dependencies. The method constructs g...

A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping.

Many single nucleotide polymorphisms (SNPs) for complex genetic diseases are genotyped by polymerase chain reaction-restriction fragment length polymo...

Optimization of the Production of Extracellular Polysaccharide from the Shiitake Medicinal Mushroom Lentinus edodes (Agaricomycetes) Using Mutation and a Genetic Algorithm-Coupled Artificial Neural Network (GA-ANN).

Exopolysaccharide (EPS) production by a strain of Lentinus edodes was studied via the effects of treatments with ultraviolet (UV) irradiation and acri...