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Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static netw...
Although principal component analysis (PCA) is widely used for the dimensional reduction of biomedical data, interpretation of PCA results remains daunting. Most existing interpretation methods attempt to expl...
Host genetic variability has been implicated in chemotherapy-induced peripheral neuropathy (CIPN). A dose-limiting toxicity for chemotherapy agents, CIPN is also a debilitating condition that may progress to c...
Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. It is highly prevalent and is characterized by symptoms including odor, discharge and irritation. No single microbe has been found t...
Biological data mining is a powerful tool that can provide a wealth of information about patterns of genetic and genomic biomarkers of health and disease. A potential disadvantage of data mining is volume and ...
Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties tha...
Larger variation exists in epigenomes than in genomes, as a single genome shapes the identity of multiple cell types. With the advent of next-generation sequencing, one of the key problems in computational epi...
Taxanes are naturally occurring compounds which belong to a powerful group of chemotherapeutic drugs with anticancer properties. Their current use, clinical efficacy, and unique mechanism of action indicate th...
The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray ...
In genome-wide studies, hundreds of thousands of hypothesis tests are performed simultaneously. Bonferroni correction and False Discovery Rate (FDR) can effectively control type I error but often yield a high ...
Biorepositories linked to de-identified electronic medical records (EMRs) have the potential to complement traditional epidemiologic studies in genotype-phenotype studies of complex human diseases and traits. ...
Accurate identification of linear B-cell epitopes plays an important role in peptide vaccine designs, immunodiagnosis, and antibody productions. Although several prediction methods have been reported, unsatisf...
Cancer is the second leading cause of death around the world after cardiovascular diseases. Over the past decades, various data mining studies have tried to predict the outcome of cancer. However, only a few r...
Drug-drug interactions (DDIs) are a major contributing factor for unexpected adverse drug events (ADEs). However, few of knowledge resources cover the severity information of ADEs that is critical for prioriti...
To facilitate the implementation of the Family Smoking Prevention and Tobacco Control Act of 2009, the Federal Drug Agency (FDA) Center for Tobacco Products (CTP) has identified research priorities under the u...
One of the most challenging tasks in genomic analysis nowadays is metagenomics. Biomedical applications of metagenomics give rise to datasets containing hundreds and thousands of samples from various body site...
Pharmacogenomics (PGx) as an emerging field, is poised to change the way we practice medicine and deliver health care by customizing drug therapies on the basis of each patient’s genetic makeup. A large volume...
When comparing diseased and non-diseased patients in order to discriminate between the aspects associated with the specific disease, it is often observed that the diseased patients have more variability than t...
Whether your interests lie in scientific arenas, the corporate world, or in government, you have certainly heard the praises of big data: Big data will give you new insights, allow you to become more efficient...
Best practice for statistical methodology in cell-based dose-response studies has yet to be established. We examine the ability of MANOVA to detect trait-associated genetic loci in the presence of gene-gene in...
Biological insights into group differences, such as disease status, have been achieved through differential co-expression analysis of microarray data. Additional understanding of group differences may be achie...
The three-dimensional structure of a protein is an essential aspect of its functionality. Despite the large diversity in protein structures and functionality, it is known that there are common patterns and pre...
The prediction of solvent accessibility could provide valuable clues for analyzing protein structure and functions, such as protein 3-Dimensional structure and B-cell epitope prediction. To fully decipher the ...
We develop a new concept that reflects how genes are connected based on microarray data using the coefficient of determination (the squared Pearson correlation coefficient). Our gene rank combines a priori kno...
Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerabl...
Vaccines have been one of the most successful public health interventions to date. The use of vaccination, however, sometimes comes with possible adverse events. The U.S. FDA/CDC Vaccine Adverse Event Reportin...
The discovery of breast cancer subtypes and subsequent development of treatments aimed at them has allowed for a great reduction in the mortality of breast cancer. But despite this progress, tumors with simila...
Identifying genetic interactions in data obtained from genome-wide association studies (GWASs) can help in understanding the genetic basis of complex diseases. The large number of single nucleotide polymorphis...
Using a collection of different terminal nodesize constructed random forests, each generating a synthetic feature, a synthetic random forest is defined as a kind of hyperforest, calculated using the new input ...
Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Se...
No abstract
The original article was published in BioData Mining 2014 7:15
A network motif is a recurring subnetwork within a network, and it takes on certain functions in practical biological macromolecule applications. Previous algorithms have focused on the computational efficienc...
Many bacterial genome sequences completed using the Sanger method may contain assembly errors due in-part to low sequence coverage driven by cost.
PGxClean is a new web application that performs quality control analyses for data produced by the Affymetrix DMET chip or other candidate gene technologies. Importantly, the software does not assume that varia...
The major histocompatibility complex (MHC) is responsible for presenting antigens (epitopes) on the surface of antigen-presenting cells (APCs). When pathogen-derived epitopes are presented by MHC class II on a...
The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called “big data” challenges traditional analytic tools and will increas...
Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions ...
Effective cancer clinical outcome prediction for understanding of the mechanism of various types of cancer has been pursued using molecular-based data such as gene expression profiles, an approach that has pro...
Genetic contributions to major depressive disorder (MDD) are thought to result from multiple genes interacting with each other. Different procedures have been proposed to detect such interactions. Which approa...
Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they co...
Alzheimer’s disease is the most common form of progressive dementia and there is currently no known cure. The cause of onset is not fully understood but genetic factors are expected to play a significant role....
Advances in genomic technologies have enabled the accumulation of vast amount of genomic data, including gene expression data for multiple species under various biological and environmental conditions. Integra...
Next generation sequencing technologies are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key to analyzing massive and complex...
The Erratum to this article has been published in BioData Mining 2014 7:30
Human Immunodeficiency Virus 1 enters host cells through interaction of its V3 loop (which is part of the gp120 protein) with the host cell receptor CD4 and one of two co-receptors, namely CCR5 or CXCR4. Entry...
The Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes—to explore whether they are linked to synd...
In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true assoc...
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