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A key challenge in the emerging field of single-cell RNA-Seq is to characterize phenotypic diversity between cells and visualize this information in an informative manner. A common technique when dealing with ...
Drug resistance testing is mandatory in antiretroviral therapy in human immunodeficiency virus (HIV) infected patients for successful treatment. The emergence of resistances against antiretroviral agents remai...
Studies exploring the potential of Chaos Game Representations (CGR) of genomic sequences to act as “genomic signatures” (to be species- and genome-specific) showed that CGR patterns of nuclear and organellar D...
Biological data such as microarrays contain a huge number of features. Thus, it is necessary to select a small number of novel features to characterize the entire dataset. All combinations of the features subs...
Metagenomics holds great promises for deepening our knowledge of key bacterial driven processes, but metagenome assembly remains problematic, typically resulting in representation biases and discarding signifi...
Copy number alteration is a main genetic structural variation that plays an important role in tumor initialization and progression. Accurate detection of copy number alterations is necessary for discovering ca...
Direct volume rendering is one of flexible and effective approaches to inspect large volumetric data such as medical and biological images. In conventional volume rendering, it is often time consuming to set u...
I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016
This article is part of a Supplement: Volume 17 Supplement 10
One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PT...
Levan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high w...
It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream using SAMtools, parses and filters the lin...
The original article was published in BMC Bioinformatics 2016 17:187
The original article was published in BMC Bioinformatics 2015 16:372
The original article was published in BMC Bioinformatics 2016 17:213
Current volumes of sequence data can lead to large numbers of hits identified on a search, typically in the range of 10s to 100s of thousands. It is often quite difficult to tell from these raw results whether...
The interplay among genetic, environment and epigenetic variation is not fully understood. Advances in high-throughput genotyping methods, high-density DNA methylation detection and well-characterized sample c...
Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respi...
The Gene Ontology (GO) is a dynamic, controlled vocabulary that describes the cellular function of genes and proteins according to tree major categories: biological process, molecular function and cellular com...
DNA methylation is an important regulator of gene expression and chromatin structure. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is commonly used to identify regions of DNA methylation in eukary...
All species live in complex ecosystems. The structure and complexity of a microbial community reflects not only diversity and function, but also the environment in which it occurs. However, traditional ecologi...
The original article was published in BMC Bioinformatics 2016 17:62
Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut...
Comparing phenotypes of heterogeneous cell populations from multiple biological conditions is at the heart of scientific discovery based on flow cytometry (FC). When the biological signal is measured by the av...
It is necessary to evaluate the efficacy of individual drugs on patients to realize personalized medicine. Testing drugs on patients in clinical trial is the only way to evaluate the efficacy of drugs. The app...
This article is part of a Supplement: Volume 17 Supplement 6
Scaffold proteins are known for being crucial regulators of various cellular functions by assembling multiple proteins involved in signaling and metabolic pathways. Identification of scaffold proteins and the ...
This article is part of a Supplement: Volume 17 Supplement 6
Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates. However, this entails a great deal of effort to clarify the interaction thro...
This article is part of a Supplement: Volume 17 Supplement 6
The original article was published in BMC Bioinformatics 2016 17:S194
Intronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding thei...
Massive biological datasets are generated in different locations all over the world. Analysis of these datasets is required in order to extract knowledge that might be helpful for biologists, physicians and ph...
This article is part of a Supplement: Volume 17 Supplement 7
Protein–protein interaction networks are receiving increased attention due to their importance in understanding life at the cellular level. A major challenge in systems biology is to understand the modular str...
This article is part of a Supplement: Volume 17 Supplement 7
Genome-wide association studies (GWAS) have effectively identified genetic factors for many diseases. Many diseases, including Alzheimer’s disease (AD), have epistatic causes, requiring more sophisticated anal...
This article is part of a Supplement: Volume 17 Supplement 7
Protein-protein interaction (PPI) extraction from published scientific articles is one key issue in biological research due to its importance in grasping biological processes. Despite considerable advances of ...
This article is part of a Supplement: Volume 17 Supplement 7
The predictive nature of the primate sensorimotor systems, for example the smooth pursuit system and their ability to compensate for long delays have been proven by many physiological experiments. However, few...
This article is part of a Supplement: Volume 17 Supplement 7
Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive t...
This article is part of a Supplement: Volume 17 Supplement 7
Abnormalities in glycan biosynthesis have been conclusively related to various diseases, whereas the complexity of the glycosylation process has impeded the quantitative analysis of biochemical experimental da...
This article is part of a Supplement: Volume 17 Supplement 7
Analyzing next-generation sequencing data is difficult because datasets are large, second generation sequencing platforms have high error rates, and because each position in the target genome (exome, transcrip...
This article is part of a Supplement: Volume 17 Supplement 7
Biomedical literature retrieval is becoming increasingly complex, and there is a fundamental need for advanced information retrieval systems. Information Retrieval (IR) programs scour unstructured materials su...
This article is part of a Supplement: Volume 17 Supplement 7
Accurate determination of protein complexes has become a key task of system biology for revealing cellular organization and function. Up to now, the protein complex prediction methods are mostly focused on sta...
This article is part of a Supplement: Volume 17 Supplement 7
When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognos...
Clustering is a common technique used by molecular biologists to group homologous sequences and study evolution. There remain issues such as how to cluster molecular sequences accurately and in particular how ...
Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) Class I molecules bind to peptide fragments of proteins degraded inside the cell and display them on the cell surface. We are interested ...
Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quan...
This article is part of a Supplement: Volume 17 Supplement 9
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for...
This article is part of a Supplement: Volume 17 Supplement 9
The planted (l, d) motif search (PMS) is an important yet challenging problem in computational biology. Pattern-driven PMS algorithms usually use k out of t input sequences as reference sequences to generate cand...
This article is part of a Supplement: Volume 17 Supplement 9
Biomedical information and knowledge, structural and non-structural, stored in different repositories can be semantically connected to form a hybrid knowledge network. How to compute relatedness between concep...
This article is part of a Supplement: Volume 17 Supplement 9
Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user’s underlying intention through keywords but also because a keyword-...
This article is part of a Supplement: Volume 17 Supplement 9
A computationally efficient tool is required for a genome-wide gene-gene interaction analysis that tests an extremely large number of single-nucleotide polymorphism (SNP) interaction pairs in genome-wide assoc...
A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, prote...
There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and pro...
It is now clearly evident that cancer outcome and response to therapy is guided by diverse immune-cell activity in tumors. Presently, a key challenge is to comprehensively identify networks of distinct immune-...
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