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Hepatitis B virus (HBV) genotypes have a distinct geographical distribution and influence disease progression and treatment outcomes. The purpose of this study was to investigate the distribution of HBV genoty...
Binning environmental shotgun reads is one of the most fundamental tasks in metagenomic studies, in which mixed reads from different species or operational taxonomical units (OTUs) are separated into different...
In this study, clustering was performed using a bitmap representation of HIV reverse transcriptase and protease sequences, to produce an unsupervised classification of HIV sequences. The classification will ai...
An important problem in computational biology is the automatic detection of protein families (groups of homologous sequences). Clustering sequences into families is at the heart of most comparative studies dea...
Structural comparison of protein-protein interfaces provides valuable insights into the functional relationship between proteins, which may not solely arise from shared evolutionary origin. A few methods that ...
PAR-CLIP is a recently developed Next Generation Sequencing-based method enabling transcriptome-wide identification of interaction sites between RNA and RNA-binding proteins. The PAR-CLIP procedure induces spe...
Microbiome studies incorporate next-generation sequencing to obtain profiles of microbial communities. Data generated from these experiments are high-dimensional with a rich correlation structure but modest sa...
A key challenge in understanding the molecular mechanisms that control gene regulation is the characterization of the specificity with which transcription factor proteins bind to specific DNA sequences. A numb...
N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation si...
β-N-Acetylhexosaminidase (GH20) from the filamentous fungus Talaromyces flavus, previously identified as a prominent enzyme in the biosynthesis of modified glycosides, lacks a high resolution three-dimensional st...
Scanning force microscopy (SFM) allows direct, rapid and high-resolution visualization of single molecular complexes; irregular shapes and differences in sizes are immediately revealed by the scanning tip in t...
Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the...
Two-dimensional differential gel electrophoresis (2D-DIGE) provides a powerful technique to separate proteins on their isoelectric point and apparent molecular mass and quantify changes in protein expression. ...
Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, ...
The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been ...
Familial binding profiles (FBPs) represent the average binding specificity for a group of structurally related DNA-binding proteins. The construction of such profiles allows the classification of novel motifs ...
Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences seq...
The function of an RNA in cellular processes is directly related to its structure. The free energy of RNA structure in another important key to its function as only some structures with a specific level of fre...
Proteins are composed of domains, protein segments that fold independently from the rest of the protein and have a specific function. During evolution the arrangement of domains can change: domains are gained,...
Short sequence mapping methods for Next Generation Sequencing consist on a combination of seeding techniques followed by local alignment based on dynamic programming approaches. Most seeding algorithms are bas...
Next-generation sequencing (NGS) is rapidly becoming common practice in clinical diagnostics and cancer research. In addition to the detection of single nucleotide variants (SNVs), information on copy number v...
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This article is part of a Supplement: Volume 16 Supplement 2
This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the...
This article is part of a Supplement: Volume 16 Supplement 2
microRNAs (miRNAs) play a vital role in development, oncogenesis, and apoptosis by binding to mRNAs to regulate the posttranscriptional level of coding genes in mammals, plants, and insects. Recent studies hav...
This article is part of a Supplement: Volume 16 Supplement 1
Photosynthetic proteins (PSPs) greatly differ in their structure and function as they are involved in numerous subprocesses that take place inside an organelle called a chloroplast. Few studies predict PSPs fr...
This article is part of a Supplement: Volume 16 Supplement 1
Characterizing the interface residues will help shed light on protein-protein interactions, which are involved in many important biological processes. Many studies focus on characterizing sequence or structure...
This article is part of a Supplement: Volume 16 Supplement 1
With the development of various high throughput technologies and analysis methods, researchers can study different aspects of a biological phenomenon simultaneously or one aspect repeatedly with different expe...
This article is part of a Supplement: Volume 16 Supplement 1
The prevalence of type 2 diabetes is increasing at an alarming rate. Various complications are associated with type 2 diabetes, with diabetic nephropathy being the leading cause of renal failure among diabetic...
This article is part of a Supplement: Volume 16 Supplement 1
With the recent development of microarray and high-throughput sequencing (HTS) technologies, a number of studies have revealed catalogs of copy number variants (CNVs) and their association with phenotypes and ...
This article is part of a Supplement: Volume 16 Supplement 1
Overlapping transcription constitutes a common mechanism for regulating gene expression. A major limitation of the overlapping transcription assays is the lack of high throughput expression data.
This article is part of a Supplement: Volume 16 Supplement 1
In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the...
This article is part of a Supplement: Volume 16 Supplement 1
In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ...
This article is part of a Supplement: Volume 16 Supplement 1
In genomics, hierarchical clustering (HC) is a popular method for grouping similar samples based on a distance measure. HC algorithms do not actually create clusters, but compute a hierarchical representation ...
Understanding the dynamics of biological processes can substantially be supported by computational models in the form of nonlinear ordinary differential equations (ODE). Typically, this model class contains ma...
With recent development in sequencing technology, a large number of genome-wide DNA methylation studies have generated massive amounts of bisulfite sequencing data. The analysis of DNA methylation patterns hel...
Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how express...
N-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family c...
The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized inf...
Quantitative molecular methods (QMMs) such as quantitative real-time polymerase chain reaction (q-PCR), reverse-transcriptase PCR (qRT-PCR) and quantitative nucleic acid sequence-based amplification (QT-NASBA)...
Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30–37, 2013; Nat Rev Genet 14:9–22, 20...
Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testin...
Protein function prediction is to assign biological or biochemical functions to proteins, and it is a challenging computational problem characterized by several factors: (1) the number of function labels (anno...
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