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Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively under...
Biological interpretation of gene/protein lists resulting from -omics experiments can be a complex task. A common approach consists of reviewing Gene Ontology (GO) annotations for entries in such lists and sea...
Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working...
This article is part of a Supplement: Volume 18 Supplement 17
Because of the short read length of high throughput sequencing data, assembly errors are introduced in genome assembly, which may have adverse impact to the downstream data analysis. Several tools have been de...
Much effort is currently made to develop the Gene Ontology (GO). Due to the dynamic nature of information it addresses, GO undergoes constant updates whose results are released at regular intervals as separate...
This article is part of a Supplement: Volume 9 Supplement 3
Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria ...
Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of c...
Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of ...
Many high throughput sequencing (HTS) approaches, such as the Roche/454 platform, produce sequences in which the quality of the sequence (as measured by a Phred-like quality scores) decreases linearly across a...
An important aspect of protein design is the ability to predict changes in protein thermostability arising from single- or multi-site mutations. Protein thermostability is reflected in the change in free energ...
Various methods for differential expression analysis have been widely used to identify features which best distinguish between different categories of samples. Multiple hypothesis testing may leave out explana...
Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules.
This article is part of a Supplement: Volume 20 Supplement 9
Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an inter...
This article is part of a Supplement: Volume 11 Supplement 1
With the explosion of data comes a proportional opportunity to identify novel knowledge with the potential for application in targeted therapies. In spite of this huge amounts of data, the solutions to treatin...
This article is part of a Supplement: Volume 18 Supplement 11
Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and ...
The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher t...
The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its fou...
This article is part of a Supplement: Volume 10 Supplement 6
Perfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between a...
Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specif...
Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only ...
Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occur approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs) that lead to am...
Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this p...
This article is part of a Supplement: Volume 18 Supplement 11
Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRN...
Drug repositioning, also known as drug repurposing, defines new indications for existing drugs and can be used as an alternative to drug development. In recent years, the accumulation of large volumes of infor...
This article is part of a Supplement: Volume 20 Supplement 10
The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typical...
Interactions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high ...
The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical...
Uncovering functional genetic variants from an allele-specific perspective is of paramount importance in advancing our understanding of gene regulation and genetic diseases. Recently, various allele-specific e...
High-dimensional data of discrete and skewed nature is commonly encountered in high-throughput sequencing studies. Analyzing the network itself or the interplay between genes in this type of data continues to ...
Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representatio...
Some proposed methods for identifying essential proteins have better results by using biological information. Gene expression data is generally used to identify essential proteins. However, gene expression dat...
The gap gene system controls the early cascade of the segmentation pathway in Drosophila melanogaster as well as other insects. Owing to its tractability and key role in embryo patterning, this system has been th...
Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data gener...
This article is part of a Supplement: Volume 20 Supplement 24
Many problems in comparative biology are, or are thought to be, best expressed as phylogenetic “networks” as opposed to trees. In trees, vertices may have only a single parent (ancestor), while networks allow ...
Automatically understanding chemical-disease relations (CDRs) is crucial in various areas of biomedical research and health care. Supervised machine learning provides a feasible solution to automatically extra...
With the generation of vast compendia of biological datasets, the challenge is how best to interpret ‘omics data alongside biochemical and other small-scale experiments to gain meaningful biological insights. ...
A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For exampl...
Digital PCR (dPCR) is a technique for estimating the concentration of a target nucleic acid by loading a sample into a large number of partitions, amplifying the target and using a fluorescent marker to identi...
RNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools a...
Single-cell RNA-sequencing technologies provide a powerful tool for systematic dissection of cellular heterogeneity. However, the prevalence of dropout events imposes complications during data analysis and, de...
DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead t...
Recent technological developments have enabled the measurement of a plethora of biomolecular data from various omics domains, and research is ongoing on statistical methods to leverage these omics data to bett...
Mathematical models of biological networks can provide important predictions and insights into complex disease. Constraint-based models of cellular metabolism and probabilistic models of gene regulatory networ...
Current -omics technologies are able to sense the state of a biological sample in a very wide variety of ways. Given the high dimensionality that typically characterises these data, relevant knowledge is often hi...
Amplicon re-sequencing based on the automated Sanger method remains popular for detection of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels) for a spectrum of genetics appl...
Data-driven cell classification is becoming common and is now being implemented on a massive scale by projects such as the Human Cell Atlas. The scale of these efforts poses a challenge. How can the results be...
This article is part of a Supplement: Volume 18 Supplement 17
A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-abs...
This article is part of a Supplement: Volume 20 Supplement 15
The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is ty...
Numerous simulation tools based on specific assumptions have been proposed to simulate populations. Here we present a simulation tool named DHOEM (densification of haplotypes by loess regression and maximum li...
RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of...
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