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Predicting a list of plant taxa most likely to be observed at a given geographical location and time is useful for many scenarios in biodiversity informatics. Since efficient plant species identification is im...
A B-cell epitope is a group of residues on the surface of an antigen which stimulates humoral responses. Locating these epitopes on antigens is important for the purpose of effective vaccine design. In recent ...
DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. Until today, a universal DNA barcode marker for plants remains elusive. The rbc L and mat K...
This article is part of a Supplement: Volume 12 Supplement 13
Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. ...
PubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating...
Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heav...
This article is part of a Supplement: Volume 15 Supplement 16
The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known protein...
Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of differ...
The Correction to this article has been published in BMC Bioinformatics 2021 22:472
Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial co...
This article is part of a Supplement: Volume 19 Supplement 15
Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused ...
This article is part of a Supplement: Volume 11 Supplement 6
In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been...
Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encod...
The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen.
Increasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence dat...
T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large p...
This article is part of a Supplement: Volume 9 Supplement 1
To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a ...
Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences...
ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without s...
One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing F...
This article is part of a Supplement: Volume 20 Supplement 2
With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving...
As genomic studies continue to implicate non-coding sequences in disease, testing the roles of these variants requires insights into the cell type(s) in which they are likely to be mediating their effects. Pri...
De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read...
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
Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and a...
Many protein structures determined in high-throughput structural genomics centers, despite their significant novelty and importance, are available only as PDB depositions and are not accompanied by a peer-revi...
Rice (Oryza sativa L.) is one of the most important cereal crops in the world and its yield is closely related to the photosynthesis efficiency. The chloroplast stromal ridge complex consisting of PsaC-PsaD-PsaE ...
Understanding the Mechanism of Action (MoA) of a compound is an often challenging but equally crucial aspect of drug discovery that can help improve both its efficacy and safety. Computational methods to aid M...
Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological applica...
The homozygous yeast deletion library includes approximately 4800 diploid strains each containing one deleted non-essential gene. Hundreds of publications have arisen through experimentation using this genome-...
Several regulators of programmed cell death (PCD) in plants encode proteins with putative lipid-binding domains. Among them, VAD1 is a regulator of PCD propagation harboring a GRAM putative lipid-binding domai...
Pairing up primers to amplify desired targets and avoid undesired cross reactions can be a combinatorial challenge. Effective prediction of specificity and inclusivity from multiplexed primers and TaqMan®/Lumi...
With the exponential increase and widespread availability of genomic, transcriptomic, and proteomic data, accessing these ‘-omics’ data is becoming increasingly difficult. The current resources for accessing a...
With the advent of low cost, fast sequencing technologies metagenomic analyses are made possible. The large data volumes gathered by these techniques and the unpredictable diversity captured in them are still,...
The life-science community faces a major challenge in handling “big data”, highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, a...
Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed eff...
This article is part of a Supplement: Volume 14 Supplement 17
Gene regulatory networks (GRNs) arise from the intricate interactions between transcription factors (TFs) and their target genes during the growth and development of organisms. The inference of GRNs can unveil...
This article is part of a Supplement: Volume 18 Supplement 9
The Correction to this article has been published in BMC Bioinformatics 2017 18:490
The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying a...
This article is part of a Supplement: Volume 9 Supplement 1
The increasing volume and complexity of genomic data pose significant challenges for effective data management and reuse. Public genomic data often undergo similar preprocessing across projects, leading to red...
Biomedical research projects deal with data management requirements from multiple sources like funding agencies’ guidelines, publisher policies, discipline best practices, and their own users’ needs. We descri...
Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene thera...
Genome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies. Such data is deposited into data repositories such as the Gene Expres...
Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinf...
The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The broad spectrum of the effects of heme makes it important to i...
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