Abstract:
:Following last year's computational vaccinology workshop in Shanghai, China, the third ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013) was held in Barcelona, Spain. ICoVax 2013 provided an international platform for the attendees to showcase their research and discuss problems and solutions in the development and application of computational vaccinology and vaccine informatics tools. The first of the three full-length papers presented at ICoVax discussed the discovery of viral "camouflage" through cross-conservation of T-cell epitopes using a tool called JanusMatrix. This important paper reports that viruses may camouflage their presence in the human body by incorporating sequences in their proteins that are highly cross-conserved at the T-cell receptor surface with human genome proteins, a discovery that has wide ranging implications for the development of vaccines against viruses that use the camouflage method. The other papers described a database for storing experimentally verified data on DNA vaccines and compared therapeutic targets of western drugs to Chinese herbal medicines for cardiovascular diseases. The short poster presentations covered various uses of informatics tools for processing the DNA and microRNA of pathogens to improve vaccine coverage, efficacy and development. A live (on-line) demonstration of the vaccine design toolkit, iVax, presented by Frances Terry of EpiVax, illustrated how computational vaccinology could be used in the design of next generation vaccines.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
De Groot AS,De Groot P,He Ydoi
10.1186/1471-2105-15-S4-I1subject
Has Abstractpub_date
2014-01-01 00:00:00pages
I1issn
1471-2105pii
1471-2105-15-S4-I1journal_volume
15 Suppl 4pub_type
abstract:BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...
journal_title:BMC bioinformatics
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abstract:BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...
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abstract:BACKGROUND:The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying...
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abstract:BACKGROUND:Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection pro...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-243
更新日期:2005-10-03 00:00:00
abstract:BACKGROUND:Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind o...
journal_title:BMC bioinformatics
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doi:10.1186/1471-2105-8-163
更新日期:2007-05-21 00:00:00
abstract:BACKGROUND:High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researchers have recently presented methods for integrating direct and indirect data for predicting interacti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Routine application of gene expression microarray technology is rapidly producing large amounts of data that necessitate new approaches of analysis. The analysis of a specific microarray experiment profits enormously from cross-comparing to other experiments. This process is generally performed by numerical ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2005-12-01 00:00:00
abstract:BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03639-7
更新日期:2020-07-14 00:00:00
abstract:BACKGROUND:Computational gene finding algorithms have proven their robustness in identifying genes in complete genomes. However, metagenomic sequencing has presented new challenges due to the incomplete and fragmented nature of the data. During the last few years, attempts have been made to extract complete and incompl...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2013-01-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03782-1
更新日期:2020-12-14 00:00:00
abstract:BACKGROUND:Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. RESULTS:The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK frame...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-266
更新日期:2009-08-25 00:00:00
abstract:BACKGROUND:Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replica...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1774-x
更新日期:2017-08-07 00:00:00
abstract:BACKGROUND: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 understandable way. RESULTS:We present a visualization method that incorporates both emission and transi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-7
更新日期:2004-01-21 00:00:00
abstract:BACKGROUND:The median of k≥3 genomes was originally defined to find a compromise genome indicative of a common ancestor. However, in gene order comparisons, the usual definitions based on minimizing the sum of distances to the input genomes lead to degenerate medians reflecting only one of the input genomes. "Near-medi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1340-y
更新日期:2016-12-15 00:00:00
abstract:BACKGROUND:The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been im...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-419
更新日期:2008-10-07 00:00:00
abstract:BACKGROUND:Many statistical algorithms combine microarray expression data and genome sequence data to identify transcription factor binding motifs in the low eukaryotic genomes. Finding cis-regulatory elements in higher eukaryote genomes, however, remains a challenge, as searching in the promoter regions of genes with ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-44
更新日期:2006-01-26 00:00:00
abstract:BACKGROUND:Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to select genes that change their relationships with other genes in different biological conditions (diffe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-20
更新日期:2009-01-15 00:00:00
abstract:BACKGROUND:Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known bindi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S7-S11
更新日期:2007-11-01 00:00:00
abstract:BACKGROUND:Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the development of effective statistical methods to calibrat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-343
更新日期:2009-10-19 00:00:00
abstract:BACKGROUND:We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to t...
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pub_type: 杂志文章
doi:10.1186/1471-2105-15-S9-S11
更新日期:2014-01-01 00:00:00
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更新日期:2005-03-22 00:00:00
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更新日期:2013-11-19 00:00:00
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更新日期:2008-12-04 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2011-03-14 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2015-08-19 00:00:00
abstract::Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as...
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更新日期:2005-05-31 00:00:00
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更新日期:2011-07-15 00:00:00