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ISSN 1386-6338 (P)
ISSN 1434-3207 (E)
In Silico Biology is a scientific research journal for the advancement of computational models and simulations applied to complex biological phenomena. We publish peer-reviewed leading-edge biological, biomedical and biotechnological research in which computer-based (i.e.,
) modeling and analysis tools are developed and utilized to predict and elucidate dynamics of biological systems, their design and control, and their evolution. Experimental support may also be provided to support the computational analyses.
In Silico Biology aims to advance the knowledge of the principles of organization of living systems. We strive to provide computational frameworks for understanding how observable biological properties arise from complex systems. In particular, we seek for integrative formalisms to decipher cross-talks underlying systems level properties, ultimate aim of multi-scale models.
Studies published in
In Silico Biology generally use theoretical models and computational analysis to gain quantitative insights into regulatory processes and networks, cell physiology and morphology, tissue dynamics and organ systems. Special areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, proliferation, differentiation and morphogenesis, among others, and the use of multi-scale modeling to connect molecular and cellular systems to the level of organisms and populations.
In Silico Biology also publishes foundational research in which novel algorithms are developed to facilitate modeling and simulations. Such research must demonstrate application to a concrete biological problem.
In Silico Biology frequently publishes special issues on seminal topics and trends. Special issues are handled by Special Issue Editors appointed by the Editor-in-Chief. Proposals for special issues should be sent to the Editor-in-Chief.
About In Silico Biology
is a pendant to
(in the living system) and
(in the test tube) biological experiments, and implies the gain of insights by computer-based simulations and model analyses.
In Silico Biology (ISB) was founded in 1998 as a purely online journal. IOS Press became the publisher of the printed journal shortly after. Today, ISB is dedicated exclusively to biological systems modeling and multi-scale simulations and is published solely by IOS Press. The previous online publisher, Bioinformation Systems, maintains a website containing studies published between 1998 and 2010 for archival purposes.
We strongly support open communications and encourage researchers to share results and preliminary data with the community. Therefore, results and preliminary data made public through conference presentations, conference proceeding or posting of unrefereed manuscripts on preprint servers will not prohibit publication in ISB. However, authors are required to modify a preprint to include the journal reference (including DOI), and a link to the published article on the ISB website upon publication.
Abstract: I-superfamily conotoxins have four-disulfide bonds with cysteine arrangement C-C-CC-CC-C-C, and they inhibit or modify ion channels of nerve cells. They have been characterized only recently and are relatively less well studied compared to other superfamily conotoxins. We have detected selective and sensitive sequence pattern for I-superfamily conotoxins. The availability of sequence pattern should be useful in protein family classification and functional annotation. We have built by homology modeling, a theoretical structural 3D…model of ViTx from Conus virgo, a typical member of I-superfamily conotoxins. The modeling was based on the available 3D structure of Janus-atracotoxin-Hv1c of Janus-atracotoxin family whose members have been suggested as possible biopesticides. A study comparing the theoretically modeled structure of ViTx, with experimentally determined structures of other toxins, which share functional similarity with ViTx, reveals the crucial role of C-terminal region of ViTx in blocking therapeutically important voltage-gated potassium channels.
Abstract: As the genome of B. mori is available in GenBank and the EST database of B. mori is expanding, identification of novel genes of B. mori was conceivable by data-mining techniques and bioinformatics tools. In this study, we used the in silico cloning method to identify eukaryotic initiation factor 5A (eIF5A) gene in B. mori. With the hypusine formation, eIF5A is involved in the regulation of cell proliferation and apoptosis. Using the computer program MEGA3, we…conducted a search for homologs of eIF5A among many eukaryotic species and confirmed that the eIF5A was conserved in all organisms investigated. This gene has been registered in GenBank under the accession number DQ104412.
Keywords: eIF5A, Bombyx mori, EST, in silico cloning
Abstract: With the advent of larger genome databases detection of horizontal gene transfer events has been transformed into an increasingly important issue. Here we present a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detect HTG (Horizontally transferred genes), which are based…on (a) the codon adaptation index, codon usage, and GC percentage (CAI/GC); (b) a distributional profile (DP) approach made by a gene search in the closely related phylogenetic genomes; (c) a Bayesian model (BM); and (d) a first-order Markov model (MM). All methods exhibit limitations although, as shown here, the BM and the MM are better approximations. Moreover, the MM has demonstrated a more accurate rate of detections when genes from closely related organisms are evaluated. The application of the MM to detect recently transferred genes in the genomes of E. coli strains K12 MG1655, O157 EDL933, and Salmonella typhimurium, shows that these organisms have undergone a rather significant amount of HTG, most of which appear to be pseudogenes. Few of these sequences that have undergone HGT appear to have well defined functions and may be involved in the organism's adaptation.
Keywords: Horizontally transferred gene, methodologies to detect HTG, first-order Markov model
Abstract: This study was undertaken to identify novel candidate genes at quantitative trait loci (QTL) on chicken chromosome Z (GGAZ) by comparing orthologous regions of chicken, human and mouse genomes. Primer sequences from marker flanking QTL positions (https://acedb.asg.wur.nl/) were obtained from www.iastate.edu/chickmap and blasted against the chicken genome (www.ensembl.org) using BLASTN. The best matches were those with the highest score, lowest E-values and highest percent identity. Orthologous regions in mice and humans, together…with genes located on or around those loci were identified using the Ensembl website. Forty-six chicken genes, 91 mouse genes and 60 human genes associated with QTL on GGAZ were identified in the current study. Among the most promising candidate genes for egg production and egg shell quality are annexin A1 (ANXA1), osteoclast stimulating factor (OSF), thrombospondin-4 (THBS4), programmed cell death proteins (PDCD), follistatin (FST), growth hormone receptor (GHR), interferon (IFN) α and β. The chicken IFN α and β were located on GGAZ around position 13,000,000 bp on the draft chicken sequence map. The neuronal nicotinic acetylcholine receptor (nAChR) is located at a QTL region for abdominal fat (GGAZ 25483091 bp). Nicotine is an agonist at the nAChRs and has been shown to decrease lipolysis and triglyceride uptake, thereby reducing net storage in adipose tissue. Therefore, the nAchRs could be used as therapeutic targets for regulating feed intake and obesity. This study has identified 197 putative candidate genes in probable QTL regions of chicken chromosome Z.
Keywords: Molecular biology databases, nucleotide sequence databases, RNA sequence databases, protein sequence databases, structure databases, genomics databases, metabolic & signaling pathways, human and vertebrate genomes, human genes and diseases, microarray data and gene expression databases, proteomics resources, organelle databases, plant databases, immunological databases
Abstract: Unicellular eukaryotes were among the first ones to be selected for complete genome sequencing because of the small size of their genomes and their interactions with humans and a broad range of animals and plants. Currently, ten completely sequenced unicellular genome sequences have been publicly released and as the number of available unicellular genomes increases, comparative genomics analysis within this group of organisms becomes more and more instructive. However, such an analysis is difficult to carry…out without a suitable platform gathering not only the original annotations but also relevant information available in public databases or obtained by applying common bioinformatics methods. With the aim of solving these difficulties, we have developed a web-accessible database named u-Genome, the unicellular genome design database. The database is unique in featuring three datasets namely (1) orthologous proteins (2) paralogous proteins and (3) statistical distributions on exons, introns, intergenic DNA and correlations between them. A tool, Uniview, designed to visualize the gene structures for individual genes in the genome is also integrated. This database is of importance in understanding unicellular genome design and architecture and evolution related studies. The database is available through a web interface at http://sege.ntu.edu.sg/wester/ugenome.