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In Silico Biology - Volume 1, issue 4

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Price: EUR N/A
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., "in silico" ) 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

The term "in silico" is a pendant to "in vivo" (in the living system) and "in vitro" (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.

Comparison of Protein Structures Reveals Monophyletic Origin of the AdoMet-Dependent Methyltransferase Family and Mechanistic Convergence Rather than Recent Differentiation of N4-Cytosine and …

Authors: Bujnicki, Janusz M.

Article Type: Short Communication

Abstract: Phylogenetic analysis of the S-adenosyl-L-methionine-dependent methyltransferases was performed based on similarity of positions of main chain á-carbon atoms in published structures of members of this superfamily.  The evolutionary tree was inferred and the problem of mono/polyphyletic origin of DNA methyltransferases from the Rossmann-fold enzymes was solved, bridging two seemingly antithetical hypotheses.  The comparison of protein structures provides evidence for an evolutionary link between widely diverged subfamilies of RNA and DNA … Show more

Keywords: AdoMet-dependent methyltransferases, dehydrogenases, Rossmann-fold proteins, structure comparison, divergent evolution, molecular phylogenetics

Citation: In Silico Biology, vol. 1, no. 4, pp. 175-182, 2000

Price: EUR 27.50

Curved DNA in Promoter Sequences

Authors: Gabrielian, Andrei E. | Landsman, David | Bolshoy, Alexander

Article Type: Research Article

Abstract: Sequence-dependent DNA curvature is known to play an important role in initiation of transcription of many genes.  We compared the distribution of predicted intrinsic curvature of Escherichia coli and human promoter sequences with the distribution of curvature of randomly selected coding and non-coding fragments from these organisms.  Different methods of curvature calculation were found to yield mostly similar overall tendencies of DNA curvature in all groups of sequences.  According to all methods of calculation, E. … Show more

Keywords: DNA curvature, bendability, sequence analysis

Citation: In Silico Biology, vol. 1, no. 4, pp. 183-196, 2000

Price: EUR 27.50

Comparative Analysis of the Arabidopsis and Rice Expressed Sequence Tag (EST) Sets

Authors: Ewing, Rob | Poirot, Olivier | Claverie, Jean-Michel

Article Type: Research Article

Abstract: Large numbers of expressed sequence tags (ESTs) have now been generated from a variety of model organisms.  In plants, substantial collections of ESTs are available for Arabidopsis and rice, in each case representing significant proportions of the estimated total numbers of genes.  Large-scale comparisons of Arabidopsis and rice sequences are especially interesting due to the fact that these two species are representatives of the two subclasses of the flowering plants (Dicotyledonae and Monocotyledonae, respectively).  Here … Show more

Keywords: Arabidopsis, rice, plant, dicot, monocot, expressed sequence tag, mRNA, transcript, cDNA, cluster, singleton, contig sequence, sequence alignment, gene family, genome, transcriptome, divergence, conservation, homolog, ortholog

Citation: In Silico Biology, vol. 1, no. 4, pp. 197-213, 2000

Price: EUR 27.50
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