In Silico Biology - Volume 5, issue 2 - Journals

In Silico Biology - Volume 5, issue 2

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.

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Knowledge Discovery and System Biology in Molecular Medicine: An Application on Neurodegenerative Diseases

Authors: Fattore, Matteo | Arrigo, Patrizio

Article Type: Research Article

Abstract: The possibility to study an organism in terms of system theory has been proposed in the past, but only the advancement of molecular biology techniques allow us to investigate the dynamical properties of a biological system in a more quantitative and rational way than before. These new techniques can gave only the basic level view of an organisms functionality. The comprehension of its dynamical behaviour depends on the possibility to perform a multiple level analysis. …Functional genomics has stimulated the interest in the investigation the dynamical behaviour of an organism as a whole. These activities are commonly known as System Biology, and its interests ranges from molecules to organs. One of the more promising applications is the 'disease modeling'. The use of experimental models is a common procedure in pharmacological and clinical researches; today this approach is supported by 'in silico' predictive methods. This investigation can be improved by a combination of experimental and computational tools. The Machine Learning (ML) tools are able to process different heterogeneous data sources, taking into account this peculiarity, they could be fruitfully applied to support a multilevel data processing (molecular, cellular and morphological) that is the prerequisite for the formal model design; these techniques can allow us to extract the knowledge for mathematical model development. The aim of our work is the development and implementation of a system that combines ML and dynamical models simulations. The program is addressed to the virtual analysis of the pathways involved in neurodegenerative diseases. These pathologies are multifactorial diseases and the relevance of the different factors has not yet been well elucidated. This is a very complex task; in order to test the integrative approach our program has been limited to the analysis of the effects of a specific protein, the Cyclin Dependent Kinase 5 (CDK5) which relies on the induction of neuronal apoptosis. The system has a modular structure centred on a textual knowledge discovery approach. The text mining is the only way to enhance the capability to extract ,from multiple data sources, the information required for the dynamical simulator. The user may access the publically available modules through the following site: http://biocomp.ge.ismac.cnr.it. Show more

Keywords: System Biology, Knowledge Discovery, integrative bioinformatics, molecular medicine, Alzheimer's diseases, CDK5, virtual screening, drug design

Citation: In Silico Biology, vol. 5, no. 2, pp. 199-208, 2005

Price: EUR 27.50

Complementing Computationally Predicted Regulatory Sites in Tractor_DB Using a Pattern Matching Approach

Authors: Guía, Marylens Hernández | Pérez, Abel González | Angarica, Vladimir Espinosa | Vasconcelos, Ana T. | Collado-Vides, Julio

Article Type: Research Article

Abstract: Prokaryotic genomes annotation has focused on genes location and function. The lack of regulatory information has limited the knowledge on cellular transcriptional regulatory networks. However, as more phylogenetically close genomes are sequenced and annotated, the implementation of phylogenetic footprinting strategies for the recognition of regulators and their regulons becomes more important. In this paper we describe a comparative genomics approach to the prediction of new gamma-proteobacterial regulon members. We take advantage of …the phylogenetic proximity of Escherichia coli and other 16 organisms of this subdivision and the intensive search of the space sequence provided by a pattern-matching strategy. Using this approach we complement predictions of regulatory sites made using statistical models currently stored in Tractor_DB, and increase the number of transcriptional regulators with predicted binding sites up to 86. All these computational predictions may be reached at Tractor_DB (www.bioinfo.cu/Tractor_DB, www.tractor.lncc.br, www.ccg.unam.mx/Computational_Genomics/tractorDB/). We also take a first step in this paper towards the assessment of the conservation of the architecture of the regulatory network in the gamma-proteobacteria through evaluating the conservation of the overall connectivity of the network. Show more

Keywords: transcriptional regulatory networks, comparative genomics, gamma-proteobacterial regulons

Citation: In Silico Biology, vol. 5, no. 2, pp. 209-219, 2005

Price: EUR 27.50

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