Articles

Unraveling functional networks: does gene clustering have a meaning?

Authors: Olga Vasieva and Roland Wolf

Function prediction of a newly extracted protein from a newly extracted lassa virus gene

Authors: LE Okoror, HT Alaiya and P Aliga

A probabilistic context-free grammar for the detection of binding sites from a protein sequence

Authors: Witold Dyrka and Jean-Christophe Nebel

Binding site locations and interaction of the isolated middle loop of snake neurotoxin I with muscle type nicotinic acetylcholine receptor: molecular dynamics and docking simulation study

Authors: Adak Nasiripourdori, Bijan Ranjbar and Hossein Naderi-manesh

The NetBuilder' project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks

Authors: Katja Wegner, Johannes Knabe, Mark Robinson, Attila Egri-Nagy, Maria Schilstra and Chrystopher Nehaniv

Data mining techniques in a CGH-based breast cancer subtype profiling: an immune perspective with comparative study

Authors: Filippo Menolascina, Stefania Tommasi, Patrizia Chiarappa, Vitoantonio Bevilacqua, Giuseppe Mastronardi and Angelo Paradiso

Inferring context-sensitive Probabilistic Boolean Networks from gene expression data under multi-biological conditions

Authors: Le Yu and Stephen Marshall

A parallel algorithm for de novo peptide sequencing

Authors: Elisa Mori, Sara Brunetti, Sonia Campa and Elena Lodi

On the correlation between drug-resistant pattern of HIV-1 protease inhibitors and binding free energy and structural changes

Authors: Kitiyaporn Wittayanarakul, Supot Hannongbua and Michael Feig

Less is more: the battle of Moore's law against Bremermann's limit on the field of systems biology

Authors: Derek Gatherer

A computational tool for directing Taxus spp. cell culture metabolism from growth to Taxol^®, a diterpene alkaloid, production

Authors: Khairiah Abd-Karim, Radia Chibani and Ferda Mavituna

Huntington's disease: from experimental results to interaction networks, patho-pathway construction and disease hypothesis

Authors: Eduardo Gonzalez-Couto, Silvia Matteoni, Stefano Gotta, Letizia Magnoni, Freddy Heitz, Roberto Raggiaschi, Georg C Terstappen and Andreas Kremer

Metabolic flux analysis for directing metabolism of Streptomyces olindensis from growth to anti-tumor drug (cosmomycin) production

Authors: Ana Katerine de Carvalho Lima Lobato, Raul Munoz-Hernandez, Renata L Araujo Furlan, Gabriel Padilla, Leandro M Garrido, Gorete Ribeiro de Macedo and Ferda Mavituna

DNA interaction with sperm cells: ODE model

Authors: Andrew Kuznetsov

Computational modelling of chemotaxis in cooperative phenomena in bacterial populations

Authors: Vinayak Doraiswamy, Martin Buist and Andrew Goryachev

ECOLITASTER: cellular biosensor

Authors: Guillermo Rodrigo, Javier Carreral and Alfonso Jaramillo

Set theoretical and algebraic model for redundancies in the genetic code

Authors: Karl Heuer

MaGnET: a software tool for integrated visualisation of functional genomic data relating to the malaria parasite

Authors: Joanna L Sharman and Dietlind L Gerloff

A bioinformatics approach for the interrogation of molecular events in single cells: transforming fluorescent time-lapse microscopy images into numbers

Authors: Imtiaz Khan, Janet Fisher, Nuria Marquez, Paul Smith and Rachel Errington

MicroRNA sequence and expression database

Authors: Koray Dogan Kaya, Gokhan Karakulah, Cengiz Yakicier and Ozlen Konu

How to formalise the meaning of a bio-model: a case study

Authors: Christian Knüpfer, Clemens Beckstein and Peter Dittrich

Abstract analysis of pathways using the BN++ software framework

Authors: Jan Küntzer, Benny Kneissl, Oliver Kohlbacher and Hans-Peter Lenhof

Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model

Authors: Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto and Hiroshi Mamitsuka

Computational design of proteins with new functions

Authors: Alfonso Jaramillo, Pablo Tortosa, Guillermo Rodrigo, Maria Suarez and Javier Carrera

Linking evolution of protein structures through fragments

Authors: Sanne Abeln and Charlotte M Deane

Arsenic biosenseor: a step further

Authors: Chris French, Judith Nicholson, Farid Bizzari, Jelena Aleksic, Yizhi Cai, Sreemati Lalgudi Seshasayee, Sergii Ivakhno, Bryony Davidson, Jen Wilson, Kim de Mora, Hongwu Ma, Laszlo Kozma-Bognar and Alistair Elfick

A global statistical test for improved detection of gene activity

Authors: David JG Bakewell and Ernst Wit

Integration and analysis of heterogeneous microarray data sources for supporting drug target identification in atherosclerosis

Authors: Anyela Camargo and Francisco Azuaje

Engineering a synthetic molecular oscillator based on the Lotka-Volterra dynamic

Authors: Christin Sander, Farah Vohra, John Chattaway, Tom Hinson, John Sy, Jiongjun Bai, Jonathan Wells, Deepti Aswani, Vincent Rouilly, Chueh-Loo Poh, Matthieu Bultelle, Kirsten Jensen, David Mann, Paul Freemont and Richard Kitney

Potential role of the glyoxalase pathway as a drug target in Leishmania infantum: an exact steady-state model analysis

Authors: Nuno Filipe Lages, Marta Sousa Silva, António EN Ferreira, Ana Maria Tomás, Carlos Cordeiro and Ana Ponces Freire

SABIO-RK: a database for biochemical reactions and their kinetics

Authors: Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann and Ulrike Wittig

Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs

Authors: Xu Gu, David Gilbert, Des Higham and Miles Houslay

Visualizing regulatory interactions in metabolic networks

Authors: Stephan Noack, Aljoscha Wahl, Marco Oldiges and Wolfgang Wiechert

Modelling genetic regulatory networks from specified behaviours

Authors: Daniel Mateus, Jean-Paul Comet, Jean-Pierre Gallois and Pascale Le Gall

Integration of SABIO-RK in workbenches for kinetic model design

Authors: Martin Golebiewski, Saqib Mir, Renate Kania, Olga Krebs, Andreas Weidemann, Ulrike Wittig and Isabel Rojas

Effect of microarray data heterogeneity on regulatory gene module discovery

Authors: Alok Mishra and Duncan Gillies

A search engine to identify pathway genes from expression data on multiple organisms

The completion of several genome projects showed that most genes have not yet been characterized, especially in multicellular organisms. Although most genes have unknown functions, a large collection of data i...

Authors: Chunnuan Chen, Matthew T Weirauch, Corey C Powell, Alexander C Zambon and Joshua M Stuart

Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas

The Allen Brain Atlas (ABA) project systematically profiles three-dimensional high-resolution gene expression in postnatal mouse brains for thousands of genes. By unveiling gene behaviors at both the cellular ...

Authors: Zheng Liu, S Frank Yan, John R Walker, Theresa A Zwingman, Tao Jiang, Jing Li and Yingyao Zhou

Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae

Control effective flux (CEF) of a reaction is the weighted sum of all fluxes through that reaction, derived from elementary flux modes (EFM) of a metabolic network. Change in CEFs under different environmental...

Authors: Tunahan Çakır, Betül Kırdar, Zİlsen Önsan, Kutlu Ö Ülgen and Jens Nielsen

An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline

The ubiquitin-proteasome system is responsible for homeostatic degradation of intact protein substrates as well as the elimination of damaged or misfolded proteins that might otherwise aggregate. During ageing...

Authors: Carole J Proctor, Maria Tsirigotis and Douglas A Gray

Predicting the connectivity of primate cortical networks from topological and spatial node properties

The organization of the connectivity between mammalian cortical areas has become a major subject of study, because of its important role in scaffolding the macroscopic aspects of animal behavior and intelligen...

Authors: Lucianoda F Costa, Marcus Kaiser and Claus C Hilgetag

Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes

Commonly employed clustering methods for analysis of gene expression data do not directly incorporate phenotypic data about the samples. Furthermore, clustering of samples with known phenotypes is typically pe...

Authors: Pierre R Bushel, Russell D Wolfinger and Greg Gibson

Dynamics of in silico leukocyte rolling, activation, and adhesion

We present a multilevel, agent based, in silico model that represents the dynamics of rolling, activation, and adhesion of individual leukocytes in vitro. Object-oriented software components were designed, ver...

Authors: Jonathan Tang, Klaus F Ley and C Anthony Hunt

Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery

Expert knowledge in journal articles is an important source of data for reconstructing biological pathways and creating new hypotheses. An important need for medical research is to integrate this data with hig...

Authors: William J Bosl

Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis

Lipids are an important and highly diverse class of molecules having structural, energy storage and signaling roles. Modern analytical technologies afford screening of many lipid molecular species in parallel....

Authors: Laxman Yetukuri, Mikko Katajamaa, Gema Medina-Gomez, Tuulikki Seppänen-Laakso, Antonio Vidal-Puig and Matej Orešič

Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge

Cellular processes are controlled by gene-regulatory networks. Several computational methods are currently used to learn the structure of gene-regulatory networks from data. This study focusses on time series ...

Authors: Florian Geier, Jens Timmer and Christian Fleck

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae

Current advances in genomics, proteomics and other areas of molecular biology make the identification and reconstruction of novel pathways an emerging area of great interest. One such class of pathways is invo...

Authors: Rui Alves and Albert Sorribas

Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility

Computational models of cell signaling networks typically are aimed at capturing dynamics of molecular components to derive quantitative insights from prior experimental data, and to make predictions concernin...

Authors: Sourabh Kharait, Sampsa Hautaniemi, Shan Wu, Akihiro Iwabu, Douglas A Lauffenburger and Alan Wells

Identification of functional modules using network topology and high-throughput data

With the advent of systems biology, biological knowledge is often represented today by networks. These include regulatory and metabolic networks, protein-protein interaction networks, and many others. At the s...

Authors: Igor Ulitsky and Ron Shamir

METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks

One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the ...

Authors: Christoph Gille, Sabrina Hoffmann and Hermann-Georg Holzhütter