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  1. Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we p...

    Authors: Sebastian Henkel, Thomas Nägele, Imke Hörmiller, Thomas Sauter, Oliver Sawodny, Michael Ederer and Arnd G Heyer
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:2
  2. Elucidating the structure and/or dynamics of gene regulatory networks from experimental data is a major goal of systems biology. Stochastic models have the potential to absorb noise, account for un-certainty, ...

    Authors: Elena S Dimitrova, Indranil Mitra and Abdul Salam Jarrah
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:1
  3. An essential phenomenon of the functional brain is synaptic plasticity which is associated with changes in the strength of synapses between neurons. These changes are affected by both extracellular and intrace...

    Authors: Tiina Manninen, Katri Hituri, Eeva Toivari and Marja-Leena Linne
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:797250
  4. We simulate the growth of neuronal networks using the two recently published tools, NETMORPH and CX3D. The goals of the work are (1) to examine and compare the simulation tools, (2) to construct a model of gro...

    Authors: J Aćimović, T Mäki-Marttunen, R Havela, H Teppola and M-L Linne
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:616382
  5. We propose a Markov chain approximation of the delayed stochastic simulation algorithm to infer properties of the mechanisms in prokaryote transcription from the dynamics of RNA levels. We model transcription ...

    Authors: Henrik Mannerstrom, Olli Yli-Harja and Andre S Ribeiro
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2011:572876
  6. Relative individual information is a measurement that scores the quality of DNA- and RNA-binding sites for biological machines. The development of analytical approaches to increase the power of this scoring me...

    Authors: Michael P. Weir and Michael D. Rice
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2010:814127
  7. To study chromosomal aberrations that may lead to cancer formation or genetic diseases, the array-based Comparative Genomic Hybridization (aCGH) technique is often used for detecting DNA copy number variants (...

    Authors: Jie Chen, Ayten Yiğiter, Yu-Ping Wang and Hong-Wen Deng
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2010:268513
  8. Bayesian network models are commonly used to model gene expression data. Some applications require a comparison of the network structure of a set of genes between varying phenotypes. In principle, separately f...

    Authors: Anthony Almudevar
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2010:947564
  9. In recent years, Boolean-network-model-based approaches to dynamical analysis of complex biological networks such as gene regulatory networks have been extensively studied. One of the fundamental problems in c...

    Authors: Koichi Kobayashi, Jun-Ichi Imura and Kunihiko Hiraishi
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2010:210685
  10. We propose an image computing-based method for quantitative analysis of continuous physiological processes that can be sensed by medical imaging and demonstrate its application to the analysis of morphological...

    Authors: Lior Shamir, Salim Rahimi, Nikita Orlov, Luigi Ferrucci and Ilya G Goldberg
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2010:107036
  11. Reconstruction of gene regulatory networks based on experimental data usually relies on statistical evidence, necessitating the choice of a statistical threshold which defines a significant biological effect. ...

    Authors: Anthony Almudevar
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2009:878013
  12. Many missing-value (MV) imputation methods have been developed for microarray data, but only a few studies have investigated the relationship between MV imputation and classification accuracy. Furthermore, the...

    Authors: Youting Sun, Ulisses Braga-Neto and Edward R. Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2010 2009:504069
  13. Computational gene regulation models provide a means for scientists to draw biological inferences from time-course gene expression data. Based on the state-space approach, we developed a new modeling tool for ...

    Authors: Chushin Koh, Fang-Xiang Wu, Gopalan Selvaraj and Anthony J. Kusalik
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:484601
  14. Circadian rhythms are ubiquitous in all eukaryotes and some prokaryotes. Several computational models with or without time delays have been developed for circadian rhythms. Exact stochastic simulations have be...

    Authors: Zhouyi Xu and Xiaodong Cai
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:386853
  15. Reverse engineering of gene regulatory networks has been an intensively studied topic in bioinformatics since it constitutes an intermediate step from explorative to causative gene expression analysis. Many me...

    Authors: Hendrik Hache, Hans Lehrach and Ralf Herwig
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:617281
  16. Understanding the mechanisms of gene transcriptional regulation through analysis of high-throughput postgenomic data is one of the central problems of computational systems biology. Various approaches have bee...

    Authors: Kuang Lin and Dirk Husmeier
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:601068
  17. A method for gene clustering from expression profiles using shape information is presented. The conventional clustering approaches such as K-means assume that genes with similar functions have similar expressi...

    Authors: Travis J Hestilow and Yufei Huang
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:195712
  18. Based on time series gene expressions, cyclic genes can be recognized via spectral analysis and statistical periodicity detection tests. These cyclic genes are usually associated with cyclic biological process...

    Authors: Wentao Zhao, Erchin Serpedin and Edward R. Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:683463
  19. Based on gene expression profiles, genes can be partitioned into clusters, which might be associated with biological processes or functions, for example, cell cycle, circadian rhythm, and so forth. This paper ...

    Authors: Wentao Zhao, Erchin Serpedin and Edward R. Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:713248
  20. There has been considerable interest recently in the application of bagging in the classification of both gene-expression data and protein-abundance mass spectrometry data. The approach is often justified by t...

    Authors: TT Vu and UM Braga-Neto
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:158368
  21. An approximate representation for the state space of a context-sensitive probabilistic Boolean network has previously been proposed and utilized to devise therapeutic intervention strategies. Whereas the full ...

    Authors: Babak Faryabi, Golnaz Vahedi, Jean-Francois Chamberland, Aniruddha Datta and EdwardR Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:360864
  22. To accomplish adaptability, all living organisms are constructed of regulatory networks on different levels which are capable to differentially respond to a variety of environmental inputs. Structure of regula...

    Authors: Dirk Repsilber, Thomas Martinetz and Mats Björklund
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:618502
  23. Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to ...

    Authors: Mingzhou(Joe) Song, Chris K. Lewis, Eric R. Lance, Elissa J. Chesler, Roumyana Kirova Yordanova, Michael A. Langston, Kerrie H. Lodowski and Susan E. Bergeson
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:545176
  24. We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize differe...

    Authors: Oliver Ebenhöh and Thomas Handorf
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:570456
  25. While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignor...

    Authors: Muhammad Shoaib B Sehgal, Iqbal Gondal, Laurence S Dooley and Ross Coppel
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:717136
  26. Gene-Gene dependency plays a very important role in system biology as it pertains to the crucial understanding of different biological mechanisms. Time-course microarray data provides a new platform useful to ...

    Authors: Xin Gao, Daniel Q. Pu and Peter X.-K. Song
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:535869
  27. Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor ...

    Authors: Wei Dai, Mona A Sheikh, Olgica Milenkovic and Richard G Baraniuk
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:162824
  28. In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work...

    Authors: P. van Nes, D. Bellomo, M.J.T. Reinders and D. de Ridder
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:630695
  29. The reverse engineering of transcription regulatory networks from expression data is gaining large interest in the bioinformatics community. An important family of inference techniques is represented by algori...

    Authors: Catharina Olsen, Patrick E Meyer and Gianluca Bontempi
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:308959
  30. Nested effects models (NEMs) are a class of probabilistic models that were designed to reconstruct a hidden signalling structure from a large set of observable effects caused by active interventions into the s...

    Authors: Cordula Zeller, Holger Fröhlich and Achim Tresch
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:195272
  31. Modelling in systems biology often involves the integration of component models into larger composite models. How to do this systematically and efficiently is a significant challenge: coupling of components ca...

    Authors: Linzhong Li, RobertM Seymour and Stephen Baigent
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:308623
  32. Differential equation models for biological oscillators are often not robust with respect to parameter variations. They are based on chemical reaction kinetics, and solutions typically converge to a fixed poin...

    Authors: Nicole Radde
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:327503
  33. Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model t...

    Authors: Sophie Schbath, Vincent Lacroix and Marie-France Sagot
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:616234
  34. We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our...

    Authors: Sandra Andorf, Tanja Gärtner, Matthias Steinfath, Hanna Witucka-Wall, Thomas Altmann and Dirk Repsilber
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:147157
  35. A Boolean network (BN) is a mathematical model of genetic networks. We propose several algorithms for control of singleton attractors in BN. We theoretically estimate the average-case time complexities of the ...

    Authors: Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Shu-Qin Zhang and Wai-Ki Ching
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:521407
  36. Recent advances in high-throughput DNA microarrays and chromatin immunoprecipitation (ChIP) assays have enabled the learning of the structure and functionality of genetic regulatory networks. In light of these...

    Authors: Wentao Zhao, Erchin Serpedin and Edward R Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:248747
  37. Time series microarray measurements of gene expressions have been exploited to discover genes involved in cell cycles. Due to experimental constraints, most microarray observations are obtained through irregul...

    Authors: Wentao Zhao, Kwadwo Agyepong, Erchin Serpedin and Edward R Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:769293
  38. The inference of genetic regulatory networks from global measurements of gene expressions is an important problem in computational biology. Recent studies suggest that such dynamical molecular systems are pois...

    Authors: Wenbin Liu, Harri Lähdesmäki, Edward R Dougherty and Ilya Shmulevich
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:780541
  39. Two-level gene regulatory networks consist of the transcription factors (TFs) in the top level and their regulated genes in the second level. The expression profiles of the regulated genes are the observed hig...

    Authors: Iosifina Pournara and Lorenz Wernisch
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:172840
  40. A key objective of gene network modeling is to develop intervention strategies to alter regulatory dynamics in such a way as to reduce the likelihood of undesirable phenotypes. Optimal stationary intervention ...

    Authors: Babak Faryabi, Golnaz Vahedi, Jean-Francois Chamberland, Aniruddha Datta and Edward R Dougherty
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:620767
  41. This paper presents a novel feature vector based on physicochemical property of amino acids for prediction protein structural classes. The proposed method is divided into three different stages. First, a discr...

    Authors: Ravi Gupta, Ankush Mittal and Kuldip Singh
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:235451
  42. Structured information provided by manual annotation of proteins with Gene Ontology concepts represents a high-quality reliable data source for the research community. However, a limited scope of proteins is a...

    Authors: S Gaudan, A Jimeno Yepes, V Lee and D Rebholz-Schuhmann
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2008:342746