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EURASIP Journal on Bioinformatics and Systems Biology

ISSN Print: 1687-4153

ISSN Online:

Website: http://bsb.eurasipjournals.com

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Subtyping glioblastoma by combining miRNA and mRNA expression data using compressed sensing-based approach

Wenlong Tang, Junbo Duan, Ji-Gang Zhang, Yu-Ping Wang

Properties of Boolean networks and methods for their tests

Johannes Georg Klotz, Ronny Feuer, Oliver Sawodny, Martin Bossert, Michael Ederer, Steffen Schober

On the dynamical properties of a model of cell differentiation

Marco Villani, Roberto Serra

Protein network-based Lasso regression model for the construction of disease-miRNA functional interactions

Ala Qabaja, Mohammed Alshalalfa, Tarek A Bismar, Reda Alhajj

From microscopy data to in silico environments for in vivo-oriented simulations

Noriko Hiroi1, Michael Klann, Keisuke Iba, Pablo Heras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi, Heinz Koeppl

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

Kirk K Durston, David KY Chiu, Andrew KC Wong, Gary CL Li

Phase computations and phase models for discrete molecular oscillators

Onder Suvak, Alper Demir

A visual analytics approach for models of heterogeneous cell populations

Jan Hasenauer, Julian Heinrich, Malgorzata Doszczak, Peter Scheurich, Daniel Weiskopf, Frank Allg？wer

A novel cost function to estimate parameters of oscillatory biochemical systems

Seyedbehzad Nabavi, Cranos M Williams

In vitro detection of adrenocorticotropic hormone levels by fluorescence correlation spectroscopy immunoassay for mathematical modeling of glucocorticoid-mediated feedback mechanisms

Martin Puchinger, Clemens Zarzer, Philipp Kügler, Erwin Gaubitzer, Gottfried K？hler

A top-down approach to classify enzyme functional classes and sub-classes using random forest

Chetan Kumar, Alok Choudhary

Determination of minimal transcriptional signatures of compounds for target prediction

Florian Nigsch, Janna Hutz, Ben Cornett, Douglas W Selinger, Gregory McAllister, Somnath Bandyopadhyay, Joseph Loureiro, Jeremy L Jenkins

Identification of CpG islands in DNA sequences using statistically optimal null filters

Rajasekhar Kakumani, Omair Ahmad, Vijay Devabhaktuni

Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway

Peteris Zikmanis, Inara Kampenusa

The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae

Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Sonia Colombo, Enzo Martegani

Map-invariant spectral analysis for the identification of DNA periodicities

Ahmad Rushdi, Jamal Tuqan, Thomas Strohmer

Dynamical modeling of drug effect using hybrid systems

Xiangfang Li, lijun Qian, Edward R Dougherty

Optimal reference sequence selection for genome assembly using minimum description length principle

Bilal Wajid, Erchin Serpedin, Mohamed Nounou, Hazem Nounou

Relations between the set-complexity and the structure of graphsand their sub-graphs

Tomasz M Ignac, Nikita A Sakhanenko, David J Galas

Fastbreak: a tool for analysis and visualization of structural variations in genomic data

Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo Knijnenburg, John Boyle, Ilya Shmulevich

Approximate maximum likelihood estimation for stochastic chemical kinetics

Aleksandr Andreychenko, Linar Mikeev, David Spieler, Verena Wolf

Modeling stochasticity and variability in gene regulatory networks

David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Seda Arat, Reinhard Laubenbacher

Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

Ronny Feuer, Katrin Gottlieb, Gero Viertel, Johannes Klotz, Steffen Schober, Martin Bossert, Oliver Sawodny, Georg Sprenger, Michael Ederer

Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation

Johannes Witt, Sandra Barisic, Oliver Sawodny, Michael Ederer, Dagmar Kulms, Thomas Sauter

Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D

J A？imovi？, T M？ki-Marttunen, R Havela, H Teppola, M-L Linne

A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana

Sebastian Henkel, Thomas N？gele, Imke H？rmiller, Thomas Sauter, Oliver Sawodny, Michael Ederer, Arnd G Heyer

Detecting controlling nodes of boolean regulatory networks

Steffen Schober, David Kracht, Reinhard Heckel, Martin Bossert

Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

Syed Baker, C Poskar, Bj？rn H Junker

Measuring and analyzing tissue specificity of human genes and protein complexes

Dorothea Emig, Tim Kacprowski, Mario Albrecht

Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems

Zhouyi Xu, Xiaodong Cai

Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks

Elena S Dimitrova, Indranil Mitra, Abdul Jarrah

Modeling Signal Transduction Leading to Synaptic Plasticity: Evaluation and Comparison of Five Models

Tiina Manninen, Katri Hituri, Eeva Toivari, Marja-Leena Linne

A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics

Tonny J Oyana

Polynomial-Time Algorithm for Controllability Test of a Class of Boolean Biological Networks

Koichi Kobayashi, Jun-Ichi Imura, Kunihiko Hiraishi

A Hypothesis Test for Equality of Bayesian Network Models

Anthony Almudevar

Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data—A Model-Based Study

Youting Sun, Ulisses Braga-Neto, EdwardR Dougherty

TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites

Michael P Weir, Michael D Rice

A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process

Jie Chen, Ayten Yi？iter, Yu-Ping Wang, Hong-Wen Deng

Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation

Henrik Mannerstrom, Olli Yli-Harja, Andre S Ribeiro

Selection of Statistical Thresholds in Graphical Models

Anthony Almudevar

Progression Analysis and Stage Discovery in Continuous Physiological Processes Using Image Computing

Lior Shamir, Salim Rahimi, Nikita Orlov, Luigi Ferrucci, Ilya G Goldberg

Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited

Babak Faryabi, Golnaz Vahedi, Jean-Francois Chamberland, Aniruddha Datta, EdwardR Dougherty

Transition Dependency: A Gene-Gene Interaction Measure for Times Series Microarray Data

Xin Gao, Daniel Q Pu, Peter X-K Song

A Hybrid Technique for the Periodicity Characterization of Genomic Sequence Data

Julien Epps

Reverse Engineering of Gene Regulatory Networks: A Comparative Study

Hendrik Hache, Hans Lehrach, Ralf Herwig

Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge

Wentao Zhao, Erchin Serpedin, Edward R Dougherty

Stochastic Simulation of Delay-Induced Circadian Rhythms in Drosophila

Zhouyi Xu, Xiaodong Cai

Network Structure and Biological Function: Reconstruction, Modeling, and Statistical Approaches

Joachim Selbig, Matthias Steinfath, Dirk Repsilber

Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks

Chushin Koh, Fang-Xiang Wu, Gopalan Selvaraj, Anthony J Kusalik

Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?

TT Vu, UM Braga-Neto

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