BMC Systems Biology - oalib

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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

主页: http://www.biomedcentral.com/bmcsystbiol

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Inference of gene pathways using mixture Bayesian networks

Younhee Ko, ChengXiang Zhai, Sandra Rodriguez-Zas

Stochastic simulation and analysis of biomolecular reaction networks

John M Frazier, Yaroslav Chushak, Brent Foy

Simple molecular networks that respond optimally to time-periodic stimulation

Axel Cournac, Jacques-Alexandre Sepulchre

mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle

Nicola Soranzo, Mattia Zampieri, Lorenzo Farina, Claudio Altafini

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Monica L Mo, Bernhard ？ Palsson, Markus J Herrg？rd

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

Melanie I Stefan, Stuart J Edelstein, Nicolas Le Novère

Adapted Boolean network models for extracellular matrix formation

Johannes Wollbold, René Huber, Dirk Pohlers, Dirk Koczan, Reinhard Guthke, Raimund W Kinne, Ulrike Gausmann

Information theoretical quantification of cooperativity in signalling complexes

Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz, Frederic Rousseau

From gene expression to gene regulatory networks in Arabidopsis thaliana

Chris J Needham, Iain W Manfield, Andrew J Bulpitt, Philip M Gilmartin, David R Westhead

Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis

Yves Fomekong-Nanfack, Marten Postma, Jaap A Kaandorp

Inferring branching pathways in genome-scale metabolic networks

Esa Pitk？nen, Paula Jouhten, Juho Rousu

Spectral affinity in protein networks

Konstantin Voevodski, Shang-Hua Teng, Yu Xia

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

Bevan Chung, Dong-Yup Lee

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks

Avi Ma'ayan, Sherry L Jenkins, Ryan L Webb, Seth I Berger, Sudarshan P Purushothaman, Noura S Abul-Husn, Jeremy M Posner, Tony Flores, Ravi Iyengar

Bifurcation analysis informs Bayesian inference in the Hes1 feedback loop

Catherine F Higham

Information processing in the transcriptional regulatory network of yeast: Functional robustness

Frank Emmert-Streib, Matthias Dehmer

Version control of pathway models using XML patches

Peter Saffrey, Richard Orton

Reconstruction of metabolic pathways for the cattle genome

Seongwon Seo, Harris A Lewin

Identifying disease-specific genes based on their topological significance in protein networks

Zoltán Dezs？, Yuri Nikolsky, Tatiana Nikolskaya, Jeremy Miller, David Cherba, Craig Webb, Andrej Bugrim

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson, Simon Daefler

Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms

Jan Baumbach, Sven Rahmann, Andreas Tauch

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3

Donatella Cimini, Kiran R Patil, Chiara Schiraldi, Jens Nielsen

Impact of environmental inputs on reverse-engineering approach to network structures

Jianhua Wu, James L Sinfield, Vicky Buchanan-Wollaston, Jianfeng Feng

Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments

Ramon Grima

How to identify essential genes from molecular networks?

Gabriel del Rio, Dirk Koschützki, Gerardo Coello

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

Dominik M Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A Lauffenburger, Steffen Klamt, Fabian J Theis

An editor for pathway drawing and data visualization in the Biopathways Workbench

Robert W Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway

Richard J Orton, Michiel E Adriaens, Amelie Gormand, Oliver E Sturm, Walter Kolch, David R Gilbert

Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

Antonio Marco, Ignacio Marín

A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism

Jen-hwa Chu, Scott T Weiss, Vincent J Carey, Benjamin A Raby

Systematic identifiability testing for unambiguous mechanistic modeling – application to JAK-STAT, MAP kinase, and NF-κB signaling pathway models

Tom Quaiser, Martin M？nnigmann

An approach to evaluate the topological significance of motifs and other patterns in regulatory networks

Bj？rn Goemann, Edgar Wingender, Anatolij P Potapov

Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

Seth B Roberts, Jennifer L Robichaux, Arvind K Chavali, Patricio A Manque, Vladimir Lee, Ana M Lara, Jason A Papin, Gregory A Buck

On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems

Lan K Nguyen, Don Kulasiri

Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway

Maria Luisa Guerriero, Anna Dudka, Nicholas Underhill-Day, John K Heath, Corrado Priami

Identification of neutral biochemical network models from time series data

Marco Vilela, Susana Vinga, Marco Maia, Eberhard O Voit, Jonas S Almeida

On gene dosage balance in protein complexes: a comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression.

Reiner A Veitia

A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation

Reza Mobini, Bengt A Andersson, Jonas Erjef？lt, Mirjana Hahn-Zoric, Michael A Langston, Andy D Perkins, Lars Cardell, Mikael Benson

A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs

Farhan Mohammad, Priyanka Singh, Abhay Sharma

Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart

Fan Wu, Daniel A Beard

Genetic and environmental pathways to complex diseases

Julia M Gohlke, Reuben Thomas, Yonqing Zhang, Michael C Rosenstein, Allan P Davis, Cynthia Murphy, Kevin G Becker, Carolyn J Mattingly, Christopher J Portier

A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana

Le Lu, Jinming Li

Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting

Amina A Qutub, Aleksander S Popel

Coordinations between gene modules control the operation of plant amino acid metabolic networks

Hadar Less, Gad Galili

Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations

Hossein Zare, Dipen Sangurdekar, Poonam Srivastava, Mostafa Kaveh, Arkady Khodursky

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension

Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano

BowTieBuilder: modeling signal transduction pathways

Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dr？ger, Adrian Schr？der, Andreas Zell

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

Jussi Paananen, Garry Wong

Protein evolution on a human signaling network

Qinghua Cui, Enrico O Purisima, Edwin Wang

Efficient, sparse biological network determination

Elias August, Antonis Papachristodoulou

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