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BMC Systems Biology

ISSN Print: 1752-0509

ISSN Online:

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

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Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility

Divyaswetha Peddinti, Bindu Nanduri, Abdullah Kaya, Jean M Feugang, Shane C Burgess, Erdogan Memili

A quantitative estimation of the global translational activity in logarithmically growing yeast cells

Tobias von der Haar

The dynamics and efficacy of antiviral RNA silencing: A model study

Marian AC Groenenboom, Paulien Hogeweg

Employing conservation of co-expression to improve functional inference

Carsten O Daub, Erik LL Sonnhammer

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

Juan Nogales, Bernhard ？ Palsson, Ines Thiele

Machine learning based analyses on metabolic networks supports high-throughput knockout screens

Kitiporn Plaimas, Jan-Phillip Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer K？nig

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

Derek Ruths, Luay Nakhleh, Prahlad T Ram

An in silico method for detecting overlapping functional modules from composite biological networks

Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos

Dynamics of receptor and protein transducer homodimerisation

Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana

Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants

David J Weston, Lee E Gunter, Alistair Rogers, Stan D Wullschleger

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

Ana Oliveira, Kiran Patil, Jens Nielsen

Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

Wei Jiang, Xia Li, Shaoqi Rao, Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, Baofeng Yang

Stochastic synchronization of genetic oscillator networks

Chunguang Li, Luonan Chen, Kazuyuki Aihara

Dynamic morphometric characterization of local connective tissue network structure in humans using ultrasound

Helene M Langevin, Donna M Rizzo, James R Fox, Gary J Badger, Junru Wu, Elisa E Konofagou, Debbie Stevens-Tuttle, Nicole A Bouffard, Martin H Krag

Non-linear dimensionality reduction of signaling networks

Sergii Ivakhno, J Douglas Armstrong

Modeling protein network evolution under genome duplication and domain shuffling

Kirill Evlampiev, Hervé Isambert

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

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

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

Pierre R Bushel, Russell D Wolfinger, Greg Gibson

Gene regulatory networks in lactation: identification of global principles using bioinformatics

Danielle G Lemay, Margaret C Neville, Michael C Rudolph, Katherine S Pollard, J German

Integration of enzyme activities into metabolic flux distributions by elementary mode analysis

Hiroyuki Kurata, Quanyu Zhao, Ryuichi Okuda, Kazuyuki Shimizu

The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli

Yohann Grondin, Derek J Raine, Vic Norris

Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana

Miyako Kusano, Atsushi Fukushima, Masanori Arita, P？r Jonsson, Thomas Moritz, Makoto Kobayashi, Naomi Hayashi, Takayuki Tohge, Kazuki Saito

CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data

Heiko Neuweger, Jan Baumbach, Stefan Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, J？rn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile, Alexander Goesmann

Master equation simulation analysis of immunostained Bicoid morphogen gradient

Yu Feng Wu, Ekaterina Myasnikova, John Reinitz

Eigengene networks for studying the relationships between co-expression modules

Peter Langfelder, Steve Horvath

New insights about host response to smallpox using microarray data

Gustavo H Esteves, Ana CQ Simoes, Estevao Souza, Rodrigo A Dias, Raydonal Ospina, Thiago M Venancio

From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data

Rainer Opgen-Rhein, Korbinian Strimmer

Threshold-dominated regulation hides genetic variation in gene expression networks

Arne B Gjuvsland, Erik Plahte, Stig W Omholt

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

Rui Alves, Albert Sorribas

Understanding network concepts in modules

Jun Dong, Steve Horvath

Dynamics of in silico leukocyte rolling, activation, and adhesion

Jonathan Tang, Klaus F Ley, C Anthony Hunt

Epstein-Barr virus latency switch in human B-cells: a physico-chemical model

Maria Werner, Ingemar Ernberg, JieZhi Zou, Jenny Almqvist, Erik Aurell

From bit to it: How a complex metabolic network transforms information into living matter

Andreas Wagner

Noise-induced switches in network systems of the genetic toggle switch

Junwei Wang, Jiajun Zhang, Zhanjiang Yuan, Tianshou Zhou

Receptor downregulation and desensitization enhance the information processing ability of signalling receptors

Harish Shankaran, H Steven Wiley, Haluk Resat

Models for synthetic biology

Yiannis N Kaznessis

Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors

Claes R Andersson, Torgeir R Hvidsten, Anders Isaksson, Mats G Gustafsson, Jan Komorowski

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

Christoph Gille, Sabrina Hoffmann, Hermann-Georg Holzhütter

Computational cell model based on autonomous cell movement regulated by cell-cell signalling successfully recapitulates the "inside and outside" pattern of cell sorting

Takuya T Maeda, Itsuki Ajioka, Kazunori Nakajima

Analysis of global control of Escherichia coli carbohydrate uptake

Andreas Kremling, Katja Bettenbrock, Ernst Gilles

Consistency analysis of metabolic correlation networks

Mark Müller-Linow, Wolfram Weckwerth, Marc-Thorsten Hütt

Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays

Najaf A Shah, Richard J Laws, Bradley Wardman, Lue Zhao, John L Hartman

Structural and functional analysis of cellular networks with CellNetAnalyzer

Steffen Klamt, Julio Saez-Rodriguez, Ernst D Gilles

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network

Ofer Meshi, Tomer Shlomi, Eytan Ruppin

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

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

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

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

Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior

Scott H Robertson, Chris K Smith, Anna L Langhans, Sara E McLinden, Matthew A Oberhardt, Karoly R Jakab, Bette Dzamba, Douglas W DeSimone, Jason A Papin, Shayn M Peirce

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

Andreas Hoppe, Sabrina Hoffmann, Hermann-Georg Holzhütter

A system for success: BMC Systems Biology, a new open access journal

Matt J Hodgkinson, Penelope A Webb

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