| | |  | Archive |
|
|
| | | | | | | |
Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Erik Alexandersson
|
| | BMC Systems Biology, Volume 1 |
|
Volume 1 Suppl 1
Meeting abstracts
Manchester, UK. 11 13 January 2007
more supplements 
Database
 
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
Camille Laibe, Nicolas Le Nov re
BMC Systems Biology 2007, 1:58 (13December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Threshold-dominated regulation hides genetic variation in gene expression networks
Arne B Gjuvsland, Erik Plahte, Stig W Omholt
BMC Systems Biology 2007, 1:57 (6December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Gene regulatory networks in lactation: identification of global principles using bioinformatics
Danielle G Lemay, Margaret C Neville, Michael C Rudolph, Katherine S Pollard, J Bruce German
BMC Systems Biology 2007, 1:56 (27November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
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 H ser, J rn Kalinowski, Sebastian Oehm, Alfred Phler, Sven Rahmann, Jochen Weile, Alexander Goesmann
BMC Systems Biology 2007, 1:55 (22November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Eigengene networks for studying the relationships between co-expression modules
Peter Langfelder, Steve Horvath
BMC Systems Biology 2007, 1:54 (21November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
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
BMC Systems Biology 2007, 1:53 (21November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Master equation simulation analysis of immunostained Bicoid morphogen gradient
Yu Feng Wu, Ekaterina Myasnikova, John Reinitz
BMC Systems Biology 2007, 1:52 (16November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment]
Methodology article
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models
Florian Steinke, Matthias Seeger, Koji Tsuda
BMC Systems Biology 2007, 1:51 (16November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Noise-induced switches in network systems of the genetic toggle switch
Junwei Wang, Jiajun Zhang, Zhanjiang Yuan, Tianshou Zhou
BMC Systems Biology 2007, 1:50 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Modeling protein network evolution under genome duplication and domain shuffling
Kirill Evlampiev, Herv Isambert
BMC Systems Biology 2007, 1:49 (13November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Receptor downregulation and desensitization enhance the information processing ability of signalling receptors
Harish Shankaran, H Steven Wiley, Haluk Resat
BMC Systems Biology 2007, 1:48 (9November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Commentary
Models for synthetic biology
Yiannis N Kaznessis
BMC Systems Biology 2007, 1:47 (6November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
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
BMC Systems Biology 2007, 1:46 (22October2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
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
BMC Systems Biology 2007, 1:45 (16October2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Consistency analysis of metabolic correlation networks
Mark Mller-Linow, Wolfram Weckwerth, Marc-Thorsten Htt
BMC Systems Biology 2007, 1:44 (24September2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
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
BMC Systems Biology 2007, 1:43 (20September2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Analysis of global control of Escherichia coli carbohydrate uptake
Andreas Kremling, Katja Bettenbrock, Ernst Dieter Gilles
BMC Systems Biology 2007, 1:42 (13September2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Editorial
A system for success: BMC Systems Biology, a new open access journal
Matt J Hodgkinson, Penelope A Webb
BMC Systems Biology 2007, 1:41 (4September2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Epstein-Barr virus latency switch in human B-cells: a physico-chemical model
Maria Werner, Ingemar Ernberg, JieZhi Zou, Jenny Almqvist, Erik Aurell
BMC Systems Biology 2007, 1:40 (31August2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Modeling gene expression regulatory networks with the sparse vector autoregressive model
Andr Fujita, Jo o R Sato, Humberto M Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari C Sogayar, Carlos E Ferreira
BMC Systems Biology 2007, 1:39 (30August2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
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
BMC Systems Biology 2007, 1:38 (24August2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
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
BMC Systems Biology 2007, 1:37 (6August2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Facile: a command-line network compiler for systems biology
Fernando Siso-Nadal, Julien F Ollivier, Peter S Swain
BMC Systems Biology 2007, 1:36 (3August2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
A data integration approach for cell cycle analysis oriented to model simulation in systems biology
Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi
BMC Systems Biology 2007, 1:35 (1August2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network
Gregory D Amoutzias, Elgar E Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L Robertson, Stephen G Oliver
BMC Systems Biology 2007, 1:34 (31July2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
From bit to it: How a complex metabolic network transforms information into living matter
Andreas Wagner
BMC Systems Biology 2007, 1:33 (30July2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms
Arne B Gjuvsland, Ben J Hayes, Theo HE Meuwissen, Erik Plahte, Stig W Omholt
BMC Systems Biology 2007, 1:32 (25July2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Integration of enzyme activities into metabolic flux distributions by elementary mode analysis
Hiroyuki Kurata, Quanyu Zhao, Ryuichi Okuda, Kazuyuki Shimizu
BMC Systems Biology 2007, 1:31 (18July2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli
Yohann Grondin, Derek J Raine, Vic Norris
BMC Systems Biology 2007, 1:30 (17July2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Metabolic network visualization eliminating node redundance and preserving metabolic pathways
Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Auber, Patrick Mary, Marie-France Sagot, Fabien Jourdan
BMC Systems Biology 2007, 1:29 (3July2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Commentary
The long journey to a Systems Biology of neuronal function
Nicolas Le Novre
BMC Systems Biology 2007, 1:28 (13June2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Non-linear dimensionality reduction of signaling networks
Sergii Ivakhno, J Douglas Armstrong
BMC Systems Biology 2007, 1:27 (8June2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
Neema Jamshidi, Bernhard  Palsson
BMC Systems Biology 2007, 1:26 (8June2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
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
BMC Systems Biology 2007, 1:25 (5June2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Understanding network concepts in modules
Jun Dong, Steve Horvath
BMC Systems Biology 2007, 1:24 (4June2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks
Andreas Hoppe, Sabrina Hoffmann, Hermann-Georg Holzhtter
BMC Systems Biology 2007, 1:23 (1June2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
RMBNToolbox: random models for biochemical networks
Tommi Aho, Olli-Pekka Smolander, Jari Niemi, Olli Yli-Harja
BMC Systems Biology 2007, 1:22 (24May2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment]
Methodology article
A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells
Zheng Li, Shireesh Srivastava, Xuerui Yang, Sheenu Mittal, Paul Norton, James Resau, Brian Haab, Christina Chan
BMC Systems Biology 2007, 1:21 (11May2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
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
BMC Systems Biology 2007, 1:20 (4May2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
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
BMC Systems Biology 2007, 1:19 (16April2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
Tunahan  ak r, Betl Krdar, Z  lsen  nsan, Kutlu  lgen, Jens Nielsen
BMC Systems Biology 2007, 1:18 (27March2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline
Carole J Proctor, Maria Tsirigotis, Douglas A Gray
BMC Systems Biology 2007, 1:17 (21March2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting the connectivity of primate cortical networks from topological and spatial node properties
Luciano da F Costa, Marcus Kaiser, Claus C Hilgetag
BMC Systems Biology 2007, 1:16 (8March2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes
Pierre R Bushel, Russell D Wolfinger, Greg Gibson
BMC Systems Biology 2007, 1:15 (23February2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Dynamics of in silico leukocyte rolling, activation, and adhesion
Jonathan Tang, Klaus F Ley, C Anthony Hunt
BMC Systems Biology 2007, 1:14 (19February2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery
William J Bosl
BMC Systems Biology 2007, 1:13 (15February2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis
Laxman Yetukuri, Mikko Katajamaa, Gema Medina-Gomez, Tuulikki Seppnen-Laakso, Antonio Vidal-Puig, Matej Ore i
BMC Systems Biology 2007, 1:12 (15February2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
Florian Geier, Jens Timmer, Christian Fleck
BMC Systems Biology 2007, 1:11 (2February2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae
Rui Alves, Albert Sorribas
BMC Systems Biology 2007, 1:10 (31January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
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
BMC Systems Biology 2007, 1:9 (29January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Identification of functional modules using network topology and high-throughput data
Igor Ulitsky, Ron Shamir
BMC Systems Biology 2007, 1:8 (26January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes
Vassilios Sotiropoulos, Yiannis N Kaznessis
BMC Systems Biology 2007, 1:7 (9January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Stochastic synchronization of genetic oscillator networks
Chunguang Li, Luonan Chen, Kazuyuki Aihara
BMC Systems Biology 2007, 1:6 (9January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks
Christoph Gille, Sabrina Hoffmann, Hermann-Georg Holzhtter
BMC Systems Biology 2007, 1:5 (9January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Qualitative networks: a symbolic approach to analyze biological signaling networks
Marc A Schaub, Thomas A Henzinger, Jasmin Fisher
BMC Systems Biology 2007, 1:4 (8January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
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 Ping Zhao, John L Hartman IV
BMC Systems Biology 2007, 1:3 (8January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Structural and functional analysis of cellular networks with CellNetAnalyzer
Steffen Klamt, Julio Saez-Rodriguez, Ernst D Gilles
BMC Systems Biology 2007, 1:2 (8January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network
Ofer Meshi, Tomer Shlomi, Eytan Ruppin
BMC Systems Biology 2007, 1:1 (8January2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
|
| 
BMC Systems Biology Volumes |
| | |
|
