Selection to minimise noise in living systems and its implications for the evolution of gene expression
Ben Lehner
doi:10.1038/msb.2008.11
Published online:
04 March 2008
Subject archive
Simulation and data analysis
2008
The role of disorder in interaction networks: a structural analysis
Philip M Kim, Andrea Sboner, Yu Xia & Mark Gerstein
doi:10.1038/msb.2008.16
Published online:
25 March 2008
Ultrasensitive gene regulation by positive feedback loops in nucleosome modification
Kim Sneppen, Mille A Micheelsen & Ian B Dodd
doi:10.1038/msb.2008.21
Published online:
15 April 2008
Recurrent design patterns in the feedback regulation of the mammalian signalling network
Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff & Nils Blüthgen
doi:10.1038/msb.2008.29
Published online:
06 May 2008
Understanding NF-
B signaling via mathematical modeling
Raymond Cheong, Alexander Hoffmann & Andre Levchenko
doi:10.1038/msb.2008.30
Published online:
06 May 2008
Gene network dynamics controlling keratinocyte migration
Hauke Busch, David Camacho-Trullio, Zbigniew Rogon, Kai Breuhahn, Peter Angel, Roland Eils & Axel Szabowski
doi:10.1038/msb.2008.36
Published online:
01 July 2008
Synopsis | Full Text | PDF (2,142K) | Supplementary information
Parasites lead to evolution of robustness against gene loss in host signaling networks
Marcel Salathé & Orkun S Soyer
doi:10.1038/msb.2008.44
Published online:
15 July 2008
Synopsis | Full Text | PDF (842K) | Supplementary information
Membrane identity and GTPase cascades regulated by toggle and cut-out switches
Perla Del Conte-Zerial, Lutz Brusch, Jochen C Rink, Claudio Collinet, Yannis Kalaidzidis, Marino Zerial & Andreas Deutsch
doi:10.1038/msb.2008.45
Published online:
15 July 2008
Synopsis | Full Text | PDF (380K) | Supplementary information
Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size
Jingshan Zhang, Sergei Maslov & Eugene I Shakhnovich
doi:10.1038/msb.2008.48
Published online:
05 August 2008
Synopsis | Full Text | PDF (1,746K) | Supplementary information
Isoform switching facilitates period control in the Neurospora crassa circadian clock
Ozgur E Akman, James C W Locke, Sanyi Tang, Isabelle Carré, Andrew J Millar & David A Rand
doi:10.1038/msb.2008.5
Published online:
12 February 2008
Synopsis | Full Text | PDF (390K) | Supplementary information
Survival of the sparsest: robust gene networks are parsimonious
Robert D Leclerc
doi:10.1038/msb.2008.52
Published online:
05 August 2008
A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves
Simona Digiuni, Swen Schellmann, Florian Geier, Bettina Greese, Martina Pesch, Katja Wester, Burcu Dartan, Valerie Mach, Bhylahalli Purushottam Srinivas, Jens Timmer, Christian Fleck & Martin Hulskamp
doi:10.1038/msb.2008.54
Published online:
02 September 2008
Synopsis | Full Text | PDF (3,600K) | Supplementary information
Analysis of pairwise cell interactions using an integrated dielectrophoretic-microfluidic system
Zhizhong Yin, David Noren, C Joanne Wang, Rob Hang & Andre Levchenko
doi:10.1038/msb.2008.69
Published online:
16 December 2008
Synopsis | Full Text | PDF (4,541K) | Supplementary information
Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops
Joshua W Williams, Xiaohui Cui, Andre Levchenko & Ann M Stevens
doi:10.1038/msb.2008.70
Published online:
16 December 2008
Synopsis | Full Text | PDF (400K) | Supplementary information
Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli
Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui & Hiroyuki Kurata
doi:10.1038/msb4100201
Published online:
15 January 2008
Synopsis | Full Text | PDF (1,965K) | Supplementary information
2007
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
Sean D Hooper, Stephanie Boué, Roland Krause, Lars J Jensen, Christopher E Mason, Murad Ghanim, Kevin P White, Eileen EM Furlong & Peer Bork
doi:10.1038/msb4100112
Published online:
16 January 2007
Synopsis | Full Text | PDF (552K) | Supplementary information
Chemical combination effects predict connectivity in biological systems
Joseph Lehár, Grant R Zimmermann, Andrew S Krueger, Raymond A Molnar, Jebediah T Ledell, Adrian M Heilbut, Glenn F Short, III, Leanne C Giusti, Garry P Nolan, Omar A Magid, Margaret S Lee, Alexis A Borisy, Brent R Stockwell & Curtis T Keith
doi:10.1038/msb4100116
Published online:
27 February 2007
Synopsis | Full Text | PDF (616K) | Supplementary information
How to infer gene networks from expression profiles
Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesi-Impiombato & Diego di Bernardo
doi:10.1038/msb4100120
Published online:
13 February 2007
Computational analysis of the synergy among multiple interacting genes
Dimitris Anastassiou
doi:10.1038/msb4100124
Published online:
13 February 2007
A systems biology dynamical model of mammalian G1 cell cycle progression
Thomas Haberichter, Britta Mädge, Renee A Christopher, Naohisa Yoshioka, Anjali Dhiman, Robert Miller, Rina Gendelman, Sergej V Aksenov, Iya G Khalil & Steven F Dowdy
doi:10.1038/msb4100126
Published online:
13 February 2007
Functioning and robustness of a bacterial circadian clock
Sébastien Clodong, Ulf Dühring, Luiza Kronk, Annegret Wilde, Ilka Axmann, Hanspeter Herzel & Markus Kollmann
doi:10.1038/msb4100128
Published online:
13 March 2007
Synopsis | Full Text | PDF (564K) | Supplementary information
Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks
Jacques Rougemont & Felix Naef
doi:10.1038/msb4100130
Published online:
13 March 2007
Revealing static and dynamic modular architecture of the eukaryotic protein interaction network
Kakajan Komurov & Michael White
doi:10.1038/msb4100149
Published online:
24 April 2007
Synopsis | Full Text | PDF (1,146K) | Supplementary information
The adapter importin-
provides flexible control of nuclear import at the expense of efficiency
Greg Riddick & Ian G Macara
doi:10.1038/msb4100160
Published online:
05 June 2007
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
Robert Schuetz, Lars Kuepfer & Uwe Sauer
doi:10.1038/msb4100162
Published online:
10 July 2007
Synopsis | Full Text | PDF (278K) | Supplementary information
Increased glycolytic flux as an outcome of whole-genome duplication in yeast
Gavin C Conant & Kenneth H Wolfe
doi:10.1038/msb4100170
Published online:
31 July 2007
Synopsis | Full Text | PDF (251K) | Supplementary information
Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator
Wilson W Wong, Tony Y Tsai & James C Liao
doi:10.1038/msb4100172
Published online:
31 July 2007
Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses
Marc R Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Babatunde A Ogunnaike, Jan B Hoek & Boris N Kholodenko
doi:10.1038/msb4100188
Published online:
13 November 2007
Synopsis | Full Text | PDF (646K) | Supplementary information
Deriving structure from evolution: metazoan segmentation
Paul François, Vincent Hakim & Eric D Siggia
doi:10.1038/msb4100192
Published online:
18 December 2007
Synopsis | Full Text | PDF (212K) | Supplementary information
2006
Noise resistance in the spindle assembly checkpoint
Andreas Doncic, Eshel Ben-Jacob & Naama Barkai
doi:10.1038/msb4100070
Published online:
16 May 2006
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
Anne Kümmel, Sven Panke & Matthias Heinemann
doi:10.1038/msb4100074
Published online:
20 June 2006
Synopsis | Full Text | PDF (182K) | Supplementary information
Noise in transcription negative feedback loops: simulation and experimental analysis
Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kümmerer, Mathilde Foglierini & Luis Serrano
doi:10.1038/msb4100081
Published online:
01 August 2006
Cell lineage transport: a mechanism for molecular gradient formation
Marta Ibañes, Yasuhiko Kawakami, Diego Rasskin-Gutman & Juan Carlos Izpisúa Belmonte
doi:10.1038/msb4100098
Published online:
17 October 2006
Synopsis | Full Text | PDF (514K) | Supplementary information
Imaging single molecules in living cells for systems biology
Yasushi Sako
doi:10.1038/msb4100100
Published online:
17 October 2006
Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades
Nick I Markevich, Mikhail A Tsyganov, Jan B Hoek & Boris N Kholodenko
doi:10.1038/msb4100108
Published online:
14 November 2006
Robustness and modular design of the Drosophila segment polarity network
Wenzhe Ma, Luhua Lai, Qi Ouyang & Chao Tang
doi:10.1038/msb4100111
Published online:
12 December 2006
Synopsis | Full Text | PDF (183K) | Supplementary information
2005
Local signaling with molecular diffusion as a decoder of Ca2+ signals in synaptic plasticity
Honda Naoki, Yuichi Sakumura & Shin Ishii
doi:10.1038/msb4100035
Published online:
13 December 2005
Synopsis | Full Text | PDF (417K) | Supplementary information
