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1.
7850 Accesses
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An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver
Linglin Xie, Brent Weichel, Joyce Ohm, Ke Zhang BMC Systems Biology 2011, 5(Suppl 3):S4 (23 December 2011)
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2.
6465 Accesses
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AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease
Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka BMC Systems Biology 2012, 6:52 (30 May 2012)
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| PubMed | Cited on BioMed Central
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Editor’s summary
AlzPathway is a publicly available database collating known Alzheimer's disease intra, inter and extra cellular signalling pathways into a comprehensive pathway map, providing a useful resource in deciphering Alzheimer's disease pathogenesis.
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3.
5362 Accesses
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Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
Daniel C Kirouac, Julio Saez-Rodriguez, Jennifer Swantek, John M Burke, Douglas A Lauffenburger, Peter K Sorger BMC Systems Biology 2012, 6:29 (1 May 2012)
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4.
5136 Accesses
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A review of imaging techniques for systems biology
Armen R Kherlopian, Ting Song, Qi Duan, Mathew A Neimark, Ming J Po, John K Gohagan, Andrew F Laine BMC Systems Biology 2008, 2:74 (12 August 2008)
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5.
5092 Accesses
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Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0
Michael Weber, Sebastian G Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J van Zoelen, Dominik Driesch BMC Systems Biology 2013, 7:1 (2 January 2013)
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6.
4931 Accesses
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Understanding network concepts in modules
Jun Dong, Steve Horvath BMC Systems Biology 2007, 1:24 (4 June 2007)
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7.
4394 Accesses
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Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis
Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui BMC Systems Biology 2012, 6:68 (15 June 2012)
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8.
4299 Accesses
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Computational codon optimization of synthetic gene for protein expression
Bevan Chung, Dong-Yup Lee BMC Systems Biology 2012, 6:134 (20 October 2012)
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Editor’s summary
A novel method for codon usage optimization in artificial gene synthesis, optimizing use of both individual codon usage and codon context approaches, is predicted to lead to improved in vitro heterologous protein expression in biotechnology applications.
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9.
4290 Accesses
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Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
Benjamin D Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P Walker BMC Systems Biology 2012, 6:55 (4 June 2012)
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| PubMed | Cited on BioMed Central
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10.
4262 Accesses
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Low-complexity regions within protein sequences have position-dependent roles
Alain Coletta, John W Pinney, David Solís, James Marsh, Steve R Pettifer, Teresa K Attwood BMC Systems Biology 2010, 4:43 (13 April 2010)
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11.
3961 Accesses
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Time-resolved metabolomics reveals metabolic modulation in rice foliage
Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, Masaru Tomita BMC Systems Biology 2008, 2:51 (18 June 2008)
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| PubMed | Cited on BioMed Central
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12.
3895 Accesses
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Crosstalk between transcription factors and microRNAs in human protein interaction network
Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang BMC Systems Biology 2012, 6:18 (13 March 2012)
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13.
3881 Accesses
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A reconfigurable NAND/NOR genetic logic gate
Angel Goñi-Moreno, Martyn Amos BMC Systems Biology 2012, 6:126 (18 September 2012)
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Editor’s summary
A novel genetic circuit is proposed and computationally tested that can be dynamically reconfigured to serve as either a NAND or NOR genetic logic gate in either single cells or cell populations.
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14.
3833 Accesses
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A general co-expression network-based approach to gene expression analysis: comparison and applications
Jianhua Ruan, Angela K Dean, Weixiong Zhang BMC Systems Biology 2010, 4:8 (2 February 2010)
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15.
3770 Accesses
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Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
Carola Huthmacher, Andreas Hoppe, Sascha Bulik, Hermann-Georg Holzhütter BMC Systems Biology 2010, 4:120 (31 August 2010)
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16.
3721 Accesses
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Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen BMC Systems Biology 2012, 6:24 (4 April 2012)
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Editor’s summary
A new genome-scale metabolic model of the industrially important yeast species Pichia stipitis and Pichia pastoris enables the modeling of growth on xylose, which is essential to optimising the production of ethanol from biomass.
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17.
3579 Accesses
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A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson, Iman Famili BMC Systems Biology 2011, 5:180 (31 October 2011)
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18.
3512 Accesses
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Network target for screening synergistic drug combinations with application to traditional Chinese medicine
Shao Li, Bo Zhang, Ningbo Zhang BMC Systems Biology 2011, 5(Suppl 1):S10 (20 June 2011)
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| PubMed | Cited on BioMed Central
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19.
3489 Accesses
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A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen
Galina Lebedeva, Azusa Yamaguchi, Simon P Langdon, Kenneth Macleod, David J Harrison BMC Systems Biology 2012, 6:138 (8 November 2012)
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Editor’s summary
A minimal mechanistic model of estrogen receptor alpha-dependent gene expression, predicts complex non-linear effects in transcriptional response to natural hormone 17 beta-estradiol and its external competitor tamoxifen under a range of biologically plausible parameter values.
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20.
3383 Accesses
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Initial characterization of the human central proteome
Thomas R Burkard, Melanie Planyavsky, Ines Kaupe, Florian P Breitwieser, Tilmann Bürckstümmer, Keiryn L Bennett, Giulio Superti-Furga, Jacques Colinge BMC Systems Biology 2011, 5:17 (26 January 2011)
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21.
3278 Accesses
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CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
Camille Terfve, Thomas Cokelaer, David Henriques, Aidan MacNamara, Emanuel Goncalves, Melody K Morris, Martijn van Iersel, Douglas A Lauffenburger, Julio Saez-Rodriguez BMC Systems Biology 2012, 6:133 (18 October 2012)
Abstract | Full text | PDF
| ePUB | PubMed | Cited on BioMed Central
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Editor’s summary
CellNOptR is an R based software package for the training of signaling networks extracted from prior knowledge using experimental data, which extends the existing CellNetOptimizer MATLAB package with further logical formalisms.
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22.
3276 Accesses
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Improving metabolic flux predictions using absolute gene expression data
Dave Lee, Kieran Smallbone, Warwick B Dunn, Ettore Murabito, Catherine L Winder, Douglas B Kell, Pedro Mendes, Neil Swainston BMC Systems Biology 2012, 6:73 (19 June 2012)
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23.
3268 Accesses
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Precise generation of systems biology models from KEGG pathways
Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell BMC Systems Biology 2013, 7:15 (21 February 2013)
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Editor’s summary
A new method allows the construction of correct BioPAX and SBML models based on data from the KEGG database, correcting KGML content and augmenting it with data from other sources to generate complete pathway models.
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24.
3265 Accesses
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The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
Ottar Rolfsson, Bernhard Ø Palsson, Ines Thiele BMC Systems Biology 2011, 5:155 (1 October 2011)
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25.
3226 Accesses
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Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii
Nanette R Boyle, John A Morgan BMC Systems Biology 2009, 3:4 (7 January 2009)
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| PubMed | Cited on BioMed Central
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