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BMC Systems Biology

ISSN: 1752--0509
Publisher: BioMed Central


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Multi-equilibrium property of metabolic networks: SSI module PDF available

Author(s): Lei Hong-Bo | Zhang Ji-Feng | Chen Luonan
Volume: 5
Issue: Suppl 1
Year: 2011
Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger PDF available

Author(s): Omony Jimmy | de Graaff Leo | van Straten Gerrit | van Boxtel Anton
Volume: 5
Issue: Suppl 1
Year: 2011
A trigger model of apoptosis induced by tumor necrosis factor signaling PDF available

Author(s): Gu Chang | Zhang Junjie | Chen Yingyu | Lei Jinzhi
Volume: 5
Issue: Suppl 1
Year: 2011
An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis PDF available

Author(s): Li Ru-Dong | Li Yuan-Yuan | Lu Ling-Yi | Ren Cong | Li Yi-Xue | Liu Lei
Volume: 5
Issue: Suppl 1
Year: 2011
Two-stage flux balance analysis of metabolic networks for drug target identification PDF available

Author(s): Li Zhenping | Wang Rui-Sheng | Zhang Xiang-Sun
Volume: 5
Issue: Suppl 1
Year: 2011
Network target for screening synergistic drug combinations with application to traditional Chinese medicine PDF available

Author(s): Li Shao | Zhang Bo | Zhang Ningbo
Volume: 5
Issue: Suppl 1
Year: 2011
Computational systems biology: integration of sequence, structure, network, and dynamics PDF available

Author(s): Wang Yong | Zhang Xiang-Sun | Chen Luonan
Volume: 5
Issue: Suppl 1
Year: 2011
Integrating multiple types of data to predict novel cell cycle-related genes PDF available

Author(s): Wang Lin | Hou Lin | Qian Minping | Li Fangting | Deng Minghua
Volume: 5
Issue: Suppl 1
Year: 2011
Conditional random field approach to prediction of protein-protein interactions using domain information PDF available

Author(s): Hayashida Morihiro | Kamada Mayumi | Song Jiangning | Akutsu Tatsuya
Volume: 5
Issue: Suppl 1
Year: 2011
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction PDF available

Author(s): Si Jingna | Zhang Zengming | Lin Biaoyang | Schroeder Michael | Huang Bingding
Volume: 5
Issue: Suppl 1
Year: 2011
Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context PDF available

Author(s): Wang Yong-Cui | Wang Yong | Yang Zhi-Xia | Deng Nai-Yang
Volume: 5
Issue: Suppl 1
Year: 2011
DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts PDF available

Author(s): Li Zhenhua | Wong Limsoon | Li Jinyan
Volume: 5
Issue: Suppl 1
Year: 2011
Regulatory link mapping between organisms PDF available

Author(s): Sharma Rachita | Evans Patricia | Bhavsar Virendrakumar
Volume: 5
Issue: Suppl 1
Year: 2011
Functional pathway mapping analysis for hypoxia-inducible factors PDF available

Author(s): Chuang Chia-Sheng | Pai Tun-Wen | Hu Chin-Hua | Tzou Wen-Shyong | Dah-Tsyr Chang Margaret | Chang Hao-Teng | Chen Chih-Chia
Volume: 5
Issue: Suppl 1
Year: 2011
Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells PDF available

Author(s): Saito Shigeru | Onuma Yasuko | Ito Yuzuru | Tateno Hiroaki | Toyoda Masashi | Hidenori Akutsu | Nishino Koichiro | Chikazawa Emi | Fukawatase Yoshihiro | Miyagawa Yoshitaka | Okita Hajime | Kiyokawa Nobutaka | Shimma Yohichi | Umezawa Akihiro | Hirabayashi Jun | Horimoto Katsuhisa | Asashima Makoto
Volume: 5
Issue: Suppl 1
Year: 2011
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression PDF available

Author(s): Zhou Huarong | Saito Shigeru | Piao Guanying | Liu Zhi-Ping | Wang Jiguang | Horimoto Katsuhisa | Chen Luonan
Volume: 5
Issue: Suppl 1
Year: 2011
Non-compartment model to compartment model pharmacokinetics transformation meta-analysis – a multivariate nonlinear mixed model PDF available

Author(s): Wang Zhiping | Kim Seongho | Quinney Sara | Zhou Jihao | Li Lang
Volume: 4
Issue: Suppl 1
Year: 2010
A novel gene network inference algorithm using predictive minimum description length approach PDF available

Author(s): Chaitankar Vijender | Ghosh Preetam | Perkins Edward | Gong Ping | Deng Youping | Zhang Chaoyang
Volume: 4
Issue: Suppl 1
Year: 2010
3D Protein structure prediction with genetic tabu search algorithm PDF available

Author(s): Zhang Xiaolong | Wang Ting | Luo Huiping | Yang Jack | Deng Youping | Tang Jinshan | Yang Mary
Volume: 4
Issue: Suppl 1
Year: 2010
A conceptual cellular interaction model of left ventricular remodelling post-MI: dynamic network with exit-entry competition strategy PDF available

Author(s): Wang Yunji | Han Hai-Chao | Yang Jack | Lindsey Merry | Jin Yufang
Volume: 4
Issue: Suppl 1
Year: 2010
Genome-wide analysis of regions similar to promoters of histone genes PDF available

Author(s): Chowdhary Rajesh | Bajic Vladimir | Dong Difeng | Wong Limsoon | Liu Jun
Volume: 4
Issue: Suppl 1
Year: 2010
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features PDF available

Author(s): Wang Liangjiang | Huang Caiyan | Yang Mary | Yang Jack
Volume: 4
Issue: Suppl 1
Year: 2010
Archaic chaos: intrinsically disordered proteins in Archaea PDF available

Author(s): Xue Bin | Williams Robert | Oldfield Christopher | Dunker A | Uversky Vladimir
Volume: 4
Issue: Suppl 1
Year: 2010
Is the transcript from the overlapping region of two converging genes part of either gene? PDF available

Author(s): Spence Alastair
Volume: 1
Issue: Suppl 1
Year: 2007
A global statistical test for improved detection of gene activity PDF available

Author(s): Bakewell David | Wit Ernst
Volume: 1
Issue: Suppl 1
Year: 2007
A quantitative model for the GCN4 translational control in Saccharomyces cerevisiae PDF available

Author(s): You Tao | Brown Alistair | Coghill George
Volume: 1
Issue: Suppl 1
Year: 2007
Gene regulatory network of human adipocyte differentiation PDF available

Author(s): Kumuthini Judit | Bessant Conrad | Wilson Paul | Crowther Daniel
Volume: 1
Issue: Suppl 1
Year: 2007
Predicting gene co-expression from CIS-regulatory regions PDF available

Author(s): Allen Jamie | Shirley Mark | Rushton Steve | Kohli Ajay | Mesbahi Ehsan
Volume: 1
Issue: Suppl 1
Year: 2007
A Cys-capping motif unique to small leucine-rich repeat proteins and proteoglycans of the extracellular matrix PDF available

Author(s): Park Hosil | Huxley-Jones Julie | Attwood Teresa | Bella Jordi
Volume: 1
Issue: Suppl 1
Year: 2007
Docking study on mammalian CTR1 copper importer motifs PDF available

Author(s): Zatulovskiy Evgeny | Samsonov Sergey | Skvortsov Alexej
Volume: 1
Issue: Suppl 1
Year: 2007
Visualising protein interaction networks with power graphs PDF available

Author(s): Royer Loïc | Reimann Matthias | Andreopoulos Bill | Schroeder Michael
Volume: 1
Issue: Suppl 1
Year: 2007
Molecular dynamics simulations studies of aurein 1.2 analogs in water and TFE/water PDF available

Author(s): Soofian Safiyeh | Naderimanesh Hossin
Volume: 1
Issue: Suppl 1
Year: 2007
Visualizing regulatory interactions in metabolic networks PDF available

Author(s): Noack Stephan | Wahl Aljoscha | Oldiges Marco | Wiechert Wolfgang
Volume: 1
Issue: Suppl 1
Year: 2007
Discrimination of proteins using graph theoretic properties PDF available

Author(s): Küçükural Alper | Sezerman O Ugur
Volume: 1
Issue: Suppl 1
Year: 2007
Prioritization of disease microRNAs through a human phenome-microRNAome network PDF available

Author(s): Jiang Qinghua | Hao Yangyang | Wang Guohua | Juan Liran | Zhang Tianjiao | Teng Mingxiang | Liu Yunlong | Wang Yadong
Volume: 4
Issue: Suppl 1
Year: 2010
PFF – an integrated database of residues and fragments critical for protein folding PDF available

Author(s): Corpas Manuel | Sinnott James | Thorne Dave | Pettifer Steve | Attwood Terri
Volume: 1
Issue: Suppl 1
Year: 2007
A computational tool for directing Taxus spp. cell culture metabolism from growth to Taxol®, a diterpene alkaloid, production PDF available

Author(s): Abd-Karim Khairiah | Chibani Radia | Mavituna Ferda
Volume: 1
Issue: Suppl 1
Year: 2007
Kinetic constraints on the sensitivity of large metabolic responses PDF available

Author(s): Ortega Fernando | Acerenza Luis
Volume: 1
Issue: Suppl 1
Year: 2007
Huntington's disease: from experimental results to interaction networks, patho-pathway construction and disease hypothesis PDF available

Author(s): Gonzalez-Couto Eduardo | Matteoni Silvia | Gotta Stefano | Magnoni Letizia | Heitz Freddy | Raggiaschi Roberto | Terstappen Georg | Kremer Andreas
Volume: 1
Issue: Suppl 1
Year: 2007
Context sensitivity in individual-based modeling PDF available

Author(s): Chen Chih-Chun | Clack Christopher | Nagl Sylvia
Volume: 1
Issue: Suppl 1
Year: 2007
Metabolic flux analysis for directing metabolism of Streptomyces olindensis from growth to anti-tumor drug (cosmomycin) production PDF available

Author(s): de Carvalho Lima Lobato Ana | Munoz-Hernandez Raul | Furlan Renata | Padilla Gabriel | Garrido Leandro | de Macedo Gorete | Mavituna Ferda
Volume: 1
Issue: Suppl 1
Year: 2007
DNA interaction with sperm cells: ODE model PDF available

Author(s): Kuznetsov Andrew
Volume: 1
Issue: Suppl 1
Year: 2007
Computational modelling of chemotaxis in cooperative phenomena in bacterial populations PDF available

Author(s): Doraiswamy Vinayak | Buist Martin | Goryachev Andrew
Volume: 1
Issue: Suppl 1
Year: 2007
Molecules for memory: modelling CaMKII PDF available

Author(s): Stefan Melanie | Le Novere Nicolas
Volume: 1
Issue: Suppl 1
Year: 2007
Integration of SABIO-RK in workbenches for kinetic model design PDF available

Author(s): Golebiewski Martin | Mir Saqib | Kania Renate | Krebs Olga | Weidemann Andreas | Wittig Ulrike | Rojas Isabel
Volume: 1
Issue: Suppl 1
Year: 2007
Progress toward the construction of a tri-stable genetic toggle switch in E. coli PDF available

Author(s): Lohmueller Jason | Hickey Brendan | Kaka Azeem | Gao Annie | Lemon Jamie | Lattanzi Victoria | Goldstein Peter | Tam Lick-Kong | Schmidt Meghan | Cumbers John | Gagnon James | Urabe Hayato | Jaklenec Ana | Wessel Gary
Volume: 1
Issue: Suppl 1
Year: 2007
ECOLITASTER: cellular biosensor PDF available

Author(s): Rodrigo Guillermo | Carreral Javier | Jaramillo Alfonso
Volume: 1
Issue: Suppl 1
Year: 2007
Fungal volatile fingerprints and machine learning: potential of discriminating and classifying dermatophyte species PDF available

Author(s): Sahgal Natasha | Monk Barry | Wasil Mohammad | Magan Naresh
Volume: 1
Issue: Suppl 1
Year: 2007
Computational simulations of interactions of the κ-hefutoxin1 with the voltage-gated potassium ion channels PDF available

Author(s): Zarrabi M | Naderi-Manesh H
Volume: 1
Issue: Suppl 1
Year: 2007
Chaos game representation of mitochondrial DNA: is it useful in phylogenetic studies? PDF available

Author(s): Tavassoly Iman | Tavassoly Omid | Rad Mohammad
Volume: 1
Issue: Suppl 1
Year: 2007
Set theoretical and algebraic model for redundancies in the genetic code PDF available

Author(s): Heuer Karl
Volume: 1
Issue: Suppl 1
Year: 2007
SHARKview: a tool for the visualization of systems biology data PDF available

Author(s): Pinney John | Starkovich John | Li Peter | Robertson David
Volume: 1
Issue: Suppl 1
Year: 2007
MaGnET: a software tool for integrated visualisation of functional genomic data relating to the malaria parasite PDF available

Author(s): Sharman Joanna | Gerloff Dietlind
Volume: 1
Issue: Suppl 1
Year: 2007
A bioinformatics approach for the interrogation of molecular events in single cells: transforming fluorescent time-lapse microscopy images into numbers PDF available

Author(s): Khan Imtiaz | Fisher Janet | Marquez Nuria | Smith Paul | Errington Rachel
Volume: 1
Issue: Suppl 1
Year: 2007
Visualising the immune repertoire PDF available

Author(s): Mollova Svetlana | Retter Ida | Müller Werner
Volume: 1
Issue: Suppl 1
Year: 2007
MicroRNA sequence and expression database PDF available

Author(s): Kaya Koray | Karakulah Gokhan | Yakicier Cengiz | Konu Ozlen
Volume: 1
Issue: Suppl 1
Year: 2007
How to formalise the meaning of a bio-model: a case study PDF available

Author(s): Knüpfer Christian | Beckstein Clemens | Dittrich Peter
Volume: 1
Issue: Suppl 1
Year: 2007
Pride Wizard: generation of standards compliant quantitative proteomics data PDF available

Author(s): Swainston Neil | Siepen Jennifer | Jones Andrew | Hart Sarah | Hermjakob Henning | Jones Phil | Hubbard Simon
Volume: 1
Issue: Suppl 1
Year: 2007
Designing a chemical program using chemical organization theory PDF available

Author(s): Matsumaru Naoki | Lenser Thorsten | Hinze Thomas | Dittrich Peter
Volume: 1
Issue: Suppl 1
Year: 2007
A flexible view of metabolic network PDF available

Author(s): Lo Ko-Yun | Dalby Andrew
Volume: 1
Issue: Suppl 1
Year: 2007
Abstract analysis of pathways using the BN++ software framework PDF available

Author(s): Küntzer Jan | Kneissl Benny | Kohlbacher Oliver | Lenhof Hans-Peter
Volume: 1
Issue: Suppl 1
Year: 2007
In silico prediction system of CYP450-mediated metabolism profile PDF available

Author(s): Han Hyesun | Oh Won | Jung Ji | Kim Doo | No Kyoung
Volume: 1
Issue: Suppl 1
Year: 2007
Variance stabilising transformations for NMR metabolomics data PDF available

Author(s): Parsons Helen | Viant Mark
Volume: 1
Issue: Suppl 1
Year: 2007
The complete denitrification pathway of Geobacillus thermoleovorans PDF available

Author(s): Molha Duarte | Hack Catherine | Marchant Roger
Volume: 1
Issue: Suppl 1
Year: 2007
Analysis of metabolome data by a maximum likelihood approach PDF available

Author(s): Choi Claudia | Hundertmark Claudia | Thielen Bernhard | Benkert Beatrice | Münch Richard | Schobert Max | Schomburg Dietmar | Jahn Dieter | Klawonn Frank
Volume: 1
Issue: Suppl 1
Year: 2007
Elementary flux modes – state-of-the-art implementation and scope of application PDF available

Author(s): Terzer Marco | Stelling Jörg
Volume: 1
Issue: Suppl 1
Year: 2007
Bayesian inference of the kinetic parameters of a realistic MAPK/ERK pathway PDF available

Author(s): Purutçuoğlu Vilda | Wit Ernst
Volume: 1
Issue: Suppl 1
Year: 2007
Towards a mathematical model of the cAMP pathway in S. cerevisiae PDF available

Author(s): Williamson Thomas | Bruggemann Frank | Kell Douglas | Stateva Lubomira
Volume: 1
Issue: Suppl 1
Year: 2007
Towards metabolic networks phylogeny using Petri Net-based expansional analysis PDF available

Author(s): Lanzeni Stefano | Messina Enza | Archetti Francesco
Volume: 1
Issue: Suppl 1
Year: 2007
Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model PDF available

Author(s): Zhu Shanfeng | Okuno Yasushi | Tsujimoto Gozoh | Mamitsuka Hiroshi
Volume: 1
Issue: Suppl 1
Year: 2007
Thermodynamically constrained steady state solution space of the E. coli metabolic network PDF available

Author(s): Fleming Ronan | Golden Aaron | Nasheuer Heinz-Peter
Volume: 1
Issue: Suppl 1
Year: 2007
Towards quantitative metabolome analysis PDF available

Author(s): Stein Nadine | Zeller Tina | Oldiges Marco
Volume: 1
Issue: Suppl 1
Year: 2007
A systems biology approach to modelling tea (Camellia sinensis) PDF available

Author(s): Marshall Alex | Gollapudi Sirisha | de Silva Jacquie | Hodgman Charlie
Volume: 1
Issue: Suppl 1
Year: 2007
Potential role of the glyoxalase pathway as a drug target in Leishmania infantum: an exact steady-state model analysis PDF available

Author(s): Lages Nuno | Silva Marta | Ferreira António | Tomás Ana | Cordeiro Carlos | Freire Ana
Volume: 1
Issue: Suppl 1
Year: 2007
Noise characteristics of interlocked repressilators PDF available

Author(s): Hemberg Martin | Barahona Mauricio
Volume: 1
Issue: Suppl 1
Year: 2007
SABIO-RK: a database for biochemical reactions and their kinetics PDF available

Author(s): Rojas Isabel | Golebiewski Martin | Kania Renate | Krebs Olga | Mir Saqib | Weidemann Andreas | Wittig Ulrike
Volume: 1
Issue: Suppl 1
Year: 2007
BacGrid: simulations of bacteria using the grid PDF available

Author(s): Lees Michael | Logan Brian | King John
Volume: 1
Issue: Suppl 1
Year: 2007
Modelling genetic regulatory networks from specified behaviours PDF available

Author(s): Mateus Daniel | Comet Jean-Paul | Gallois Jean-Pierre | Le Gall Pascale
Volume: 1
Issue: Suppl 1
Year: 2007
Metabolic flux analysis to study the production of a non-ribosomal lipopeptide, CDA, by Streptomyces coelicolor PDF available

Author(s): Munoz-Hernandez Raul | de Carvalho Lima Lobato Ana | Kim Hong | Mavituna Ferda
Volume: 1
Issue: Suppl 1
Year: 2007
Effect of microarray data heterogeneity on regulatory gene module discovery PDF available

Author(s): Mishra Alok | Gillies Duncan
Volume: 1
Issue: Suppl 1
Year: 2007
Computational design of proteins with new functions PDF available

Author(s): Jaramillo Alfonso | Tortosa Pablo | Rodrigo Guillermo | Suarez Maria | Carrera Javier
Volume: 1
Issue: Suppl 1
Year: 2007
Navigational control of bacteria: the design of a synthetic chemotactic biological system PDF available

Author(s): Brown James
Volume: 1
Issue: Suppl 1
Year: 2007
The relationship between domain-domain interaction orientation and sequence similarity PDF available

Author(s): Jefferson Emily | Barton Geoffrey
Volume: 1
Issue: Suppl 1
Year: 2007
Linking evolution of protein structures through fragments PDF available

Author(s): Abeln Sanne | Deane Charlotte
Volume: 1
Issue: Suppl 1
Year: 2007
Arsenic biosenseor: a step further PDF available

Author(s): French Chris | Nicholson Judith | Bizzari Farid | Aleksic Jelena | Cai Yizhi | Seshasayee Sreemati | Ivakhno Sergii | Davidson Bryony | Wilson Jen | de Mora Kim | Ma Hongwu | Kozma-Bognar Laszlo | Elfick Alistair
Volume: 1
Issue: Suppl 1
Year: 2007
New tools for self-organized pattern formation PDF available

Author(s): Bernhardt Kaj | Chand Nikhilesh | Carter Elizabeth | Lee Jisun | Xu Yang | Zhu Xueni | Rowe Duncan | Ajioka JW | Goncalves JM | Haseloff J | Micklem G
Volume: 1
Issue: Suppl 1
Year: 2007
rHVDM – a fast and user-friendly R package to predict transcription factor targets from microarray time series data PDF available

Author(s): Barenco Martino | Shah Sonia | Brewer Daniel | Callard Robin | Stark Jaroslav | Miller Crispin | Hubank Michael
Volume: 1
Issue: Suppl 1
Year: 2007
Unraveling functional networks: does gene clustering have a meaning? PDF available

Author(s): Vasieva Olga | Wolf Roland
Volume: 1
Issue: Suppl 1
Year: 2007
Modeling the arsenic biosensor system PDF available

Author(s): Cai Yizhi | Davidson Bryony | Ma Hongwu | French Chris
Volume: 1
Issue: Suppl 1
Year: 2007
Function prediction of a newly extracted protein from a newly extracted lassa virus gene PDF available

Author(s): Okoror LE | Alaiya HT | Aliga P
Volume: 1
Issue: Suppl 1
Year: 2007
ChIPMonk: software for viewing and analysing ChIP-on-chip data PDF available

Author(s): Andrews Simon
Volume: 1
Issue: Suppl 1
Year: 2007
Computational identification of tumour suppressor protein p53 target genes PDF available

Author(s): Fong Siew | Paulin Fiona | Thompson Alastair
Volume: 1
Issue: Suppl 1
Year: 2007
Registry of BioBricks models using CellML PDF available

Author(s): Rouilly Vincent | Canton Barry | Nielsen Poul | Kitney Richard
Volume: 1
Issue: Suppl 1
Year: 2007
A probabilistic context-free grammar for the detection of binding sites from a protein sequence PDF available

Author(s): Dyrka Witold | Nebel Jean-Christophe
Volume: 1
Issue: Suppl 1
Year: 2007
Flux balance analysis and its applications PDF available

Author(s): Papp Balazs | Simeonidis Evangelos
Volume: 1
Issue: Suppl 1
Year: 2007
Rate control analysis of the translation initiation pathway in S. cerevisiae PDF available

Author(s): Sangthong Padchanee | Hughes John | McCarthy John
Volume: 1
Issue: Suppl 1
Year: 2007
Identification of phenotypes in patient microarrays PDF available

Author(s): Vass J Keith | Kalna Gabriela | Higham Des
Volume: 1
Issue: Suppl 1
Year: 2007
Applications of sensitivity analysis for drug discovery and development in the ErbB receptor network PDF available

Author(s): Harms B | Lee A | Paxson R | Nielsen UB | Schoeberl B
Volume: 1
Issue: Suppl 1
Year: 2007
The NetBuilder' project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks PDF available

Author(s): Wegner Katja | Knabe Johannes | Robinson Mark | Egri-Nagy Attila | Schilstra Maria
Volume: 1
Issue: Suppl 1
Year: 2007
Modelling the comet assay PDF available

Author(s): McArt Darragh | Cairns Robert | Wasson Gillian | Saetzler Kurt
Volume: 1
Issue: Suppl 1
Year: 2007
Data mining techniques in a CGH-based breast cancer subtype profiling: an immune perspective with comparative study PDF available

Author(s): Menolascina Filippo | Tommasi Stefania | Chiarappa Patrizia | Bevilacqua Vitoantonio | Mastronardi Giuseppe | Paradiso Angelo
Volume: 1
Issue: Suppl 1
Year: 2007
Modelling gradient perception and polarization in chemotaxing Dictyostelium cells PDF available

Author(s): Krishnan Jawahar
Volume: 1
Issue: Suppl 1
Year: 2007
Using the protein interaction network to predict protein folds without homology PDF available

Author(s): Saeed Ramazan | Deane Charlotte
Volume: 1
Issue: Suppl 1
Year: 2007
Design of novel semisynethetic metalloenzyme from thermolysin PDF available

Author(s): Rahman Mohd | Jaafar Ahmad | Basri Mahiran | Rahman Raja | Salleh Abu | Wahab Habibah
Volume: 1
Issue: Suppl 1
Year: 2007
Microarrays expression measurement PDF available

Author(s): Pearson Richard
Volume: 1
Issue: Suppl 1
Year: 2007
Prediction and ranking of human protein-protein interactions within a Bayesian framework PDF available

Author(s): Scott Michelle | Barton Geoffrey
Volume: 1
Issue: Suppl 1
Year: 2007
Mathematical modelling of multi-site protein-ligand interactions PDF available

Author(s): Valeyev Najl | Kotov Nikolai | Postlethwaite Ian | Bates Declan
Volume: 1
Issue: Suppl 1
Year: 2007
Simulating epidermal growth factor receptor interaction with ligand PDF available

Author(s): McIntyre Emmet
Volume: 1
Issue: Suppl 1
Year: 2007
A Bayesian framework for integrating genomic data to aid function prediction PDF available

Author(s): Bridson Chris | Morris Richard
Volume: 1
Issue: Suppl 1
Year: 2007
A parallel algorithm for de novo peptide sequencing PDF available

Author(s): Mori Elisa | Brunetti Sara | Campa Sonia | Lodi Elena
Volume: 1
Issue: Suppl 1
Year: 2007
Computer aided multi-parameter gene design: impact of synthetic dnas on protein expression enhancement PDF available

Author(s): Notka Frank | Leikam Doris | Bauer Asli | Raab David | Graf Marcus | Wagner Ralf
Volume: 1
Issue: Suppl 1
Year: 2007
Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs PDF available

Author(s): Gu Xu | Gilbert David | Higham Des | Houslay Miles
Volume: 1
Issue: Suppl 1
Year: 2007
Similarity in expression accounts for correlated evolution of interacting proteins PDF available

Author(s): Hakes Luke | Lovell Simon | Oliver Stephen | Robertson David
Volume: 1
Issue: Suppl 1
Year: 2007
Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

Author(s): Jack John | Wambaugh John | Shah Imran
Volume: 5
Issue: 1
Year: 2011
Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella

Author(s): Yoon Hyunjin | Ansong Charles | McDermott Jason | Gritsenko Marina | Smith Richard | Heffron Fred | Adkins Joshua
Volume: 5
Issue: 1
Year: 2011
Automated Bayesian model development for frequency detection in biological time series

Author(s): Granqvist Emma | Oldroyd Giles | Morris Richard
Volume: 5
Issue: 1
Year: 2011
An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability

Author(s): Wei XN | Han BC | Zhang JX | Liu XH | Tan CY | Jiang YY | Low BC | Tidor B | Chen YZ
Volume: 5
Issue: 1
Year: 2011
Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting

Author(s): Valgepea Kaspar | Adamberg Kaarel | Vilu Raivo
Volume: 5
Issue: 1
Year: 2011
Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells

Author(s): Beurton-Aimar Marie | Beauvoit Bertrand | Monier Antoine | Vallée François | Dieuaide-Noubhani Martine | Colombié Sophie
Volume: 5
Issue: 1
Year: 2011
Combined logical and data-driven models for linking signalling pathways to cellular response

Author(s): Melas Ioannis | Mitsos Alexander | Messinis Dimitris | Weiss Thomas | Alexopoulos Leonidas
Volume: 5
Issue: 1
Year: 2011
Integrative network analysis reveals active microRNAs and their functions in gastric cancer

Author(s): Tseng Chien-Wei | Lin Chen-Ching | Chen Chiung-Nien | Huang Hsuan-Cheng | Juan Hsueh-Fen
Volume: 5
Issue: 1
Year: 2011
An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro

Author(s): Fang Hai | Jin Wen | Yang Ying | Jin Ying | Zhang Ji | Wang Kankan
Volume: 5
Issue: 1
Year: 2011
Analysis of complex metabolic behavior through pathway decomposition

Author(s): Ip Kuhn | Colijn Caroline | Lun Desmond
Volume: 5
Issue: 1
Year: 2011
Systematic quantitative characterization of cellular responses induced by multiple signals

Author(s): Al-Shyoukh Ibrahim | Yu Fuqu | Feng Jiaying | Yan Karen | Dubinett Steven | Ho Chih-Ming | Shamma Jeff | Sun Ren
Volume: 5
Issue: 1
Year: 2011
Symbolic flux analysis for genome-scale metabolic networks

Author(s): Schryer David | Vendelin Marko | Peterson Pearu
Volume: 5
Issue: 1
Year: 2011
Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes

Author(s): Chu Jen-hwa | Lazarus Ross | Carey Vincent | Raby Benjamin
Volume: 5
Issue: 1
Year: 2011
Hierarchical Cluster-based Partial Least Squares Regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models

Author(s): Tøndel Kristin | Indahl Ulf | Gjuvsland Arne | Vik Jon | Hunter Peter | Omholt Stig | Martens Harald
Volume: 5
Issue: 1
Year: 2011
Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems

Author(s): Wu Rongling | Cao Jiguo | Huang Zhongwen | Wang Zhong | Gai Junyi | Vallejos Eduardo
Volume: 5
Issue: 1
Year: 2011
From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli

Author(s): Toni Tina | Jovanovic Goran | Huvet Maxime | Buck Martin | Stumpf Michael
Volume: 5
Issue: 1
Year: 2011
Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization

Author(s): Luo Weijun | Friedman Michael | Hankenson Kurt | Woolf Peter
Volume: 5
Issue: 1
Year: 2011
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network

Author(s): Li Zhenpeng | Li Fei | Ni Ming | Li Peng | Bo Xiaochen | Wang Shengqi
Volume: 5
Issue: 1
Year: 2011
Structurally robust biological networks

Author(s): Blanchini Franco | Franco Elisa
Volume: 5
Issue: 1
Year: 2011
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Author(s): Fang Kechi | Zhao Hansheng | Sun Changyue | Lam Carolyn | Chang Suhua | Zhang Kunlin | Panda Gurudutta | Godinho Miguel | Martins dos Santos Vítor | Wang Jing
Volume: 5
Issue: 1
Year: 2011
A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana

Author(s): Meier Stuart | Tzfadia Oren | Vallabhaneni Ratnakar | Gehring Chris | Wurtzel Eleanore
Volume: 5
Issue: 1
Year: 2011
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus

Author(s): Overton Ian | Graham Shirley | Gould Katherine | Hinds Jason | Botting Catherine | Shirran Sally | Barton Geoffrey | Coote Peter
Volume: 5
Issue: 1
Year: 2011
A General Life History Theory for Effects of Caloric Restriction on Health Maintenance

Author(s): Hou Chen | Bolt Kendra | Bergman Aviv
Volume: 5
Issue: 1
Year: 2011
Cell functional enviromics: Unravelling the function of environmental factors

Author(s): Teixeira Ana | Dias João | Carinhas Nuno | Sousa Marcos | Clemente João | Cunha António | von Stosch Moritz | Alves Paula | Carrondo Manuel | Oliveira Rui
Volume: 5
Issue: 1
Year: 2011
A computational model of the hypothalamic - pituitary - gonadal axis in female fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol and 17β-trenbolone

Author(s): Li Zhenhong | Kroll Kevin | Jensen Kathleen | Villeneuve Daniel | Ankley Gerald | Brian Jayne | Sepúlveda María | Orlando Edward | Lazorchak James | Kostich Mitchell | Armstrong Brandon | Denslow Nancy | Watanabe Karen
Volume: 5
Issue: 1
Year: 2011
Expanding a dynamic flux balance model of yeast fermentation to genome-scale

Author(s): Vargas Felipe | Pizarro Francisco | Pérez-Correa J Ricardo | Agosin Eduardo
Volume: 5
Issue: 1
Year: 2011
Improved functional overview of protein complexes using inferred epistatic relationships

Author(s): Ryan Colm | Greene Derek | Guénolé Aude | van Attikum Haico | Krogan Nevan | Cunningham Pádraig | Cagney Gerard
Volume: 5
Issue: 1
Year: 2011
A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes

Author(s): Bucher Joachim | Riedmaier Stephan | Schnabel Anke | Marcus Katrin | Vacun Gabriele | Weiss Thomas | Thasler Wolfgang | Nüssler Andreas | Zanger Ulrich | Reuss Matthias
Volume: 5
Issue: 1
Year: 2011
Thermodynamically consistent model calibration in chemical kinetics

Author(s): Jenkinson Garrett | Goutsias John
Volume: 5
Issue: 1
Year: 2011
Inference of gene regulatory networks from time series by Tsallis entropy

Author(s): Lopes Fabrício | de Oliveira Evaldo | Cesar Roberto
Volume: 5
Issue: 1
Year: 2011
A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer

Author(s): Shen Changyu | Huang Yiwen | Liu Yunlong | Wang Guohua | Zhao Yuming | Wang Zhiping | Teng Mingxiang | Wang Yadong | Flockhart David | Skaar Todd | Yan Pearlly | Nephew Kenneth | Huang Tim | Li Lang
Volume: 5
Issue: 1
Year: 2011
A deterministic map of Waddington's epigenetic landscape for cell fate specification

Author(s): Bhattacharya Sudin | Zhang Qiang | Andersen Melvin
Volume: 5
Issue: 1
Year: 2011
Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition

Author(s): Xiao Xiaolin | Dawson Neil | MacIntyre Lynsey | Morris Brian | Pratt Judith | Watson David | Higham Desmond
Volume: 5
Issue: 1
Year: 2011
Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

Author(s): Larsen Peter | Sreedasyam Avinash | Trivedi Geetika | Podila Gopi | Cseke Leland | Collart Frank
Volume: 5
Issue: 1
Year: 2011
Statistical Inference Methods for Sparse Biological Time Series Data

Author(s): Ndukum Juliet | Fonseca Luís | Santos Helena | Voit Eberhard | Datta Susmita
Volume: 5
Issue: 1
Year: 2011
Network-based scoring system for genome-scale metabolic reconstructions

Author(s): Serrano M Ángeles | Sagués Francesc
Volume: 5
Issue: 1
Year: 2011
Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions

Author(s): Li Bo | Cao Weiguo | Zhou Jizhong | Luo Feng
Volume: 5
Issue: 1
Year: 2011
A protein network-guided screen for cell cycle regulators in Drosophila

Author(s): Guest Stephen | Yu Jingkai | Liu Dongmei | Hines Julie | Kashat Maria | Finley Russell
Volume: 5
Issue: 1
Year: 2011
Transcriptional robustness and protein interactions are associated in yeast

Author(s): Bekaert Michaël | Conant Gavin
Volume: 5
Issue: 1
Year: 2011
Combining experimental and mathematical modeling to reveal mechanisms of macrophage-dependent left ventricular remodeling

Author(s): Jin Yu-Fang | Han Hai- Chao | Berger Jamie | Dai Qiuxia | Lindsey Merry
Volume: 5
Issue: 1
Year: 2011
Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis

Author(s): Vempati Prakash | Popel Aleksander | Mac Gabhann Feilim
Volume: 5
Issue: 1
Year: 2011
Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease

Author(s): Pandey Priyanka | Qin Shan | Ho Jacqueline | Zhou Jing | Kreidberg Jordan
Volume: 5
Issue: 1
Year: 2011
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

Author(s): Zhang Wangshu | Chen Yong | Sun Fengzhu | Jiang Rui
Volume: 5
Issue: 1
Year: 2011
Theoretical basis of the community effect in development

Author(s): Saka Yasushi | Lhoussaine Cédric | Kuttler Celine | Ullner Ekkehard | Thiel Marco
Volume: 5
Issue: 1
Year: 2011
TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM)

Author(s): Nie Jeff | Stewart Ron | Zhang Hang | Thomson James | Ruan Fang | Cui Xiaoqi | Wei Hairong
Volume: 5
Issue: 1
Year: 2011
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network

Author(s): Ryu Taewoo | Mavromatis Charalampos | Bayer Till | Voolstra Christian | Ravasi Timothy
Volume: 5
Issue: 1
Year: 2011
A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress

Author(s): Achcar Fiona | Camadro Jean-Michel | Mestivier Denis
Volume: 5
Issue: 1
Year: 2011
Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

Author(s): Gómez Antonio | Cedano Juan | Amela Isaac | Planas Antoni | Piñol Jaume | Querol Enrique
Volume: 5
Issue: 1
Year: 2011
A Systems Biology Strategy for Predicting Similarities and Differences of Drug Effects: Evidence for Drug-specific Modulation of Inflammation in Atherosclerosis

Author(s): Kleemann Robert | Bureeva Svetlana | Perlina Ally | Kaput Jim | Verschuren Lars | Wielinga Peter | Hurt-Camejo Eva | Nikolsky Yuri | van Ommen Ben | Kooistra Teake
Volume: 5
Issue: 1
Year: 2011
A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Author(s): Carbonell Pablo | Planson Anne-Gaëlle | Fichera Davide | Faulon Jean-Loup
Volume: 5
Issue: 1
Year: 2011
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli

Author(s): Madar Daniel | Dekel Erez | Bren Anat | Alon Uri
Volume: 5
Issue: 1
Year: 2011
The coupling of pathways and processes through shared components

Author(s): Seaton Daniel | Krishnan J
Volume: 5
Issue: 1
Year: 2011
Inferring causal genomic alterations in breast cancer using gene expression data

Author(s): Tran Linh | Zhang Bin | Zhang Zhan | Zhang Chunsheng | Xie Tao | Lamb John | Dai Hongyue | Schadt Eric | Zhu Jun
Volume: 5
Issue: 1
Year: 2011
Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

Author(s): Durzinsky Markus | Wagler Annegret | Marwan Wolfgang
Volume: 5
Issue: 1
Year: 2011
Construction of a computable cell proliferation network focused on non-diseased lung cells

Author(s): Westra Jurjen | Schlage Walter | Frushour Brian | Gebel Stephan | Catlett Natalie | Han Wanjiang | Eddy Sean | Hengstermann Arnd | Matthews Andrea | Mathis Carole | Lichtner Rosemarie | Poussin Carine | Talikka Marja | Veljkovic Emilija | Van Hooser Aaron | Wong Benjamin | Maria Michael | Peitsch Manuel | Deehan Renee | Hoeng Julia
Volume: 5
Issue: 1
Year: 2011
An integrative approach to inferring biologically meaningful gene modules

Author(s): Cho Ji-Hoon | Wang Kai | Galas David
Volume: 5
Issue: 1
Year: 2011
Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis

Author(s): Vélez de Mendizábal Nieves | Carneiro Jorge | Solé Ricard | Goñi Joaquín | Bragard Jean | Martinez-Forero Ivan | Martinez-Pasamar Sara | Sepulcre Jorge | Torrealdea Javier | Bagnato Francesca | Garcia-Ojalvo Jordi | Villoslada Pablo
Volume: 5
Issue: 1
Year: 2011
Is RNA-dependent RNA polymerase essential for transposon control?

Author(s): Crombach Anton | Hogeweg Paulien
Volume: 5
Issue: 1
Year: 2011
Proteomic patterns of cervical cancer cell lines, a network perspective

Author(s): Higareda-Almaraz Juan | Enríquez-Gasca María | Hernández-Ortiz Magdalena | Resendis-Antonio Osbaldo | Encarnación-Guevara Sergio
Volume: 5
Issue: 1
Year: 2011
iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

Author(s): Imam Saheed | Yilmaz Safak | Sohmen Ugur | Gorzalski Alexander | Reed Jennifer | Noguera Daniel | Donohue Timothy
Volume: 5
Issue: 1
Year: 2011
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle

Author(s): Smith Anthony | Robinson Alan
Volume: 5
Issue: 1
Year: 2011
Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue

Author(s): Yde Pernille | Mengel Benedicte | Jensen Mogens | Krishna Sandeep | Trusina Ala
Volume: 5
Issue: 1
Year: 2011
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92

Author(s): Charusanti Pep | Chauhan Sadhana | McAteer Kathleen | Lerman Joshua | Hyduke Daniel | Motin Vladimir | Ansong Charles | Adkins Joshua | Palsson Bernhard
Volume: 5
Issue: 1
Year: 2011
Network analysis of microRNAs and their regulation in human ovarian cancer

Author(s): Schmeier Sebastian | Schaefer Ulf | Essack Magbubah | Bajic Vladimir
Volume: 5
Issue: 1
Year: 2011
Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination

Author(s): Ferreira Ana | Dias João | Teixeira Ana | Carinhas Nuno | Portela Rui | Isidro Inês | von Stosch Moritz | Oliveira Rui
Volume: 5
Issue: 1
Year: 2011
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

Author(s): Bordbar Aarash | Feist Adam | Usaite-Black Renata | Woodcock Joseph | Palsson Bernhard | Famili Iman
Volume: 5
Issue: 1
Year: 2011
Regulation of the yeast metabolic cycle by transcription factors with periodic activities

Author(s): Rao Aliz | Pellegrini Matteo
Volume: 5
Issue: 1
Year: 2011
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation

Author(s): Wangorsch Gaby | Butt Elke | Mark Regina | Hubertus Katharina | Geiger Jörg | Dandekar Thomas | Dittrich Marcus
Volume: 5
Issue: 1
Year: 2011
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae

Author(s): Glatigny Annie | Mathieu Lise | Herbert Christopher | Dujardin Geneviève | Meunier Brigitte | Mucchielli-Giorgi Marie-Hélène
Volume: 5
Issue: 1
Year: 2011
Identifying cancer biomarkers by network-constrained support vector machines

Author(s): Chen Li | Xuan Jianhua | Riggins Rebecca | Clarke Robert | Wang Yue
Volume: 5
Issue: 1
Year: 2011
Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance

Author(s): Svensson J Peter | Pesudo Laia | Fry Rebecca | Adeleye Yeyejide | Carmichael Paul | Samson Leona
Volume: 5
Issue: 1
Year: 2011
Removing bias against membrane proteins in interaction networks

Author(s): Brito Glauber | Andrews David
Volume: 5
Issue: 1
Year: 2011
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

Author(s): Tzamali Eleftheria | Poirazi Panayiota | Tollis Ioannis | Reczko Martin
Volume: 5
Issue: 1
Year: 2011
A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

Author(s): Schlage Walter | Westra Jurjen | Gebel Stephan | Catlett Natalie | Mathis Carole | Frushour Brian | Hengstermann Arnd | Van Hooser Aaron | Poussin Carine | Wong Ben | Lietz Michael | Park Jennifer | Drubin David | Veljkovic Emilija | Peitsch Manuel | Hoeng Julia | Deehan Renee
Volume: 5
Issue: 1
Year: 2011
Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network

Author(s): Liu Hui | Su Jianzhong | Li Junhua | Liu Hongbo | Lv Jie | Li Boyan | Qiao Hong | Zhang Yan
Volume: 5
Issue: 1
Year: 2011
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

Author(s): Rolfsson Ottar | Palsson Bernhard | Thiele Ines
Volume: 5
Issue: 1
Year: 2011
Noise characteristics of the Escherichia coli rotary motor

Author(s): Clausznitzer Diana | Endres Robert
Volume: 5
Issue: 1
Year: 2011
How yeast re-programmes its transcriptional profile in response to different nutrient impulses

Author(s): Dikicioglu Duygu | Karabekmez Erkan | Rash Bharat | Pir Pınar | Kirdar Betul | Oliver Stephen
Volume: 5
Issue: 1
Year: 2011
Noise and crosstalk in two quorum-sensing inputs of Vibrio fischeri

Author(s): Pérez Pablo | Weiss Joel | Hagen Stephen
Volume: 5
Issue: 1
Year: 2011
Computational modelling elucidates the mechanism of ciliary regulation in health and disease

Author(s): Kotov Nikolay | Bates Declan | Gizatullina Antonina | Gilaziev Bulat | Khairullin Rustem | Chen Michael | Drozdov Ignat | Umezawa Yoshinori | Hundhausen Christian | Aleksandrov Alexey | Yan Xing-gang | Spurgeon Sarah | Smales C Mark | Valeyev Najl
Volume: 5
Issue: 1
Year: 2011
Systemic remodeling of the redox regulatory network due to RNAi perturbations of glutaredoxin 1, thioredoxin 1, and glucose-6-phosphate dehydrogenase

Author(s): Kippner Linda | Finn Nnenna | Shukla Shreya | Kemp Melissa
Volume: 5
Issue: 1
Year: 2011
How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex

Author(s): Setty Yaki | Chen Chih-Chun | Secrier Maria | Skoblov Nikita | Kalamatianos Dimitrios | Emmott Stephen
Volume: 5
Issue: 1
Year: 2011
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

Author(s): Hädicke Oliver | Grammel Hartmut | Klamt Steffen
Volume: 5
Issue: 1
Year: 2011
Identifying Tmem59 related gene regulatory network of mouse neural stem cell from a compendium of expression profiles

Author(s): Zhang Luwen | Ju Xiangchun | Cheng Yumin | Guo Xiuyun | Wen Tieqiao
Volume: 5
Issue: 1
Year: 2011
Systems biology applied to vaccine and immunotherapy development

Author(s): Buonaguro Luigi | Wang Ena | Tornesello Maria | Buonaguro Franco | Marincola Francesco
Volume: 5
Issue: 1
Year: 2011
Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects

Author(s): Wu Wu-Hsiung | Wang Feng-Sheng | Chang Maw-Shang
Volume: 5
Issue: 1
Year: 2011
Efficient characterization of high-dimensional parameter spaces for systems biology

Author(s): Zamora-Sillero Elías | Hafner Marc | Ibig Ariane | Stelling Joerg | Wagner Andreas
Volume: 5
Issue: 1
Year: 2011
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer

Author(s): Kaur Mandeep | MacPherson Cameron | Schmeier Sebastian | Narasimhan Kothandaraman | Choolani Mahesh | Bajic Vladimir
Volume: 5
Issue: 1
Year: 2011
Environmental versatility promotes modularity in genome-scale metabolic networks

Author(s): Samal Areejit | Wagner Andreas | Martin Olivier
Volume: 5
Issue: 1
Year: 2011
Optimality and evolution of transcriptionally regulated gene expression

Author(s): Poelwijk Frank | Heyning Philip | de Vos Marjon | Kiviet Daniel | Tans Sander
Volume: 5
Issue: 1
Year: 2011
Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells

Author(s): Jennen Danyel | Ruiz-Aracama Ainhoa | Magkoufopoulou Christina | Peijnenburg Ad | Lommen Arjen | van Delft Joost | Kleinjans Jos
Volume: 5
Issue: 1
Year: 2011
MiR-206-mediated dynamic mechanism of the mammalian circadian clock

Author(s): Zhou Wei | Li Yan | Wang Xia | Wu Lianqi | Wang Yonghua
Volume: 5
Issue: 1
Year: 2011
Degeneration of penicillin production in ethanol-limited chemostat cultivations of Penicillium chrysogenum: A systems biology approach

Author(s): Douma Rutger | Batista Joana | Touw Kai | Kiel Jan | Krikken Arjen | Zhao Zheng | Veiga Tânia | Klaassen Paul | Bovenberg Roel | Daran Jean-Marc | Heijnen Joseph | van Gulik Walter
Volume: 5
Issue: 1
Year: 2011
Fluxomers: a new approach for 13C metabolic flux analysis

Author(s): Srour Orr | Young Jamey | Eldar Yonina
Volume: 5
Issue: 1
Year: 2011
Biological interaction networks are conserved at the module level

Author(s): Zinman Guy | Zhong Shan | Bar-Joseph Ziv
Volume: 5
Issue: 1
Year: 2011
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Author(s): Milne Caroline | Eddy James | Raju Ravali | Ardekani Soroush | Kim Pan-Jun | Senger Ryan | Jin Yong-Su | Blaschek Hans | Price Nathan
Volume: 5
Issue: 1
Year: 2011
Mechanisms of gap gene expression canalization in the Drosophila blastoderm

Author(s): Gursky Vitaly | Panok Lena | Myasnikova Ekaterina | Manu | Samsonova Maria | Reinitz John | Samsonov Alexander
Volume: 5
Issue: 1
Year: 2011
Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

Author(s): Pozo Carlos | Marín-Sanguino Alberto | Alves Rui | Guillén-Gosálbez Gonzalo | Jiménez Laureano | Sorribas Albert
Volume: 5
Issue: 1
Year: 2011
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

Author(s): Casey Fergal | Krogan Nevan | Shields Denis | Cagney Gerard
Volume: 5
Issue: 1
Year: 2011
Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle

Author(s): Eriksson Olivia | Andersson Tom | Zhou Yishao | Tegnér Jesper
Volume: 5
Issue: 1
Year: 2011
Analysing GCN4 translational control in yeast by stochastic chemical kinetics modelling and simulation

Author(s): You Tao | Stansfield Ian | Romano M Carmen | Brown Alistair | Coghill George
Volume: 5
Issue: 1
Year: 2011
Integrating systems biology models and biomedical ontologies

Author(s): Hoehndorf Robert | Dumontier Michel | Gennari John | Wimalaratne Sarala | de Bono Bernard | Cook Daniel | Gkoutos Georgios
Volume: 5
Issue: 1
Year: 2011
MicroRNAs coordinately regulate protein complexes

Author(s): Sass Steffen | Dietmann Sabine | Burk Ulrike | Brabletz Simone | Lutter Dominik | Kowarsch Andreas | Mayer Klaus | Brabletz Thomas | Ruepp Andreas | Theis Fabian | Wang Yu
Volume: 5
Issue: 1
Year: 2011
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

Author(s): Ruths Derek | Nakhleh Luay | Ram Prahlad
Volume: 2
Issue: 1
Year: 2008
Multiway modeling and analysis in stem cell systems biology

Author(s): Yener Bülent | Acar Evrim | Aguis Pheadra | Bennett Kristin | Vandenberg Scott | Plopper George
Volume: 2
Issue: 1
Year: 2008
Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A

Author(s): Jouhten Paula | Rintala Eija | Huuskonen Anne | Tamminen Anu | Toivari Mervi | Wiebe Marilyn | Ruohonen Laura | Penttilä Merja | Maaheimo Hannu
Volume: 2
Issue: 1
Year: 2008
Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways

Author(s): De Rajat | Das Mouli | Mukhopadhyay Subhasis
Volume: 2
Issue: 1
Year: 2008
Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

Author(s): Dias João | Oehmen Adrian | Serafim Luísa | Lemos Paulo | Reis Maria | Oliveira Rui
Volume: 2
Issue: 1
Year: 2008
A systems approach to model natural variation in reactive properties of bacterial ribosomes

Author(s): Jackson Julius | Schmidt Thomas | Herring Patricia
Volume: 2
Issue: 1
Year: 2008
Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data

Author(s): Huang Zuyi | Senocak Fatih | Jayaraman Arul | Hahn Juergen
Volume: 2
Issue: 1
Year: 2008
Seeded Bayesian Networks: Constructing genetic networks from microarray data

Author(s): Djebbari Amira | Quackenbush John
Volume: 2
Issue: 1
Year: 2008
The effects of protein interactions, gene essentiality and regulatory regions on expression variation

Author(s): Zhou Linqi | Ma Xiaotu | Sun Fengzhu
Volume: 2
Issue: 1
Year: 2008
Systematic reconstruction of TRANSPATH data into Cell System Markup Language

Author(s): Nagasaki Masao | Saito Ayumu | Li Chen | Jeong Euna | Miyano Satoru
Volume: 2
Issue: 1
Year: 2008
Time-resolved metabolomics reveals metabolic modulation in rice foliage

Author(s): Sato Shigeru | Arita Masanori | Soga Tomoyoshi | Nishioka Takaaki | Tomita Masaru
Volume: 2
Issue: 1
Year: 2008
Can single knockouts accurately single out gene functions?

Author(s): Deutscher David | Meilijson Isaac | Schuster Stefan | Ruppin Eytan
Volume: 2
Issue: 1
Year: 2008
Mathematical modeling and analysis of insulin clearance in vivo

Author(s): Koschorreck Markus | Gilles Ernst
Volume: 2
Issue: 1
Year: 2008
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach

Author(s): Valeyev Najl | Bates Declan | Heslop-Harrison Pat | Postlethwaite Ian | Kotov Nikolay
Volume: 2
Issue: 1
Year: 2008
Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory

Author(s): Heuett William | Beard Daniel | Qian Hong
Volume: 2
Issue: 1
Year: 2008
Extraction of elementary rate constants from global network analysis of E. coli central metabolism

Author(s): Zhao Jiao | Ridgway Douglas | Broderick Gordon | Kovalenko Andriy | Ellison Michael
Volume: 2
Issue: 1
Year: 2008
Defining a Modular Signalling Network from the Fly Interactome

Author(s): Baudot Anaïs | Angelelli Jean-Baptiste | Guénoche Alain | Jacq Bernard | Brun Christine
Volume: 2
Issue: 1
Year: 2008
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

Author(s): Dräger Andreas | Hassis Nadine | Supper Jochen | Schröder Adrian | Zell Andreas
Volume: 2
Issue: 1
Year: 2008
Phenotype prediction in regulated metabolic networks

Author(s): Kaleta Christoph | Centler Florian | di Fenizio Pietro | Dittrich Peter
Volume: 2
Issue: 1
Year: 2008
An ultrasensitive sorting mechanism for EGF Receptor Endocytosis

Author(s): Schmidt-Glenewinkel Hannah | Vacheva Ivayla | Hoeller Daniela | Dikic Ivan | Eils Roland
Volume: 2
Issue: 1
Year: 2008
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway

Author(s): Vera Julio | Bachmann Julie | Pfeifer Andrea | Becker Verena | Hormiga Jose | Darias Nestor | Timmer Jens | Klingmüller Ursula | Wolkenhauer Olaf
Volume: 2
Issue: 1
Year: 2008
Using genetic markers to orient the edges in quantitative trait networks: The NEO software

Author(s): Aten Jason | Fuller Tova | Lusis Aldons | Horvath Steve
Volume: 2
Issue: 1
Year: 2008
Extracting expression modules from perturbational gene expression compendia

Author(s): Maere Steven | Van Dijck Patrick | Kuiper Martin
Volume: 2
Issue: 1
Year: 2008
Hybrid optimization method with general switching strategy for parameter estimation

Author(s): Balsa-Canto Eva | Peifer Martin | Banga Julio | Timmer Jens | Fleck Christian
Volume: 2
Issue: 1
Year: 2008
Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility

Author(s): Peddinti Divyaswetha | Nanduri Bindu | Kaya Abdullah | Feugang Jean | Burgess Shane | Memili Erdogan
Volume: 2
Issue: 1
Year: 2008
OptCircuit: An optimization based method for computational design of genetic circuits

Author(s): Dasika Madhukar | Maranas Costas
Volume: 2
Issue: 1
Year: 2008
Parameter optimization in S-system models

Author(s): Vilela Marco | Chou I-Chun | Vinga Susana | Vasconcelos Ana | Voit Eberhard | Almeida Jonas
Volume: 2
Issue: 1
Year: 2008
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

Author(s): Thum Karen | Shin Michael | Gutiérrez Rodrigo | Mukherjee Indrani | Katari Manpreet | Nero Damion | Shasha Dennis | Coruzzi Gloria
Volume: 2
Issue: 1
Year: 2008
Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification

Author(s): Yang Tae Hoon | Frick Oliver | Heinzle Elmar
Volume: 2
Issue: 1
Year: 2008
On cycles in the transcription network of Saccharomyces cerevisiae

Author(s): Jeong Jieun | Berman Piotr
Volume: 2
Issue: 1
Year: 2008
Global parameter search reveals design principles of the mammalian circadian clock

Author(s): Locke James | Westermark Pål | Kramer Achim | Herzel Hanspeter
Volume: 2
Issue: 1
Year: 2008
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants

Author(s): Weston David | Gunter Lee | Rogers Alistair | Wullschleger Stan
Volume: 2
Issue: 1
Year: 2008
Linking the ovarian cancer transcriptome and immunome

Author(s): Rapberger Ronald | Perco Paul | Sax Cornelia | Pangerl Thomas | Siehs Christian | Pils Dietmar | Bernthaler Andreas | Lukas Arno | Mayer Bernd | Krainer Michael
Volume: 2
Issue: 1
Year: 2008
Eigengene networks for studying the relationships between co-expression modules

Author(s): Langfelder Peter | Horvath Steve
Volume: 1
Issue: 1
Year: 2007
Evidence of probabilistic behaviour in protein interaction networks

Author(s): Ivanic Joseph | Wallqvist Anders | Reifman Jaques
Volume: 2
Issue: 1
Year: 2008
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae

Author(s): Guzmán-Vargas Lev | Santillán Moisés
Volume: 2
Issue: 1
Year: 2008
Equilibrium model selection: dTTP induced R1 dimerization

Author(s): Radivoyevitch Tomas
Volume: 2
Issue: 1
Year: 2008
Annotating novel genes by integrating synthetic lethals and genomic information

Author(s): Schöner Daniel | Kalisch Markus | Leisner Christian | Meier Lukas | Sohrmann Marc | Faty Mahamadou | Barral Yves | Peter Matthias | Gruissem Wilhelm | Bühlmann Peter
Volume: 2
Issue: 1
Year: 2008
Identification of gene interactions associated with disease from gene expression data using synergy networks

Author(s): Watkinson John | Wang Xiaodong | Zheng Tian | Anastassiou Dimitris
Volume: 2
Issue: 1
Year: 2008
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction

Author(s): Franke Raimo | Müller Melanie | Wundrack Nicole | Gilles Ernst-Dieter | Klamt Steffen | Kähne Thilo | Naumann Michael
Volume: 2
Issue: 1
Year: 2008
Dissecting the logical types of network control in gene expression profiles

Author(s): Marr Carsten | Geertz Marcel | Hütt Marc-Thorsten | Muskhelishvili Georgi
Volume: 2
Issue: 1
Year: 2008
Receptor downregulation and desensitization enhance the information processing ability of signalling receptors

Author(s): Shankaran Harish | Wiley H Steven | Resat Haluk
Volume: 1
Issue: 1
Year: 2007
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models

Author(s): Steinke Florian | Seeger Matthias | Tsuda Koji
Volume: 1
Issue: 1
Year: 2007
Threshold-dominated regulation hides genetic variation in gene expression networks

Author(s): Gjuvsland Arne | Plahte Erik | Omholt Stig
Volume: 1
Issue: 1
Year: 2007
A simple principle concerning the robustness of protein complex activity to changes in gene expression

Author(s): Semple Jennifer | Vavouri Tanya | Lehner Ben
Volume: 2
Issue: 1
Year: 2008
Regulatory network reconstruction using an integral additive model with flexible kernel functions

Author(s): Novikov Eugene | Barillot Emmanuel
Volume: 2
Issue: 1
Year: 2008
Master equation simulation analysis of immunostained Bicoid morphogen gradient

Author(s): Wu Yu Feng | Myasnikova Ekaterina | Reinitz John
Volume: 1
Issue: 1
Year: 2007
CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data

Author(s): Neuweger Heiko | Baumbach Jan | Albaum Stefan | Bekel Thomas | Dondrup Michael | Hüser Andrea | Kalinowski Jörn | Oehm Sebastian | Pühler Alfred | Rahmann Sven | Weile Jochen | Goesmann Alexander
Volume: 1
Issue: 1
Year: 2007
Gene regulatory networks in lactation: identification of global principles using bioinformatics

Author(s): Lemay Danielle | Neville Margaret | Rudolph Michael | Pollard Katherine | German J
Volume: 1
Issue: 1
Year: 2007
Modeling protein network evolution under genome duplication and domain shuffling

Author(s): Evlampiev Kirill | Isambert Hervé
Volume: 1
Issue: 1
Year: 2007
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior

Author(s): Robertson Scott | Smith Chris | Langhans Anna | McLinden Sara | Oberhardt Matthew | Jakab Karoly | Dzamba Bette | DeSimone Douglas | Papin Jason | Peirce Shayn
Volume: 1
Issue: 1
Year: 2007
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors

Author(s): Andersson Claes | Hvidsten Torgeir | Isaksson Anders | Gustafsson Mats | Komorowski Jan
Volume: 1
Issue: 1
Year: 2007
Epstein-Barr virus latency switch in human B-cells: a physico-chemical model

Author(s): Werner Maria | Ernberg Ingemar | Zou JieZhi | Almqvist Jenny | Aurell Erik
Volume: 1
Issue: 1
Year: 2007
Analysis of global control of Escherichia coli carbohydrate uptake

Author(s): Kremling Andreas | Bettenbrock Katja | Gilles Ernst
Volume: 1
Issue: 1
Year: 2007
Modeling gene expression regulatory networks with the sparse vector autoregressive model

Author(s): Fujita André | Sato João | Garay-Malpartida Humberto | Yamaguchi Rui | Miyano Satoru | Sogayar Mari | Ferreira Carlos
Volume: 1
Issue: 1
Year: 2007
Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms

Author(s): Gjuvsland Arne | Hayes Ben | Meuwissen Theo | Plahte Erik | Omholt Stig
Volume: 1
Issue: 1
Year: 2007
A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Author(s): Alfieri Roberta | Merelli Ivan | Mosca Ettore | Milanesi Luciano
Volume: 1
Issue: 1
Year: 2007
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network

Author(s): Amoutzias Gregory | Pichler Elgar | Mian Nina | De Graaf David | Imsiridou Anastasia | Robinson-Rechavi Marc | Bornberg-Bauer Erich | Robertson David | Oliver Stephen
Volume: 1
Issue: 1
Year: 2007
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