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BMC Systems Biology, Volume 5
Volume 5, 2011
- Atsushi Fukushima
, Miyako Kusano
, Henning Redestig
, Masanori Arita, Kazuki Saito
:
Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. 1 - Patrik Sahlin, Pontus Melke, Henrik Jönsson:
Models of sequestration and receptor cross-talk for explaining multiple mutants in plant stem cell regulation. 2 - John H. Gauthier, Phillip I. Pohl:
A general framework for modeling growth and division of mammalian cells. 3 - Olaf Wolkenhauer
, Darryl Shibata, Mihajlo D. Mesarovic:
A stem cell niche dominance theorem. 4 - Lope A. Flórez, Katrin Gunka, Rafael Polanía
, Stefan Tholen
, Jörg Stülke
:
SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants. 5 - Shiek S. S. J. Ahmed, Abdul R. Ahameethunisa, Winkins Santosh, Srinivasa Chakravarthy, Suresh Kumar:
Systems biological approach on neurological disorders: a novel molecular connectivity to aging and psychiatric diseases. 6 - Sergey Kozhenkov, Mayya Sedova
, Yulia Dubinina, Amarnath Gupta, Animesh Ray
, Julia V. Ponomarenko
, Michael Baitaluk:
BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies. 7 - Ines Thiele
, Daniel R. Hyduke, Benjamin Steeb, Guy Fankam, Douglas K. Allen
, Susanna Bazzani, Pep Charusanti
, Feng-Chi Chen, Ronan M. T. Fleming
, Chao A. Hsiung, Sigrid C. J. De Keersmaecker
, Yu-Chieh Liao
, Kathleen Marchal
, Monica L. Mo, Emre Özdemir
, Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir
, Jonas Steinmann, Suresh Sudarsan
, Neil Swainston, Inge M. Thijs, Karsten Zengler
, Bernhard O. Palsson, Joshua N. Adkins
, Dirk Bumann:
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. 8 - Konstantinos Biliouris, Prodromos Daoutidis, Yiannis N. Kaznessis
:
Stochastic simulations of the tetracycline operon. 9 - Sylvia Haus, Sara Jabbari
, Thomas Millat
, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R. King
, Olaf Wolkenhauer
:
A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture. 10 - Marc Weber
, Javier Buceta
:
Noise regulation by quorum sensing in low mRNA copy number systems. 11 - Özlem Ates
, Ebru Oner, Kazim Yalçin Arga
:
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. 12 - Choujun Zhan, Lam Fat Yeung
:
Parameter estimation in systems biology models using spline approximation. 14 - Ché S. Pillay
, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer
:
The logic of kinetic regulation in the thioredoxin system. 15 - Spyros K. Stamatelos, Christopher J. Brinkerhoff, Sastry S. Isukapalli, Panos G. Georgopoulos:
Mathematical model of uptake and metabolism of arsenic(III) in human hepatocytes - Incorporation of cellular antioxidant response and threshold-dependent behavior. 16 - Thomas R. Burkard
, Melanie Planyavsky, Ines Kaupe, Florian P. Breitwieser
, Tilmann Bürckstümmer
, Keiryn L. Bennett, Giulio Superti-Furga
, Jacques Colinge
:
Initial characterization of the human central proteome. 17 - Sayantari Ghosh, Kamakshi Sureka
, Bhaswar Ghosh, Indrani Bose, Joyoti Basu, Manikuntala Kundu:
Phenotypic heterogeneity in mycobacterial stringent response. 18 - Giulia Cuccato, Athanasios Polynikis, Velia Siciliano, Mafalda Graziano, Mario di Bernardo
, Diego di Bernardo
:
Modeling RNA interference in mammalian cells. 19 - Stephan Pabinger
, Robert Rader, Rasmus Agren, Jens Nielsen, Zlatko Trajanoski:
MEMOSys: Bioinformatics platform for genome-scale metabolic models. 20 - Jan Krumsiek, Karsten Suhre
, Thomas Illig, Jerzy Adamski
, Fabian J. Theis
:
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. 21 - Tatiana T. Marquez-Lago, André Leier
:
Stochastic adaptation and fold-change detection: from single-cell to population behavior. 22 - Yunjiao Wang, Pawel Paszek
, Caroline A. Horton, Douglas B. Kell
, Michael R. H. White
, David S. Broomhead, Mark R. Muldoon
:
Interactions among oscillatory pathways in NF-kappa B signaling. 23 - Christos Josephides, Alan M. Moses:
Modeling the evolution of a classic genetic switch. 24 - Wynand S. Verwoerd
:
A new computational method to split large biochemical networks into coherent subnets. 25 - Shakti Gupta, Mano Ram Maurya, Alfred H. Merrill Jr., Christopher K. Glass, Shankar Subramaniam:
Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. 26 - Rotem Ben-Hamo, Sol Efroni
:
The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features. 27 - Vinay Satish Kumar, James G. Ferry, Costas D. Maranas
:
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. 28 - Yoshimi Naruo, Takeshi Nagashima, Ryoko Ushikoshi-Nakayama
, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hiroshi Tanaka, Shih-Feng Tsai, Mariko Okada-Hatakeyama:
Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity. 29 - Tom Quaiser, Anna Dittrich
, Fred Schaper
, Martin Mönnigmann
:
A simple work flow for biologically inspired model reduction - application to early JAK-STAT signaling. 30 - Paul Rees
, M. Rowan Brown
, Huw D. Summers
, Mark D. Holton, Rachel J. Errington, Sally C. Chappell, Paul J. Smith:
A transfer function approach to measuring cell inheritance. 31 - Yogendra Patel, Catherine A. Heyward
, Michael R. H. White
, Douglas B. Kell
:
Predicting the points of interaction of small molecules in the NF-κB pathway. 32 - Roberto Olivares-Hernández
, Sergio Bordel
, Jens Nielsen
:
Codon usage variability determines the correlation between proteome and transcriptome fold changes. 33 - Nuno Carinhas
, Vicente Bernal
, Ana P. Teixeira
, Manuel J. T. Carrondo
, Paula M. Alves
, Rui Oliveira
:
Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products. 34 - Shivashankar H. Nagaraj, Antonio Reverter:
A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer. 35 - Oksana Sorokina, Florence Corellou
, David Dauvillée
, Anatoly A. Sorokin
, Igor Goryanin
, Steven Ball
, François-Yves Bouget, Andrew J. Millar
:
Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. 36 - Yueheng Lan, Igor Mezic
:
On the architecture of cell regulation networks. 37 - Dieter Maier, Wenzel Kalus, Martin Wolff, Susana G. Kalko
, Josep Roca
, Igor Marín de Mas
, Nil Turan, Marta Cascante, Francesco Falciani, Miguel Hernandez, Jordi Villà-Freixa
, Sascha Losko
:
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. 38 - João F. Matias Rodrigues
, Andreas Wagner:
Genotype networks, innovation, and robustness in sulfur metabolism. 39 - Nikolaus Sonnenschein
, Marcel Geertz, Georgi Muskhelishvili, Marc-Thorsten Hütt:
Analog regulation of metabolic demand. 40 - Thanneer M. Perumal
, Rudiyanto Gunawan
:
Understanding dynamics using sensitivity analysis: caveat and solution. 41 - Nataly Kravchenko-Balasha
, Françoise Remacle
, Ayelet Gross, Varda Rotter, Alexander Levitzki, Raphael D. Levine:
Convergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach. 42 - Christopher C. Park
, Greg D. Gale, Simone de Jong
, Anatole Ghazalpour, Brian J. Bennett
, Charles R. Farber
, Peter Langfelder, Andy Lin, Arshad H. Khan, Eleazar Eskin, Steve Horvath
, Aldons J. Lusis, Roel A. Ophoff, Desmond J. Smith:
Gene networks associated with conditional fear in mice identified using a systems genetics approach. 43 - Rui-Sheng Wang
, Réka Albert:
Elementary signaling modes predict the essentiality of signal transduction network components. 44 - Rolf Lindén, Ville-Pekka Eronen, Tero Aittokallio
:
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis. 45 - Francisco Azuaje, Haiying Wang
, Huiru Zheng
, Frédérique Léonard, Magali Rolland-Turner, Lu Zhang, Yvan Devaux, Daniel R. Wagner:
Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. 46 - Nicola Bernabò
, Paolo Berardinelli, Annunziata Mauro
, Valentina Russo
, Pia Lucidi, Mauro Mattioli, Barbara Barboni:
The role of actin in capacitation-related signaling: an in silico and in vitro study. 47 - Bertrand R. Caré, Hédi Soula:
Impact of receptor clustering on ligand binding. 48 - Antonio Gómez Moruno
, Juan Cedano
, Isaac Amela, Antoni Planas
, Jaume Piñol
, Enrique Querol:
Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks. 49 - Shengchao Ding, Wei Wang:
Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. 50 - Fiona Achcar
, Jean-Michel Camadro
, Denis Mestivier:
A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress. 51 - Rita Gupta, Anna Stincone, Philipp Antczak
, Sarah Durant, Roy Bicknell
, Andreas Bikfalvi, Francesco Falciani:
A computational framework for gene regulatory network inference that combines multiple methods and datasets. 52 - Jeff Nie, Ron M. Stewart, Hang Zhang, James A. Thomson, Fang Ruan, Xiaoqi Cui, Hairong Wei:
TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). 53 - Yasushi Saka, Cédric Lhoussaine, Céline Kuttler, Ekkehard Ullner
, Marco Thiel:
Theoretical basis of the community effect in development. 54 - Wangshu Zhang, Yong Chen, Fengzhu Sun, Rui Jiang
:
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. 55 - Priyanka Pandey, Shan Qin, Jacqueline Ho, Jing Zhou, Jordan A. Kreidberg:
Systems biology approach to identify transcriptome reprogramming and candidate microRNA targets during the progression of polycystic kidney disease. 56 - Juliet Ndukum, Luís L. Fonseca
, Helena Santos
, Eberhard O. Voit, Susmita Datta:
Statistical Inference Methods for Sparse Biological Time Series Data. 57 - Taewoo Ryu, Charalampos Mavromatis, Till Bayer
, Christian R. Voolstra
, Timothy Ravasi
:
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network. 58 - Prakash Vempati, Aleksander S. Popel
, Feilim Mac Gabhann:
Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis. 59 - Yufang Jin
, Hai-Chao Han
, Jamie Berger, Qiuxia Dai, Merry Lindsey
:
Combining experimental and mathematical modeling to reveal mechanisms of macrophage-dependent left ventricular remodeling. 60 - Fabrício Martins Lopes, Evaldo Araújo de Oliveira, Roberto M. Cesar
:
Inference of gene regulatory networks from time series by Tsallis entropy. 61 - Michaël Bekaert
, Gavin C. Conant
:
Transcriptional robustness and protein interactions are associated in yeast. 62 - Zhenhong Li
, Kevin J. Kroll
, Kathleen M. Jensen, Daniel L. Villeneuve, Gerald T. Ankley, Jayne V. Brian, María S. Sepúlveda, Edward F. Orlando, James M. Lazorchak
, Mitchell Kostich, Brandon Armstrong, Nancy D. Denslow, Karen H. Watanabe
:
A computational model of the hypothalamic - pituitary - gonadal axis in female fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol and 17#946;-trenbolone. 63 - W. Garrett Jenkinson, John Goutsias:
Thermodynamically consistent model calibration in chemical kinetics. 64 - Stephen Guest, Jingkai Yu, Dongmei Liu, Julie A. Hines, Maria A. Kashat, Russell L. Finley Jr.
:
A protein network-guided screen for cell cycle regulators in Drosophila. 65 - Joachim Bucher, Stephan Riedmaier, Anke Schnabel, Katrin Marcus, Gabriele Vacun, Thomas S. Weiss
, Wolfgang E. Thasler, Andreas K. Nüssler, Ulrich M. Zanger, Matthias Reuss:
A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes. 66 - Changyu Shen, Yi-Wen Huang, Yunlong Liu, Guohua Wang, Yuming Zhao, Zhiping Wang, Mingxiang Teng
, Yadong Wang, David A. Flockhart, Todd C. Skaar, Pearlly Yan, Kenneth P. Nephew, Tim Hui-Ming Huang, Lang Li:
A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. 67 - Ian M. Overton
, Shirley Graham
, Katherine A. Gould
, Jason Hinds
, Catherine H. Botting, Sally Shirran
, Geoffrey J. Barton
, Peter J. Coote
:
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. 68 - Tina Toni, Goran N. Jovanovic
, Maxime Huvet, Martin Buck, Michael P. H. Stumpf:
From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli. 69 - Peter E. Larsen, Avinash Sreedasyam, Geetika Trivedi, Gopi K. Podila, Leland J. Cseke, Frank Collart
:
Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. 70 - Michael Klann, Alexei Lapin, Matthias Reuss:
Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants. 71 - Xiaolin Xiao, Neil Dawson
, Lynsey MacIntyre, Brian J. Morris, Judith A. Pratt, David G. Watson, Desmond J. Higham:
Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition. 72 - Bo Li, Weiguo Cao, Jizhong Zhou
, Feng Luo:
Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions. 73 - Franco Blanchini
, Elisa Franco
:
Structurally robust biological networks. 74 - Felipe A. Vargas, Francisco Pizarro, José Ricardo Pérez-Correa
, Eduardo Agosin
:
Expanding a dynamic flux balance model of yeast fermentation to genome-scale. 75 - M. Ángeles Serrano
, Francesc Sagués
:
Network-based scoring system for genome-scale metabolic reconstructions. 76 - Stuart Meier, Oren Tzfadia
, Ratnakar Vallabhaneni, Chris Gehring
, Eleanore T. Wurtzel
:
A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana. 77 - Chen Hou
, Kendra Bolt, Aviv Bergman:
A General Life History Theory for Effects of Caloric Restriction on Health Maintenance. 78 - Xin Yao, Han Hao
, Yanda Li, Shao Li
:
Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. 79 - Colm J. Ryan
, Derek Greene
, Aude Guénolé, Haico van Attikum
, Nevan J. Krogan, Pádraig Cunningham
, Gerard Cagney
:
Improved functional overview of protein complexes using inferred epistatic relationships. 80 - David W. Schryer, Marko Vendelin
, Pearu Peterson
:
Symbolic flux analysis for genome-scale metabolic networks. 81 - Weijun Luo, Michael S. Friedman, Kurt D. Hankenson
, Peter J. Woolf:
Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. 82 - Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn M. C. Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A. P. Martins dos Santos
, Jing Wang:
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. 83 - Rongling Wu, Jiguo Cao
, Zhongwen Huang, Zhong Wang, Junyi Gai, C. Eduardo Vallejos:
Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems. 84 - Sudin Bhattacharya
, Qiang Zhang, Melvin E. Andersen
:
A deterministic map of Waddington's epigenetic landscape for cell fate specification. 85 - Angel Alvarez, Peter J. Woolf:
Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks. 86 - Steven X. Ge
:
Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes. 87 - Ibrahim Al-Shyoukh, Fuqu Yu, Jiaying Feng, Karen Yan, Steven Dubinett, Chih-Ming Ho
, Jeff S. Shamma, Ren Sun:
Systematic quantitative characterization of cellular responses induced by multiple signals. 88 - Jen-hwa Chu
, Ross Lazarus
, Vincent J. Carey, Benjamin A. Raby:
Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes. 89 - Kristin Tøndel, Ulf G. Indahl, Arne B. Gjuvsland
, Jon Olav Vik
, Peter J. Hunter
, Stig W. Omholt, Harald Martens
:
Hierarchical Cluster-based Partial Least Squares Regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models. 90 - Kuhn Ip, Caroline Colijn, Desmond S. Lun:
Analysis of complex metabolic behavior through pathway decomposition. 91 - Ana P. Teixeira
, João M. L. Dias, Nuno Carinhas
, Marcos Sousa, José Clemente
, António Cunha
, Moritz von Stosch, Paula M. Alves
, Manuel J. T. Carrondo
, Rui Oliveira
:
Cell functional enviromics: Unravelling the function of environmental factors. 92 - Zhenpeng Li, Fei Li, Ming Ni
, Peng Li, Xiaochen Bo
, Shengqi Wang:
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network. 93 - Ambarish Nag
, Monte Lunacek, Peter A. Graf, Christopher H. Chang
:
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation. 94 - Marie Beurton-Aimar
, Bertrand Beauvoit
, Antoine Monier, François Vallée, Martine Dieuaide-Noubhani, Sophie Colombié:
Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells. 95 - Juan Higareda-Almaraz, María Enríquez-Gasca, Magdalena Hernández-Ortiz, Osbaldo Resendis-Antonio
, Sergio Encarnación-Guevara
:
Proteomic patterns of cervical cancer cell lines, a network perspective. 96 - Emma Granqvist, Giles E. D. Oldroyd, Richard J. Morris
:
Automated Bayesian model development for frequency detection in biological time series. 97 - Kazuhiro Takemoto
, Tatsuya Niwa
, Hideki Taguchi
:
Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement. 98 - Chien-Wei Tseng, Chen-Ching Lin, Chiung-Nien Chen
, Hsuan-Cheng Huang
, Hsueh-Fen Juan
:
Integrative network analysis reveals active microRNAs and their functions in gastric cancer. 99 - Hyunjin Yoon, Charles Ansong, Jason E. McDermott
, Marina A. Gritsenko, Richard D. Smith
, Fred Heffron, Joshua N. Adkins
:
Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella. 100 - Jong Park, Tae Kim, Sang Lee
:
Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production. 101 - Anthony C. Smith
, Alan J. Robinson:
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. 102 - Daniel D. Seaton
, Jawahar Krishnan:
The coupling of pathways and processes through shared components. 103 - Anton Crombach
, Paulien Hogeweg:
Is RNA-dependent RNA polymerase essential for transposon control? 104 - Jurjen Willem Westra, Walter K. Schlage, Brian P. Frushour, Stephan Gebel, Natalie L. Catlett, Wan-Jiang Han, Sean F. Eddy
, Arnd Hengstermann, Andrea L. Matthews, Carole Mathis, Rosemarie B. Lichtner, Carine Poussin, Marja Talikka, Emilija Veljkovic, Aaron A. Van Hooser, Benjamin Wong, Michael J. Maria, Manuel C. Peitsch
, Renee Deehan, Julia Hoeng:
Construction of a computable cell proliferation network focused on non-diseased lung cells. 105 - Kaspar Valgepea
, Kaarel Adamberg
, Raivo Vilu:
Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting. 106 - Ioannis N. Melas
, Alexander Mitsos, Dimitris E. Messinis
, Thomas S. Weiss
, Leonidas G. Alexopoulos
:
Combined logical and data-driven models for linking signalling pathways to cellular response. 107 - Hai Fang, Wen Jin, Ying Yang, Ying Jin, Ji Zhang, Kankan Wang:
An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro. 108 - John Jack, John Wambaugh
, Imran Shah
:
Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles. 109 - Aarash Bordbar
, Neema Jamshidi
, Bernhard O. Palsson:
iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. 110 - Daniel Madar
, Erez Dekel, Anat Bren, Uri Alon:
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. 111 - XiaoNa Wei, Bu-Cong Han, Jing-Xian Zhang, X. H. Liu, C. Y. Tan, Yu Yang Jiang, Boon Chuan Low
, Bruce Tidor, Yuzong Chen
:
An Integrated Mathematical Model of Thrombin-, Histamine-and VEGF-Mediated Signalling in Endothelial Permeability. 112