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BMC Systems Biology, Volume 6
Volume 6, 2012
- Bettina M. Länger, Cristina Pou-Barreto, Carlos González-Alcón
, Basilio Valladares, Bettina Wimmer, Néstor V. Torres:
Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies. 1 - Kevin M. D'Auria, Gina M. Donato, Mary C. Gray
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. 2 - Rotem Ben-Hamo, Sol Efroni
Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies. 3 - Pinar Pir
The genetic control of growth rate: a systems biology study in yeast. 4 - Liang-Chun Chen, Hsiang-Yuan Yeh, Cheng-Yu Yeh, Carlos Arias, Von-Wun Soo:
Identifying co-targets to fight drug resistance based on a random walk model. 5 - Jörg Linde, Peter Hortschansky, Eugen Fazius, Axel A. Brakhage, Reinhard Guthke, Hubertus Haas:
Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. 6 - Stefanie Widder
Evolvability of feed-forward loop architecture biases its abundance in transcription networks. 7 - Joost Boele
FAME, the Flux Analysis and Modeling Environment. 8 - Jan Schellenberger, Daniel C. Zielinski
Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. 9 - Pablo Carbonell
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. 10 - Josef Thingnes, Timothy J. Lavelle, Arne B. Gjuvsland
Towards a quantitative understanding of the MITF-PIAS3-STAT3 connection. 11 - Naveed Aslam, Harel Z. Shouval:
Regulation of cytoplasmic polyadenylation can generate a bistable switch. 12 - Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling
In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems. 13 - Irina Surovtsova, Natalia Simus, Katrin Hübner
Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. 14 - Min Li, Hanhui Zhang, Jianxin Wang, Yi Pan
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. 15 - Sabrina Kleessen, Zoran Nikoloski
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. 16 - Joji M. Otaki:
Structural analysis of eyespots: dynamics of morphogenic signals that govern elemental positions in butterfly wings. 17 - Chen-Ching Lin, Ya-Jen Chen, Cho-Yi Chen
Crosstalk between transcription factors and microRNAs in human protein interaction network. 18 - Tian Xia, Jiansong Tong, Shailendra S. Rathore, Xun Gu, Julie A. Dickerson
Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis. 19 - (Withdrawn) Predicting new molecular targets for rhein using network pharmacology. 20
- Skylar W. Marvel, Cranos M. Williams
Set membership experimental design for biological systems. 21 - Milan van Hoek, Roeland Merks
Redox balance is key to explaining full vs. partial switching to low-yield metabolism. 22 - Chao-Yi Dong, Kwang-Hyun Cho:
An optimally evolved connective ratio of neural networks that maximizes the occurrence of synchronized bursting behavior. 23 - Luis Caspeta
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. 24 - Mikolaj Rybinski
Tav4SB: integrating tools for analysis of kinetic models of biological systems. 25 - Barbara Szomolay
Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation. 26 - Arvind K. Chavali, Anna S. Blazier, Jose L. Tlaxca, Paul A. Jensen, Richard D. Pearson, Jason A. Papin
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. 27 - Jason E. McDermott
Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis. 28 - Daniel C. Kirouac
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. 29 - Jeffrey D. Orth, Bernhard Ø. Palsson:
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. 30 - Man-Sun Kim, Jeong-Rae Kim
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. 31 - Zuguang Gu
Gene regulation is governed by a core network in hepatocellular carcinoma. 32 - Hendrik Rohn, Anja Hartmann, Astrid Junker
FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks. 33 - Dapeng Hao, Cong Ren, Chuanxing Li
Revisiting the variation of clustering coefficient of biological networks suggests new modular structure. 34 - Nicolás Loira, Thierry Dulermo, Jean-Marc Nicaud
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. 35 - Iain Hepburn
STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. 36 - Verônica A. Grieneisen
Morphogengineering roots: comparing mechanisms of morphogen gradient formation. 37 - Ricardo de Matos Simoes
Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. 38 - Philipp Thomas
The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions. 39 - Zhengzhang Chen
Spice: discovery of phenotype-determining component interplays. 40 - Nikolaus Sonnenschein
A network perspective on metabolic inconsistency. 41 - Michael J. McAnulty
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. 42 - Scott B. Crown
Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells. 43 - Davide Luciani, Gianfranco Bazzoni:
From networks of protein interactions to networks of functional dependencies. 44 - Maria Bravo
Modeling of human factor Va inactivation by activated protein C. 45 - Pedro Gonnet
A specialized ODE integrator for the efficient computation of parameter sensitivities. 46 - Rachel S. Koh, Mary J. Dunlop:
Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network. 47 - Kevin B. Wood
Trade-offs between drug toxicity and benefit in the multi-antibiotic resistance system underlie optimal growth of E. coli. 48 - Seung Sohn, Tae Kim, Jay H. Lee
Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. 49 - Ricardo J. Flores, Yiting Li, Alexander Yu, Jianhe Shen, Pulivarthi H. Rao, Serrine S. Lau, Marina Vannucci, Ching C. Lau, Tsz-Kwong Man
A systems biology approach reveals common metastatic pathways in osteosarcoma. 50 - Paola Lecca
Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics. 51 - Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yukiko Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka:
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. 52 - Michalis K. Titsias, Antti Honkela, Neil D. Lawrence
Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison. 53 - Florian Martin, Ty M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. 54 - Benjamin D. Heavner
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. 55 - Zuguang Gu
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. 56 - Nicole Radde
Analyzing fixed points of intracellular regulation networks with interrelated feedback topology. 57 - Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N. Kaznessis
Stochastic simulations of a synthetic bacteria-yeast ecosystem. 58 - Alexander Wentzel
Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2). 59 - Ralph Patrick
Mapping the stabilome: a novel computational method for classifying metabolic protein stability. 60 - Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. 61 - Nizamul Morshed, Madhu Chetty
Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique. 62 - Michael C. Oldham
Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. 63 - Wenting Li
Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level. 64 - Yu Liu
Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. 65 - Tian Hong
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. 66 - Sarp A. Coskun, Xinjian Qi, Ali Cakmak
PathCase-SB: integrating data sources and providing tools for systems biology research. 67 - Jihong Fu, Wentao Tang, Peng Du, Guanghui Wang, Wei Chen, Jingming Li, Yunxiang Zhu, Jun Gao, Long Cui
Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis. 68 - Bruce A. Rosa, Yuhua Jiao, Sookyung Oh, Beronda L. Montgomery, Wensheng Qin, Jin Chen:
Frequency-based time-series gene expression recomposition using PRIISM. 69 - Sherry-Ann Brown
Computational analysis of calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons associated with ataxia. 70 - Amornpan Klanchui, Chiraphan Khannapho
iAK692: A genome-scale metabolic model of Spirulina platensis C1. 71 - Daniela Beisser, Markus A. Grohme
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. 72 - Dave Lee, Kieran Smallbone
Improving metabolic flux predictions using absolute gene expression data. 73 - Angelyn Lao
Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease. 74 - Alejandro Fernández Villaverde
A cooperative strategy for parameter estimation in large scale systems biology models. 75 - Brian Drawert, Stefan Engblom
URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. 76 - Brandilyn Stigler
A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegans development. 77 - Rohan D. Gidvani, Peter Sudmant
A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. 78 - Carlos Vilas
Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. 79 - Hee Lee, Taejeong Bae
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. 80 - Steffen Waldherr
Efficient parametric analysis of the chemical master equation through model order reduction. 81 - Uddipan Sarma, Indira Ghosh:
Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. 82 - Aiman Alam-Nazki, Jawahar Krishnan:
An investigation of spatial signal transduction in cellular networks. 83 - I-Chun Chou, Eberhard O. Voit:
Estimation of dynamic flux profiles from metabolic time series data. 84 - Tamás Székely
A higher-order numerical framework for stochastic simulation of chemical reaction systems. 85 - Jürgen Pahle, Joseph D. Challenger
Biochemical fluctuations, optimisation and the linear noise approximation. 86 - Wei Peng, Jianxin Wang, Weiping Wang, Qing Liu, Fang-Xiang Wu
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. 87 - Kristin Tøndel, Ulf G. Indahl, Arne B. Gjuvsland
Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models. 88 - Neil R. Clark
Sets2Networks: network inference from repeated observations of sets. 89 - Larry Croft, Damian Szklarczyk, Lars Juhl Jensen
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. 90 - Edward Kent, Stefan Hoops, Pedro Mendes
Condor-COPASI: high-throughput computing for biochemical networks. 91 - Jishnu Das
HINT: High-quality protein interactomes and their applications in understanding human disease. 92 - Lei Zhang, Arthur D. Lander, Qing Nie:
A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. 93 - Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang:
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database. 94 - Daniel Schmidl, Sabine Hug, Wei Li, Matthias B. Greiter
Bayesian model selection validates a biokinetic model for zirconium processing in humans. 95 - Tomás Helikar
The Cell Collective: Toward an open and collaborative approach to systems biology. 96 - Eduardo Tejera
Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis. 97 - Vijay Chickarmane, Victor Olariu, Carsten Peterson:
Probing the role of stochasticity in a model of the embryonic stem cell - heterogeneous gene expression and reprogramming efficiency. 98 - Daniel Kaschek, Jens Timmer:
A variational approach to parameter estimation in ordinary differential equations. 99 - Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree
Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model. 100 - Kenneth Lo, Adrian E. Raftery, Kenneth M. Dombek, Jun Zhu, Eric E. Schadt, Roger Eugene Bumgarner, Ka Yee Yeung
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. 101 - Tzu-Hsien Yang
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. 102 - Christian Jungreuthmayer, Jürgen Zanghellini
Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. 103 - Marcel H. Schulz
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. 104 - Yushu Liu, Pei-Wen Tsai, Yong Wang, Tan-Chi Fan, Chia-Hung Hsieh, Margaret Dah-Tsyr Chang, Tun-Wen Pai, Chien-Fu Huang, Chung-Yu Lan
Chemoattraction of macrophages by secretory molecules derived from cells expressing the signal peptide of eosinophil cationic protein. 105 - Jong Myoung Park, Hye Min Park, Won Jun Kim, Hyun Uk Kim
Flux variability scanning based on enforced objective flux for identifying gene amplification targets. 106 - Matthew S. Creamer, Edward C. Stites, Meraj Aziz, James A. Cahill, Chin Wee Tan
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. 107 - Thomas Williamson, Delali A. Adiamah, Jean-Marc Schwartz
Exploring the genetic control of glycolytic oscillations in Saccharomyces Cerevisiae. 108 - Marc R. Birtwistle
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. 109 - Joaquín Sanz
Topological effects of data incompleteness of gene regulatory networks. 110 - Yonatan Savir, Nir Waysbort, Yaron E. Antebi
Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback. 111 - Mohammed Alshalalfa, Gary D. Bader
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. 112 - Jinghang Liang, Jie Han:
Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks. 113 - Anja Karlstädt
CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism. 114 - Giuseppe Facchetti, Mattia Zampieri
Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer. 115 - Gautier Stoll
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. 116 - Jason E. Shoemaker
Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs. 117 - Susanna Bazzani, Andreas Hoppe
Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. 118 - Nishanth G. Chemmangattuvalappil
An integer optimization algorithm for robust identification of non-linear gene regulatory networks. 119 - Clemens Kreutz
Likelihood based observability analysis and confidence intervals for predictions of dynamic models. 120 - Nicolae Radu Zabet
System size reduction in stochastic simulations of the facilitated diffusion mechanism. 121 - Ji-Young Hong, Geun-Hong Kim, Jun-Woo Kim, Soon-Sung Kwon, Eisuke F. Sato, Kwang-Hyun Cho, Eun Bo Shim:
Computational modeling of apoptotic signaling pathways induced by cisplatin. 122 - Shyamesh Kumar
Nuclear Factor kappa B is central to Marek's Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo. 123 - Shingo Tsuji, Sigeo Ihara, Hiroyuki Aburatani:
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. 124 - Rainer Poltz, Michael Naumann
Dynamics of p53 and NF-κ. 125 - Ángel Goñi-Moreno
A reconfigurable NAND/NOR genetic logic gate. 126 - David Byrne, Alexandra Dumitriu
Comparative multi-goal tradeoffs in systems engineering of microbial metabolism. 127 - Leandra M. Brettner, Joanna Masel
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. 128 - Changki Hong, Minho Lee
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network. 129 - Mark Mc Auley, Darren J. Wilkinson
A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. 130 - Carla Bosia
Gene autoregulation via intronic microRNAs and its functions. 131 - Isaac Crespo
Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease. 132 - Camille Terfve
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. 133 - Bevan Chung, Dong-Yup Lee
Computational codon optimization of synthetic gene for protein expression. 134 - Magbubah Essack
Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. 135 - Bor-Sen Chen, Chih-Yuan Hsu:
Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing. 136 - André Fujita, Patricia Severino
Functional clustering of time series gene expression data by Granger causality. 137 - Galina Lebedeva, Azusa Yamaguchi, Simon P. Langdon, Kenneth Macleod, David J. Harrison
A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen. 138 - Hendrik Rohn, Astrid Junker
VANTED v2: a framework for systems biology applications. 139 - Elad Noor
A proof for loop-law constraints in stoichiometric metabolic networks. 140 - Tatiana A. Karelina, Kirill V. Zhudenkov
Regulation of leukotriene and 5oxoETE synthesis and the effect of 5-lipoxygenase inhibitors: a mathematical modeling approach. 141 - Gengjie Jia, Gregory Stephanopoulos, Rudiyanto Gunawan
Incremental parameter estimation of kinetic metabolic network models. 142 - Hye-Won Kang:
A multiscale approximation in a heat shock response model of E. coli. 143 - Michal Kolár
GraphAlignment: Bayesian pairwise alignment of biological networks. 144 - Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. 145 - Mariano Beguerisse-Díaz
Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells. 146 - Sebastian Vlaic, Wolfgang Schmidt-Heck, Madlen Matz-Soja
The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes. 147 - Nadine Töpfer
Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. 148 - Andreas Kremling, Katharina Pflüger-Grau, Max Chavarría
Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida. 149 - Ali Navid
Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach. 150 - Ana Luisa B. Cruz, Marit Hebly, Giang-Huong Duong, Sebastian A. Wahl
Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics? 151 - ShengJun Fan, Qiang Geng, Zhen-Yu Pan, Xin Li, Lu Tie, Yan Pan, Xuejun Li:
Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach. 152 - Yuliang Wang
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. 153 - Shibin Mathew, Maria Jaramillo, Xinan Zhang, Li Zhang, Alejandro Soto-Gutiérrez, Ipsita Banerjee:
Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences. 154 - Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee
Metabolic Flux-Based Modularity using Shortest Retroactive distances. 155
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