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ORCIDBMC Systems Biology, Volume 9
Volume 9, 2015
- Chao Ye
, Nan Xu, Haiqin Chen, Yong Q. Chen, Wei Chen, Liming Liu:
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina. 1 - A. K. M. Azad, Alfons Lawen, Jonathan M. Keith:
Prediction of signaling cross-talks contributing to acquired drug resistance in breast cancer cells by Bayesian statistical modeling. 2 - Takahide Ota, Masayo Maeda, Mayumi Okamoto, Masaaki Tatsuka:
Positive regulation of Rho GTPase activity by RhoGDIs as a result of their direct interaction with GAPs. 3 - Wenjuan Mo, Chao Tong, Yan Zhang, Hong Lu:
microRNAs' differential regulations mediate the progress of Human Papillomavirus (HPV)-induced Cervical Intraepithelial Neoplasia (CIN). 4 - Gautham Vivek Sridharan, Ehsan Ullah, Soha Hassoun, Kyongbum Lee:
Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity. 5 - Stina K. Lien, Sebastian Niedenführ, Håvard Sletta, Katharina Nöh, Per Bruheim:
Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA. 6 - Tim Sands:
Annual acknowledgement of reviewers. 7 - Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga:
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. 8 - Patrick Weber, Mariana Hornjik, Monilola A. Olayioye, Angelika Hausser, Nicole Radde:
A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells. 9 - Anna Zhukova, David James Sherman:
Mimoza: web-based semantic zooming and navigation in metabolic networks. 10 - Li-Ying Wang, Jun Liu, Yuan Li, Bing Li, Yingying Zhang, Zhi-Wei Jing, Ya-Nan Yu, Hai-Xia Li, Shan-Shan Guo, Yi-Jun Zhao, Zhong Wang, Yongyan Wang:
Time-dependent variation of pathways and networks in a 24-hour window after cerebral ischemia-reperfusion injury. 11 - Avichai Tendler, Avraham E. Mayo, Uri Alon:
Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells. 12 - Traci L. Marin, Brendan Gongol, Marcy Martin, Stephanie J. King, Lemar Smith, David A. Johnson, Shankar Subramaniam, Shu Chien, John Shyy:
Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome. 13 - Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu:
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. 14 - John A. Cole, Lars Kohler, Jamila Hedhli, Zaida Luthey-Schulten:
Spatially-resolved metabolic cooperativity within dense bacterial colonies. 15 - Lifang Huang, Zhanjiang Yuan, Peijiang Liu, Tianshou Zhou:
Effects of promoter leakage on dynamics of gene expression. 16 - Joseph P. Dexter, Ping Xu, Jeremy Gunawardena, Megan N. McClean:
Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae. 17 - André Schultz, Amina A. Qutub:
Predicting internal cell fluxes at sub-optimal growth. 18 - Madison Brandon, Brad Howard, Christopher Lawrence, Reinhard C. Laubenbacher:
Iron acquisition and oxidative stress response in aspergillus fumigatus. 19 - Jose Davila-Velderrain, Carlos Villarreal, Elena R. Álvarez-Buylla:
Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates. 20 - Ricardo de Matos Simoes, Sabine Dalleau, Kate E. Williamson, Frank Emmert-Streib:
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. 21 - Elisenda Feliu, Carsten Wiuf:
Finding the positive feedback loops underlying multi-stationarity. 22 - Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi:
Increased robustness of early embryogenesis through collective decision-making by key transcription factors. 23 - Jakob Wieczorek, Rahuman S. Malik-Sheriff, Yessica Fermin, Hernán E. Grecco, Eli Zamir, Katja Ickstadt:
Uncovering distinct protein-network topologies in heterogeneous cell populations. 24 - Cielito Reyes-Gibby, Christine Yuan, Jian Wang, Sai-Ching Yeung, Sanjay Shete:
Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction. 25 - Zichen Wang, Neil R. Clark, Avi Ma'ayan:
Dynamics of the discovery process of protein-protein interactions from low content studies. 26 - Qing Wang, David J. Klinke II, Zhijun Wang:
CD8 + T cell response to adenovirusvaccination and subsequent suppression of tumor growth: modeling, simulation and analysis. 27 - Clémence Chamard-Jovenin, Alain Jung, Amand Chesnel, Joseph Abecassis, Stéphane Flament, Sonia Ledrappier, Christine Macabre, Taha Boukhobza, Hélène Dumond:
From ERα66 to ERα36: a generic method for validating a prognosis marker of breast tumor progression. 28 - Ye Chen, Cheng Lv, Fangting Li, Tiejun Li:
Distinguishing the rates of gene activation from phenotypic variations. 29 - Devin H. Currie, Babu Raman, Christopher M. Gowen, Timothy J. Tschaplinski, Miriam L. Land, Steven D. Brown, Sean F. Covalla, Dawn M. Klingeman, Zamin K. Yang, Nancy L. Engle, Courtney M. Johnson, Miguel Rodriguez, A. Shaw, William R. Kenealy, Lee R. Lynd, Stephen S. Fong, Jonathan R. Mielenz, Brian H. Davison, David A. Hogsett, Christopher D. Herring:
Genome-scale resources for Thermoanaerobacterium saccharolyticum. 30 - Jovan Tanevski, Ljupco Todorovski, Yannis Kalaidzidis, Saso Dzeroski:
Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis. 31 - Dicle Hasdemir, Huub C. J. Hoefsloot, Age K. Smilde:
Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions. 32 - Katherine Wolstencroft, Stuart Owen, Olga Krebs, Quyen Nguyen, Natalie J. Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lihua An, David Shockley, Jacky L. Snoep, Wolfgang Müller, Carole A. Goble:
SEEK: a systems biology data and model management platform. 33 - Aristotelis Kittas, Amélie Barozet, Jekaterina Sereshti, Niels Grabe, Sophia Tsoka:
CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks. 34 - Manuel Garcia-Albornoz, Jens Nielsen:
Finding directionality and gene-disease predictions in disease associations. 35 - Randolph Faustino, Saranya Wyles, Jody Groenendyk, Marek Michalak, Andre Terzic, Carmen Perez-Terzic:
Systems biology surveillance decrypts pathological transcriptome remodeling. 36 - Soudabeh Sabetian, Mohd Shahir Shamsir:
Identification of putative drug targets for human sperm-egg interaction defect using protein network approach. 37 - Stuart Johnston, Esha Shah, Lisa Chopin, D. L. Sean McElwain, Matthew J. Simpson:
Estimating cell diffusivity and cell proliferation rate by interpreting IncuCyte ZOOM™ assay data using the Fisher-Kolmogorov model. 38 - Kaveh Yousef, Adam Streck, Christof Schütte, Heike Siebert, Regine Hengge, Max von Kleist:
Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. 39 - Sushil Tripathi, Åsmund Flobak, Konika Chawla, Anaïs Baudot, Torunn Bruland, Liv Thommesen, Martin Kuiper, Astrid Lægreid:
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. 40 - Joseph Cursons, Jerry Gao, Daniel G. Hurley, Cristin G. Print, P. Rod Dunbar, Marc Jacobs, Edmund J. Crampin:
Regulation of ERK-MAPK signaling in human epidermis. 41 - Sergio Pérez-Landero, Santiago Sandoval-Motta, Claudia Martínez-Anaya, Runying Yang, Jorge Folch-Mallol, Luz Martínez, Larissa Ventura, Karina Guillén-Navarro, Maximino Aldana-González, Jorge Nieto-Sotelo:
Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA in Saccharomyces cerevisiae: experimental and computational evidences. 42 - Mohammad Tajparast, Dominic Frigon:
Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. 43 - Khuram Shahzad, Jay E. Mittenthal, Gustavo Caetano-Anollés:
The organization of domains in proteins obeys Menzerath-Altmann's law of language. 44 - Tomoya Mori, Max Flöttmann, Marcus Krantz, Tatsuya Akutsu, Edda Klipp:
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks. 45 - Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev:
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. 46 - Weronika Wronowska, Agata Charzynska, Karol Nienaltowski, Anna Gambin:
Computational modeling of sphingolipid metabolism. 47 - Philipp Erdrich, Ralf Steuer, Steffen Klamt:
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. 48 - Weiwei Yin, Swetha Garimalla, Alberto Moreno, Mary R. Galinski, Mark P. Styczynski:
A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems. 49 - Yue Deng, Lin Gao, Bingbo Wang:
Erratum to: ppiPre: predicting protein-protein interactions by combining heterogeneous features. 50 - Stanislav Sokolenko, Marc Aucoin:
A correction method for systematic error in 1 H-NMR time-course data validated through stochastic cell culture simulation. 51 - Markus Karlsson, David Janzén, Lucia Durrieu, Alejandro Colman-Lerner, Maria Kjellsson, Gunnar Cedersund:
Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it. 52 - Justin M. Fear, Michelle N. Arbeitman, Matthew Salomon, Justin Dalton, John Tower, Sergey V. Nuzhdin, Lauren M. McIntyre:
The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster. 53 - Kun-Nan Tsai, Shu-Hsi Lin, Wei-Chung Liu, Daryi Wang:
Inferring microbial interaction network from microbiome data using RMN algorithm. 54 - R. Joseph Bender, Feilim Mac Gabhann:
Dysregulation of the vascular endothelial growth factor and semaphorin ligand-receptor families in prostate cancer metastasis. 55 - Di Chen, Xi Liu, Yiping Yang, Hongjun Yang, Peng Lu:
Systematic synergy modeling: understanding drug synergy from a systems biology perspective. 56 - Christopher Garay, Jonathan M. Dreyfuss, James E. Galagan:
Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis. 57 - Francisco Peñagaricano, Bruno Valente, Juan P. Steibel, Ronald O. Bates, Catherine W. Ernst, Hasan Khatib, Guilherme J. M. Rosa:
Exploring causal networks underlying fat deposition and muscularity in pigs through the integration of phenotypic, genotypic and transcriptomic data. 58 - Andrew E. Blanchard, Ting Lu:
Bacterial social interactions drive the emergence of differential spatial colony structures. 59 - Lydia M. Rickett, Nick Pullen, Matthew Hartley, Cyril Zipfel, Sophien Kamoun, József Baranyi, Richard J. Morris:
Incorporating prior knowledge improves detection of differences in bacterial growth rate. 60 - Michael K. Strasser, Justin Feigelman, Fabian J. Theis, Carsten Marr:
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy. 61 - Claudia Cava, Gloria Bertoli, Isabella Castiglioni:
Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. 62 - Daniel Botman, Fredrik Jansson, Eric Röttinger, Mark Q. Martindale, Johann de Jong, Jaap A. Kaandorp:
Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development. 63 - Pierre Millard, Jean-Charles Portais, Pedro Mendes:
Impact of kinetic isotope effects in isotopic studies of metabolic systems. 64 - Karol Nienaltowski, Michal Wlodarczyk, Tomasz Lipniacki, Michal Komorowski:
Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics. 65 - Weiruo Zhang, Ritesh Kolte, David L. Dill:
Towards in vivo estimation of reaction kinetics using high-throughput metabolomics data: a maximum likelihood approach. 66 - Ivan Kryven, Susanna Röblitz, Christof Schütte:
Solution of the chemical master equation by radial basis functions approximation with interface tracking. 67 - Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, Andreas Zell:
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. 68 - Michael Reed, Mary Gamble, Megan Hall, H. Nijhout:
Mathematical analysis of the regulation of competing methyltransferases. 69 - Fortunato Bianconi, Elisa Baldelli, Vienna Ludovini, Emanuel F. Petricoin, Lucio Crinò, Paolo Valigi:
Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology. 70 - Daniel Cook, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli:
Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes. 71 - Martin Kavscek, Govindprasad Bhutada, Tobias Madl, Klaus Natter:
Optimization of lipid production with a genome-scale model of Yarrowia lipolytica. 72 - Meiyappan Lakshmanan, Tae Yong Kim, Bevan Kai-Sheng Chung, Sang Yup Lee, Dong-Yup Lee:
Flux-sum analysis identifies metabolite targets for strain improvement. 73 - Attila Gábor, Julio R. Banga:
Robust and efficient parameter estimation in dynamic models of biological systems. 74 - Christopher J. Mitchell, Derese Getnet, Min Sik Kim, Srinivas Manda Srikanth, Praveen Kumar, Tai-Chung Huang, Sneha M. Pinto, Nirujogi Raja Sekhar, Mio Iwasaki, Patrick G. Shaw, Xinyan Wu, Jun Zhong, Raghothama Chaerkady, Arivusudar Marimuthu, Babylakshmi Muthusamy, Nandini A. Sahasrabuddhe, Rajesh Raju, Caitlyn Bowman, Ludmila V. Danilova, Jevon Cutler, Dhanashree S. Kelkar, Charles G. Drake, T. S. Keshava Prasad, Luigi Marchionni, Peter N. Murakami, Alan F. Scott, Leming Shi, Jean Thierry-Mieg, Danielle Thierry-Mieg, Rafael A. Irizarry, Leslie Cope, Yasushi Ishihama, Charles Wang, Harsha Gowda, Akhilesh Pandey:
A multi-omic analysis of human naïve CD4+ T cells. 75 - Sarah L. Field, Tathagata Dasgupta, Michele Cummings, Richard S. Savage, Julius Adebayo, Hema McSara, Jeremy Gunawardena, Nicolas M. Orsi:
Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networks in vivo. 76 - D. B. R. K. Gupta Udatha, Evangelos Topakas, Margarita Salazar, Lisbeth Olsson, Mikael R. Andersen, Gianni Panagiotou:
Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. 77 - Anuprabha Bhargava, Hanspeter Herzel, Bharath Ananthasubramaniam:
Mining for novel candidate clock genes in the circadian regulatory network. 78 - Elsje Pienaar, Véronique Dartois, Jennifer J. Linderman, Denise E. Kirschner:
In silico evaluation and exploration of antibiotic tuberculosis treatment regimens. 79 - Megha Padi, John Quackenbush:
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. 80 - Jukka Intosalmi, Helena Ahlfors, Sini Rautio, Henrik Mannerström, Zhi Jane Chen, Riitta Lahesmaa, Brigitta Stockinger, Harri Lähdesmäki:
Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. 81 - Tatsuya Ando, Ryuji Kato, Hiroyuki Honda:
Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation. 82 - Kerstin Abshagen, Matthias König, Andreas Hoppe, Isabell Müller, Matthias Ebert, Honglei Weng, Hermann-Georg Holzhütter, Ulrich M. Zanger, Johannes G. Bode, Brigitte Vollmar, Maria Thomas, Steven Dooley:
Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice. 83 - Mahsa Ghanbari, Julia Lasserre, Martin Vingron:
Reconstruction of gene networks using prior knowledge. 84 - Sonja E. M. Boas, María I. Navarro Jimenez, Roeland M. H. Merks, Joke G. Blom:
A global sensitivity analysis approach for morphogenesis models. 85 - Sonja E. M. Boas, Roeland M. H. Merks:
Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis. 86 - Jae Kyoung Kim, Kresimir Josic, Matthew R. Bennett:
The relationship between stochastic and deterministic quasi-steady state approximations. 87 - Nima Abedpour, Markus Kollmann:
Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks. 88 - Carl D. Christensen, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer:
Tracing regulatory routes in metabolism using generalised supply-demand analysis. 89 - Yuya Hattori, Akinari Yokoya, Ritsuko Watanabe:
Cellular automaton-based model for radiation-induced bystander effects. 90 - Ruijie Song, Weilin Peng, Ping Liu, Murat Acar:
A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells. 91 - Pu Li, Quoc Dong Vu:
A simple method for identifying parameter correlations in partially observed linear dynamic models. 92 - Lucas Marmiesse, Rémi Peyraud, Ludovic Cottret:
FlexFlux: combining metabolic flux and regulatory network analyses. 93 - Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee, Soha Hassoun:
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. 94 - Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer:
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. 95 - Shahin Mohammadi, Baharak Saberidokht, Shankar Subramaniam, Ananth Grama:
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. 96 - Katja Kolar, Hanna M. Wischhusen, Konrad Müller, Maria Karlsson, Wilfried Weber, Matias D. Zurbriggen:
A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. 97
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