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ORCIDBMC Systems Biology, Volume 7
Volume 7, 2013
- Michael Weber, Sebastian Henkel, Sebastian Vlaic, Reinhard Guthke, Everardus J. van Zoelen, Dominik Driesch:
Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. 1 - Max Hoffmann, Ulrich S. Schwarz
:
A kinetic model for RNA-interference of focal adhesions. 2 - Ulf W. Liebal, Thomas Millat, Jon Marles-Wright, Richard J. Lewis, Olaf Wolkenhauer:
Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. 3 - Xia Zhang, M. Heather West Greenlee, Jeanne M. Serb:
EnRICH: Extraction and Ranking using Integration and Criteria Heuristics. 4 - Dario Ghersi, Mona Singh:
Disentangling function from topology to infer the network properties of disease genes. 5 - Marc Weber, Javier Buceta:
Dynamics of the quorum sensing switch: stochastic and non-stationary effects. 6 - Dávid Fazekas, Mihály Koltai, Dénes Türei, Dezsö Módos, Máté Pálfy, Zoltán Dúl, Lilian Zsákai, Máté Szalay-Beko, Katalin Lenti, Illés J. Farkas, Tibor Vellai, Peter Csermely, Tamás Korcsmáros:
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. 7 - Annette Krengel, Jan Hauth, Marja-Riitta Taskinen, Martin Adiels, Mats Jirstrand:
A continuous-time adaptive particle filter for estimations under measurement time uncertainties with an application to a plasma-leucine mixed effects model. 8 - Hyunju Cho, Ming Wu, Linxia Zhang, Ryan Thompson, Aritro Nath, Christina Chan:
Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells. 9 - Jennifer E. Dent, Christine Nardini:
From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials. 10 - Anna Bershteyn, Philip A. Eckhoff:
A model of HIV drug resistance driven by heterogeneities in host immunity and adherence patterns. 11 - Gaurav Kumar, Edmond J. Breen, Shoba Ranganathan:
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. 12 - Elena Kutumova, Andrei Yu. Zinovyev, Ruslan N. Sharipov, Fedor A. Kolpakov:
Model composition through model reduction: a combined model of CD95 and NF-κ. 13 - Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini:
Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties. 14 - Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell:
Precise generation of systems biology models from KEGG pathways. 15 - Kamil Erguler, Myrtani Pieri, Constantinos Deltas:
A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis. 16 - Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J. Heijnen, Walter M. van Gulik, Pau Ferrer, Joan Albiol, Aljoscha Wahl:
Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis. 17 - Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Yu. Zinovyev:
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. 18 - Sven E. F. Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind M. Jakobsen, Per Bruheim, Trond E. Ellingsen, Jens Nielsen, Svein Valla:
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling. 19 - Weiwei Yin, Eberhard O. Voit:
Function and design of the Nox1 system in vascular smooth muscle cells. 20 - John M. O. Ranola, Peter Langfelder, Kenneth Lange, Steve Horvath:
Cluster and propensity based approximation of a network. 21 - Fatemeh Vafaee, Daniela Rosu, Fiona Broackes-Carter, Igor Jurisica:
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. 22 - Alexandra V. Pokhilko, Paloma Mas, Andrew J. Millar:
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. 23 - Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Falconi, Daniela Besozzi, Paolo Plevani:
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. 24 - Vladimir Trifonov, Laura Pasqualucci, Riccardo Dalla Favera, Raul Rabadan:
MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples. 25 - William A. Bryant, Michael J. E. Sternberg, John W. Pinney:
AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response. 26 - Anat Bren, Yuval Hart, Erez Dekel, Daniel Koster, Uri Alon:
The last generation of bacterial growth in limiting nutrient. 27 - Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li, Yi Pan:
An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation. 28 - Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun:
Probabilistic strain optimization under constraint uncertainty. 29 - Kyungchul Noh, Kyung Soon Shin, Dongkwan Shin, Jae Yeon Hwang, June Sic Kim, Joon Hwan Jang, Chun Kee Chung, Jun Soo Kwon, Kwang-Hyun Cho:
Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of schizophrenia. 30 - Alexei Vazquez:
Optimization of personalized therapies for anticancer treatment. 31 - Jihua Ran, Hui Li, Jianfeng Fu, Ling Liu, Yanchao Xing, Xiumei Li, Hongming Shen, Yan Chen, Xiaofang Jiang, Yan Li, Huiwu Li:
Construction and analysis of the protein-protein interaction network related to essential hypertension. 32 - S. Alexander Riemer, Rene Rex, Dietmar Schomburg:
A metabolite-centric view on flux distributions in genome-scale metabolic models. 33 - Sara Martinez-Pasamar, Elena Abad, Beatriz Moreno, Nieves Vélez de Mendizábal, Ivan Martinez-Forero, Jordi García-Ojalvo, Pablo Villoslada:
Dynamic cross-regulation of antigen-specific effector and regulatory T cell subpopulations and microglia in brain autoimmunity. 34 - Tim Sands:
Annual acknowledgement of reviewers. 35 - Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen:
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. 36 - Debjit Ray, Yongchun Su, Ping Ye:
Dynamic modeling of yeast meiotic initiation. 37 - Emily Greenfest-Allen, Jeffrey Malik, James Palis, Christian J. Stoeckert Jr.:
Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis. 38 - Luca Salerno, Carlo Cosentino, Alessio Merola, Declan G. Bates, Francesco Amato:
Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics. 39 - Kevin Gonzales, Ömür Kayikçi, David G. Schaeffer, Paul M. Magwene:
Modeling mutant phenotypes and oscillatory dynamics in the Saccharomyces cerevisiae cAMP-PKA pathway. 40 - Graham R. Smith, Daryl P. Shanley:
Computational modelling of the regulation of Insulin signalling by oxidative stress. 41 - Mario A. Marchisio, Moreno Colaiacovo, Ellis Whitehead, Jörg Stelling:
Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. 42 - Christian Knüpfer, Clemens Beckstein, Peter Dittrich, Nicolas Le Novère:
Structure, function, and behaviour of computational models in systems biology. 43 - F. Alex Feltus, Stephen P. Ficklin, Scott M. Gibson, Melissa C. Smith:
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. 44 - Jaewook Joo, Steven J. Plimpton, Jean-Loup Faulon:
Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κ. 45 - David J. Baumler, Bing Ma, Jennifer L. Reed, Nicole T. Perna:
Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. 46 - Soo-Jin Kim, JungWoo Ha, Byoung-Tak Zhang:
Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning. 47 - Sabrina Hock, Yen-Kar Ng, Jan Hasenauer, Dominik M. Wittmann, Dominik Lutter, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis:
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. 48 - Yaling Nie, Jingkai Yu:
Mining breast cancer genes with a network based noise-tolerant approach. 49 - Miranda D. Stobbe, Morris A. Swertz, Ines Thiele, Trebor Rengaw, Antoine H. C. van Kampen, Perry D. Moerland:
Consensus and conflict cards for metabolic pathway databases. 50 - Jessica M. Winkler, Howard S. Fox:
Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer's disease. 51 - Katherine Lawler, Kim E. Hammond-Kosack, Alvis Brazma, Richard M. R. Coulson:
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum. 52 - Cihan Oguz, Teeraphan Laomettachit, Katherine C. Chen, Layne T. Watson, William T. Baumann, John J. Tyson:
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. 53 - Gaël Yvert, Shinsuke Ohnuki, Satoru Nogami, Yasutaka Imanaga, Steffen Fehrmann, Joseph Schacherer, Yoshikazu Ohya:
Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast. 54 - Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard R. Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger:
The systems biology simulation core algorithm. 55 - Oleg O. Demin, Sergey V. Smirnov, Victor V. Sokolov, Lourdes Cucurull-Sanchez, César Pichardo-Almarza, M. Victoria Flores, Neil Benson, Oleg V. Demin:
Modeling of celiac disease immune response and the therapeutic effect of potential drugs. 56 - Tapesh Santra, Walter Kolch, Boris N. Kholodenko:
Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology. 57 - Max Flöttmann, Falko Krause, Edda Klipp, Marcus Krantz:
Reaction-contingency based bipartite Boolean modelling. 58 - Inna Pertsovskaya, Elena Abad, Núria Domedel-Puig, Jordi García-Ojalvo, Pablo Villoslada:
Transient oscillatory dynamics of interferon beta signaling in macrophages. 59 - Dagmar Iber, Christian Geyter:
Computational modelling of bovine ovarian follicle development. 60 - Shide Liang, Dandan Zheng, Daron M. Standley, Huarong Guo, Chi Zhang:
A novel function prediction approach using protein overlap networks. 61 - Jon Pey, Luis Tobalina, Joaquín Prada J. de Cisneros, Francisco J. Planes:
A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype. 62 - Francisco G. Vital-Lopez, Anders Wallqvist, Jaques Reifman:
Bridging the gap between gene expression and metabolic phenotype via kinetic models. 63 - Tien-Chueh Kuo, Tze-Feng Tian, Yufeng Jane Tseng:
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. 64 - Hsu Kiang Ooi, Lan Ma:
Modeling heterogeneous responsiveness of intrinsic apoptosis pathway. 65 - Sharmin Nilufar, Anne Morrow, Jonathan Lee, Theodore J. Perkins:
FiloDetect: automatic detection of filopodia from fluorescence microscopy images. 66 - Marta N. Bogdal, Beata Hat, Marek Kochanczyk, Tomasz Lipniacki:
Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate. 67 - Christopher D. Lasher, Padmavathy Rajagopalan, T. M. Murali:
Summarizing cellular responses as biological process networks. 68 - Nicolas Tchitchek, Amie J. Eisfeld, Jennifer Tisoncik-Go, Laurence Josset, Lisa E. Gralinski, Christophe Bécavin, Susan C. Tilton, Bobbie-Jo M. Webb-Robertson, Martin T. Ferris, Allison L. Totura, Chengjun Li, Gabriele Neumann, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Ralph S. Baric, Yoshihiro Kawaoka, Michael G. Katze:
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. 69 - Chao Cheng, Yao Fu, Linsheng Shen, Mark Gerstein:
Identification of yeast cell cycle regulated genes based on genomic features. 70 - Peter C. St. John, Francis J. Doyle:
Estimating confidence intervals in predicted responses for oscillatory biological models. 71 - Stuart Aitken, Ozgur E. Akman:
Nested sampling for parameter inference in systems biology: application to an exemplar circadian model. 72 - Andrea Pinna, Sandra Heise, Robert J. Flassig, Alberto de la Fuente, Steffen Klamt:
Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. 73 - Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson, Daniel R. Hyduke:
COBRApy: COnstraints-Based Reconstruction and Analysis for Python. 74 - Treenut Saithong, Oratai Rongsirikul, Saowalak Kalapanulak, Porntip Chiewchankaset, Wanatsanan Siriwat, Supatcharee Netrphan, Malinee Suksangpanomrung, Asawin Meechai, Supapon Cheevadhanarak:
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration. 75 - Maria Rodriguez-Fernandez, Markus Rehberg, Andreas Kremling, Julio R. Banga:
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. 76 - Walter de Back, Roland Zimm, Lutz Brusch:
Transdifferentiation of pancreatic cells by loss of contact-mediated signaling. 77 - Michael Bockmayr, Frederick Klauschen, Balazs Györffy, Carsten Denkert, Jan Budczies:
New network topology approaches reveal differential correlation patterns in breast cancer. 78 - Yu-Chao Wang, Che Lin, Ming-Ta Chuang, Wen-Ping Hsieh, Chung-Yu Lan, Yung-Jen Chuang, Bor-Sen Chen:
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study. 79 - Ruoting Yang, Bernie J. Daigle Jr., Seid Y. Muhie, Rasha Hammamieh, Marti Jett, Linda R. Petzold, Francis J. Doyle III:
Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder. 80 - Nadine S. Schaadt, Anke Steinbach, Rolf W. Hartmann, Volkhard Helms:
Rule-based regulatory and metabolic model for Quorum sensing in P. aeruginosa. 81 - Hannes Hettling, David J. C. Alders, Jaap Heringa, Thomas W. Binsl, A. B. Johan Groeneveld, Johannes H. G. M. van Beek:
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies. 82 - Yong-Jun Shin, Kai-Yuan Chen, Ali H. Sayed, Brandon Hencey, Xiling Shen:
Post-translational regulation enables robust p53 regulation. 83 - Shahin Mohammadi, Shankar Subramaniam, Ananth Grama:
Inferring the effective TOR-dependent network: a computational study in yeast. 84 - Asfar S. Azmi, Aliccia Bollig-Fischer, Bin Bao, Bum-Joon Park, Sun-Hye Lee, Gyu Yong-Song, Gregory Dyson, Chandan K. Reddy, Fazlul H. Sarkar, Ramzi M. Mohammad:
Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25. 85 - Taejeong Bae, Kyoohyoung Rho, Jin Woo Choi, Katsuhisa Horimoto, Wan Kyu Kim, Sunghoon Kim:
Identification of upstream regulators for prognostic expression signature genes in colorectal cancer. 86 - Juliana Oliveira, Anderson de Brito, Carla Braconi, Caio de Melo Freire, Atila Iamarino, Paolo de Andrade Zanotto:
Modularity and evolutionary constraints in a baculovirus gene regulatory network. 87 - Sarp A. Coskun, A. Ercüment Çiçek, Nicola Lai, Ranjan K. Dash, Z. Meral Özsoyoglu, Gultekin Özsoyoglu:
An online model composition tool for system biology models. 88 - Saheed Imam, Daniel R. Noguera, Timothy J. Donohue:
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. 89 - Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder:
Topology of molecular interaction networks. 90 - Pu Li, Quoc Dong Vu:
Identification of parameter correlations for parameter estimation in dynamic biological models. 91 - Yousuke Nishio, Soichi Ogishima, Masao Ichikawa, Yohei Yamada, Yoshihiro Usuda, Tadashi Masuda, Hiroshi Tanaka:
Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli. 92 - Prashant K. Srivastava, Richard P. Hull, Jacques Behmoaras, Enrico Petretto, Timothy J. Aitman:
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis. 93 - Omar P. Tabbaa, German Nudelman, Stuart C. Sealfon, Fernand Hayot, Ciriyam Jayaprakash:
Noise propagation through extracellular signaling leads to fluctuations in gene expression. 94 - Sirus Palsson, Timothy P. Hickling, Erica L. Bradshaw-Pierce, Michael Zager, Karin Jooss, Peter O'Brien, Mary E. Spilker, Bernhard Ø. Palsson, Paolo Vicini:
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. 95 - Maria I. Klapa, Kalliopi Tsafou, Evangelos Theodoridis, Athanasios K. Tsakalidis, Nicholas K. Moschonas:
Reconstruction of the experimentally supported human protein interactome: what can we learn? 96 - Yukiko Matsuoka, Hiromi Matsumae, Manami Katoh, Amie J. Eisfeld, Gabriele Neumann, Takeshi Hase, Samik Ghosh, Jason E. Shoemaker, Tiago J. S. Lopes, Tokiko Watanabe, Shinji Watanabe, Satoshi Fukuyama, Hiroaki Kitano, Yoshihiro Kawaoka:
A comprehensive map of the influenza A virus replication cycle. 97 - Edwin H. Wintermute, Tami D. Lieberman, Pamela A. Silver:
An objective function exploiting suboptimal solutions in metabolic networks. 98 - Matthieu Barba, Raphaël Dutoit, Christianne Legrain, Bernard Labedan:
Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism. 99 - Inna Kuperstein, David P. A. Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev:
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. 100 - Hongbo Shi, Juan Xu, Guangde Zhang, Liangde Xu, Chunquan Li, Li Wang, Zheng Zhao, Wei Jiang, Zheng Guo, Xia Li:
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. 101 - Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson:
Antibacterial mechanisms identified through structural systems pharmacology. 102 - Francesco Alessandro Massucci, Mauro DiNuzzo, Federico Giove, Bruno Maraviglia, Isaac Pérez Castillo, Enzo Marinari, Andrea De Martino:
Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective. 103 - Kazuhiko Bessho, Kumar Shanmukhappa, Rachel Sheridan, Pranavkumar Shivakumar, Reena Mourya, Stephanie Walters, Vivek Kaimal, Eric Dilbone, Anil G. Jegga, Jorge A. Bezerra:
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia. 104 - Suoqin Jin, Xiufen Zou:
Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization. 105 - Janusz Slawek, Tomasz Arodz:
ENNET: inferring large gene regulatory networks from expression data using gradient boosting. 106 - Helen L. Kotze, Emily G. Armitage, Kieran J. Sharkey, James William Allwood, Warwick B. Dunn, Kaye J. Williams, Royston Goodacre:
A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions. 107 - Javier Carrera, Alfonso Jaramillo:
Automated design of bacterial genome sequences. 108 - Yi-Ying Lee, Chih-Yuan Hsu, Ling-Jiun Lin, Chih-Chun Chang, Hsiao-Chun Cheng, Tsung-Hsien Yeh, Rei-Hsing Hu, Che Lin, Zhen Xie, Bor-Sen Chen:
Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries. 109 - Holger Husi, Maria Sanchez-Niño, Christian Delles, William Mullen, Antonia Vlahou, Alberto Ortiz Arduan, Harald Mischak:
A combinatorial approach of Proteomics and Systems Biology in unravelling the mechanisms of acute kidney injury (AKI): involvement of NMDA receptor GRIN1 in murine AKI. 110 - Andrea Rau, Florence Jaffrézic, Grégory Nuel:
Joint estimation of causal effects from observational and intervention gene expression data. 111 - Pengping Li, Xu Hua, Zhen Zhang, Jie Li, Jin Wang:
Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks. 112 - Gonzalo Guillén-Gosálbez, Antoni Miró, Rui Alves, Albert Sorribas, Laureano Jiménez:
Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization. 113 - Miguel Ponce de Leon, Francisco Montero, Juli Peretó:
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. 114 - Torsten Vogt, Tobias Czauderna, Falk Schreiber:
Translation of SBGN maps: Process Description to Activity Flow. 115 - Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère:
Path2Models: large-scale generation of computational models from biochemical pathway maps. 116 - Axel Krinner, Ingo Roeder, Markus Loeffler, Markus Scholz:
Merging concepts - coupling an agent-based model of hematopoietic stem cells with an ODE model of granulopoiesis. 117 - David M. Simcha, Laurent Younes, Martin J. Aryee, Donald Geman:
Identification of direction in gene networks from expression and methylation. 118 - ClarLynda R. Williams-DeVane, David M. Reif, Elaine Cohen Hubal, Pierre R. Bushel, Edward E. Hudgens, Jane E. Gallagher, Stephen W. Edwards:
Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. 119 - Qinghua Wang, Keerthi Venkataramanan, Hongzhan Huang, Eleftherios T. Papoutsakis, Cathy H. Wu:
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. 120 - Anatoly L. Mayburd, Ancha V. Baranova:
Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer's disease. 121 - Ke-ning Li, Zi-hui Li, Ning Zhao, Yaoqun Xu, Yongjing Liu, Yuanshuai Zhou, Desi Shang, Fujun Qiu, Rui Zhang, Zhi-qiang Chang, Yan Xu:
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer. 122 - Partho Sen, Henri J. Vial, Ovidiu Radulescu:
Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways. 123 - Michael Weber, Ana M. Sotoca, Peter Kupfer, Reinhard Guthke, Everardus J. van Zoelen:
Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation. 124 - Gabriel Gelius-Dietrich, Abdelmoneim Amer Desouki, Claus Fritzemeier, Martin J. Lercher:
sybil - Efficient constraint-based modelling in R. 125 - Ashish Misra, Ganesh Sriram:
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. 126 - Julio A. Freyre-González, Alejandra M. Manjarrez-Casas, Enrique Merino, Mario Martinez-Nuñez, Ernesto Pérez-Rueda, Rosa-María Gutiérrez-Ríos:
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis. 127 - Derek Gatherer, Vashti Galpin:
Rosen's (M, R) system in process algebra. 128 - Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun:
MC3: a steady-state model and constraint consistency checker for biochemical networks. 129 - Mieczyslaw Torchala, Przemyslaw Chelminiak, Michal Kurzynski, Paul A. Bates:
RaTrav: a tool for calculating mean first-passage times on biochemical networks. 130 - Fei He, Vincent Fromion, Hans V. Westerhoff:
(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis. 131 - Soma Ghosh, Priyanka Baloni, Sumanta Mukherjee, Praveen Anand, Nagasuma R. Chandra:
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. 132 - Ozan Kahramanogullari, James F. Lynch:
Stochastic flux analysis of chemical reaction networks. 133 - Jon Pey, Kaspar Valgepea, Angel Rubio, John E. Beasley, Francisco J. Planes:
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. 134 - Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar:
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. 135 - Daniel Madar, Erez Dekel, Anat Bren, Anat Zimmer, Ziv Porat, Uri Alon:
Promoter activity dynamics in the lag phase of Escherichia coli. 136 - Katrina K. Treloar, Matthew J. Simpson, Parvathi Haridas, Kerry J. Manton, David I. Leavesley, Donald L. S. McElwain, Ruth E. Baker:
Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies. 137 - Yi Zhou, Alexei Vázquez, Aaron Wise, Tomoko Warita, Katsuhiko Warita, Ziv Bar-Joseph, Zoltán N. Oltvai:
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells. 138 - Francesco Iorio, Julio Saez-Rodriguez, Diego di Bernardo:
Network based elucidation of drug response: from modulators to targets. 139 - Isaac Crespo, Thanneer M. Perumal, Wiktor Jurkowski, Antonio del Sol:
Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks. 140 - Meeta Pradhan, Akshay Desai, Mathew J. Palakal:
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. 141 - Thomas J. Mueller, Bertram M. Berla, Himadri B. Pakrasi, Costas D. Maranas:
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. 142
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