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ORCIDBMC Systems Biology, Volume 10
Volume 10, 2016
- Edelmira Valero
, Hermenegilda Macià, Ildefonso M. De la Fuente, José-Antonio Hernández, María-Isabel González-Sánchez, Francisco García-Carmona:
Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. 11
- Julia Lima Fleck, Ana B. Pavel, Christos G. Cassandras:
Integrating mutation and gene expression cross-sectional data to infer cancer progression. 12 - Jimmy Omony, Astrid R. Mach-Aigner, Gerrit van Straten, Anton J. B. van Boxtel:
Quantitative modeling and analytic assessment of the transcription dynamics of the XlnR regulon in Aspergillus niger. 13 - Aleksander Jankowski, Paulina Obara, Utsav Mathur, Jerzy Tiuryn:
Enhanceosome transcription factors preferentially dimerize with high mobility group proteins. 14 - Dan Tian, Isaiah Mitchell, Pamela K. Kreeger:
Quantitative analysis of insulin-like growth factor 2 receptor and insulin-like growth factor binding proteins to identify control mechanisms for insulin-like growth factor 1 receptor phosphorylation. 15 - Ana B. Pavel, Dmitriy Sonkin, Anupama Reddy:
Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity. 16 - Marc Mangel, Michael B. Bonsall, Aziz Aboobaker:
Feedback control in planarian stem cell systems. 17 - Bor-Sen Chen, Cheng-Wei Li:
Constructing an integrated genetic and epigenetic cellular network for whole cellular mechanism using high-throughput next-generation sequencing data. 18 - William Bains:
Low potency toxins reveal dense interaction networks in metabolism. 19 - Katarzyna M. Tyc, Sanna E. Herwald, Jennifer A. Hogan, Jessica V. Pierce, Edda Klipp, Carol A. Kumamoto:
The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. 20 - Jin Chen, Jose A. Gomez, Kai Höffner, Poonam Phalak, Paul I. Barton, Michael A. Henson:
Spatiotemporal modeling of microbial metabolism. 21 - Jonathan Legrand, Jean-Benoist Léger, Stéphane Robin, Teva Vernoux, Yann Guédon:
Modelling the influence of dimerisation sequence dissimilarities on the auxin signalling network. 22 - Eleftherios Ouzounoglou, Dimitra D. Dionysiou, Georgios S. Stamatakos:
Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. 23 - Fortunato Bianconi, Elisa Baldelli, Vienna Ludovini, Emanuel F. Petricoin, Lucio Crinò, Paolo Valigi:
Erratum to: 'Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology'. 24 - Alberto Calderone, Matteo Formenti, Federica Aprea, Michele Papa, Lilia Alberghina, Anna Maria Colangelo, Paola Bertolazzi:
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. 25 - Elizabeth Brunk, Nathan Mih, Jonathan Monk, Zhen Zhang, Edward J. O'Brien, Spencer E. Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne, Bernhard O. Palsson:
Systems biology of the structural proteome. 26 - Yadira Boada, Gilberto Reynoso-Meza, Jesús Picó, Alejandro Vignoni:
Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case. 27 - Katrin Kolczyk, Carsten Conradi:
Challenges in horizontal model integration. 28 - Timothy R. Sands:
Annual Acknowledgement of Reviewers. 29 - Jovan Tanevski, Ljupco Todorovski, Saso Dzeroski:
Learning stochastic process-based models of dynamical systems from knowledge and data. 30 - Andrew Iverson, Erin Garza, Ryan Manow, Jinhua Wang, Yuanyuan Gao, Scott Grayburn, Shengde Zhou:
Engineering a synthetic anaerobic respiration for reduction of xylose to xylitol using NADH output of glucose catabolism by Escherichia coli AI21. 31 - Diana V. Salakhieva, Ildar I. Sadreev, Michael Z. Q. Chen, Yoshinori Umezawa, Aleksandr I. Evstifeev, Gavin I. Welsh, Nikolay V. Kotov:
Kinetic regulation of multi-ligand binding proteins. 32 - Peter Andorfer, Alexander Heuwieser, Andreas Heinzel, Arno Lukas, Bernd Mayer, Paul Perco:
Vascular endothelial growth factor A as predictive marker for mTOR inhibition in relapsing high-grade serous ovarian cancer. 33 - Matthew Oremland, Kathryn R. Michels, Alexandra M. Bettina, Christopher Lawrence, Borna Mehrad, Reinhard C. Laubenbacher:
A computational model of invasive aspergillosis in the lung and the role of iron. 34 - Heiko Babel, Ilka B. Bischofs:
Molecular and cellular factors control signal transduction via switchable allosteric modulator proteins (SAMPs). 35 - Jing Yang, Su-Juan Wu, Shao-You Yang, Jia-Wei Peng, Shi-Nuo Wang, Fu-Yan Wang, Yu-Xing Song, Ting Qi, Yi-Xue Li, Yuan-Yuan Li:
DNetDB: The human disease network database based on dysfunctional regulation mechanism. 36 - Lucas Sánchez, Claudine Chaouiya:
Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells. 37 - Barbara Di Camillo, Azzurra Carlon, Federica Eduati, Gianna Maria Toffolo:
A rule-based model of insulin signalling pathway. 38 - Nikolay Martyushenko, Sigurd Hagen Johansen, Cheol-Min Ghim, Eivind Almaas:
Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability. 39 - Bin Du, Daniel C. Zielinski, Erol S. Kavvas, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla E. Ruggiero, Garri A. Arzumanyan, Bernhard O. Palsson:
Evaluation of rate law approximations in bottom-up kinetic models of metabolism. 40 - Yulin Wang, Na Lu, Hongyu Miao:
Structural identifiability of cyclic graphical models of biological networks with latent variables. 41 - Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc Paulevé:
Qualitative dynamics semantics for SBGN process description. 42 - Tom Serge Weber, Mark Dukes, Denise C. Miles, Stefan P. Glaser, Shalin H. Naik, Ken R. Duffy:
Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system. 43 - Yeimy Morales, Gabriel Bosque, Josep Vehí, Jesús Picó, Francisco Llaneras:
PFA toolbox: a MATLAB tool for Metabolic Flux Analysis. 46 - Joanna Lewis, Charles E. Breeze, Jane Charlesworth, Oliver J. Maclaren, Jonathan Cooper:
Where next for the reproducibility agenda in computational biology? 52 - Teresa Vaz Martins, Matthew J. Evans, Derin B. Wysham, Richard J. Morris:
Nuclear pores enable sustained perinuclear calcium oscillations. 55 - Stefano Schivo, Jetse Scholma, Paul E. van der Vet, Marcel Karperien, Janine N. Post, Jaco van de Pol, Rom Langerak:
Modelling with ANIMO: between fuzzy logic and differential equations. 56 - Yan Huang, Li Wang, Lin-sen Zan:
ARN: analysis and prediction by adipogenic professional database. 57 - Anders Wallqvist, Xin Fang, Shivendra G. Tewari, Ping Ye, Jaques Reifman:
Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle. 58 - Fleur Jeanquartier, Claire Jean-Quartier, David Cemernek, Andreas Holzinger:
In silico modeling for tumor growth visualization. 59 - Hao Zhang, Yanpu Li, Yuanning Liu, Haiming Liu, Hongyu Wang, Wen Jin, Yanmei Zhang, Chao Zhang, Dong Xu:
Role of plant MicroRNA in cross-species regulatory networks of humans. 60 - Ines Wilms, Christophe Croux:
Robust sparse canonical correlation analysis. 72 - Xiaoqiang Sun, Jiajun Zhang, Qi Zhao, Xing Chen, Wenbo Zhu, Guangmei Yan, Tianshou Zhou:
Stochastic modeling suggests that noise reduces differentiation efficiency by inducing a heterogeneous drug response in glioma differentiation therapy. 73 - Núria Ballber Torres, Claudio Altafini:
Drug combinatorics and side effect estimation on the signed human drug-target network. 74 - Katarzyna Jonak, Monika Kurpas, Katarzyna Szoltysek, Patryk Janus, Agata Abramowicz, Krzysztof Puszynski:
A novel mathematical model of ATM/p53/NF- κB pathways points to the importance of the DDR switch-off mechanisms. 75 - Robert Pesch, Ralf Zimmer:
Cross-species Conservation of context-specific networks. 76 - Xuefeng Gao, Christophe Arpin, Jacqueline Marvel, Sotiris A. Prokopiou, Olivier Gandrillon, Fabien Crauste:
IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study. 77 - Xiao Gan, Réka Albert:
Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation. 78 - Douglas Brubaker, Alethea Barbaro, Mark R. Chance, Sam Mesiano:
A dynamical systems model of progesterone receptor interactions with inflammation in human parturition. 79 - Anna Fiedler, Sebastian Raeth, Fabian J. Theis, Angelika Hausser, Jan Hasenauer:
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. 80 - Oleg Lenive, Paul D. W. Kirk, Michael P. H. Stumpf:
Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation. 81 - Anastasiya Börsch, Jörg Schaber:
How time delay and network design shape response patterns in biochemical negative feedback systems. 82 - Yung-Keun Kwon:
Properties of Boolean dynamics by node classification using feedback loops in a network. 83 - Simona Catozzi, Juan Pablo Di-Bella, Alejandra C. Ventura, Jacques-A. Sepulchre:
Signaling cascades transmit information downstream and upstream but unlikely simultaneously. 84 - Ashley A. Jermusyk, Nicholas P. Murphy, Gregory T. Reeves:
Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo. 85 - Philippe Nimmegeers, Dries Telen, Filip Logist, Jan F. M. Van Impe:
Dynamic optimization of biological networks under parametric uncertainty. 86 - Xun Yue, Xing Guo Li, Xin-Qi Gao, Xiang Yu Zhao, Yu Xiu Dong, Chao Zhou:
The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes. 87 - Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed, Volkhard Helms:
Identification of key player genes in gene regulatory networks. 88 - David M. Budden, Edmund J. Crampin:
Information theoretic approaches for inference of biological networks from continuous-valued data. 89 - Poonam Phalak, Jin Chen, Ross P. Carlson, Michael A. Henson:
Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species. 90 - Stanislav Sokolenko, Marco Quattrociocchi, Marc Aucoin:
Identifying model error in metabolic flux analysis - a generalized least squares approach. 91 - Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond A. Jonckheere, David B. Agus, Shannon M. Mumenthaler, Paul Macklin:
Quantifying differences in cell line population dynamics using CellPD. 92 - Jason E. McDermott, Hugh D. Mitchell, Lisa E. Gralinski, Amie J. Eisfeld, Laurence Josset, Armand Bankhead III, Gabriele Neumann, Susan C. Tilton, Alexandra Schäfer, Chengjun Li, Shufang Fan, Shannon K. McWeeney, Ralph S. Baric, Michael G. Katze, Katrina M. Waters:
The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus. 93 - David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Reinhard C. Laubenbacher:
Identification of control targets in Boolean molecular network models via computational algebra. 94 - Sang-Mok Choo, Kwang-Hyun Cho:
An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network. 95 - Sung-Hwan Cho, Sang-Min Park, Hosung Lee, Hwang-Yeol Lee, Kwang-Hyun Cho:
Attractor landscape analysis of colorectal tumorigenesis and its reversion. 96 - Sayed-Rzgar Hosseini, Andreas Wagner:
The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism. 97 - Alexander Lück, Verena Wolf:
Generalized method of moments for estimating parameters of stochastic reaction networks. 98:1-98:12 - Katarzyna Jonak, Monika Kurpas, Katarzyna Szoltysek, Patryk Janus, Agata Abramowicz, Krzysztof Puszynski:
Erratum to: A novel mathematical model of ATM/p53/NF-κB pathways points to the importance of the DDR switch-off mechanisms. 99 - Bram Thijssen, T. M. H. Dijkstra, Tom Heskes, Lodewyk F. A. Wessels:
BCM: toolkit for Bayesian analysis of Computational Models using samplers. 100 - Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan L. Archibald, Tahar Ait-Ali:
Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus. 101 - Veronique Beckers, Lisa Maria Dersch, Katrin Lotz, Guido Melzer, Oliver E. Bläsing, Regine Fuchs, Thomas Ehrhardt, Christoph Wittmann:
In silico metabolic network analysis of Arabidopsis leaves. 102 - Edson Luiz Folador, Paulo Vinícius Sanches Daltro de Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, M. Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Ariston de Carvalho Azevedo, Richard Röttger:
In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. 103:1-103:9 - Zrinka Raguz Nakic, Gerhard Seisenbacher, Francesc Posas, Uwe Sauer:
Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae. 104:1-104:15 - Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng, Herbert M. Lachman:
Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. 105:1-105:20 - Andrew McKenzie, Igor Katsyv, Won-Min Song, Minghui Wang, Bin Zhang:
DGCA: A comprehensive R package for Differential Gene Correlation Analysis. 106:1-106:25 - Xiaoyuan Zhou, Christine Nardini:
A method for automated pathogenic content estimation with application to rheumatoid arthritis. 107:1-107:8 - Wenrui Hao, Avner Friedman:
Mathematical model on Alzheimer's disease. 108:1-108:18 - Min K. Roh, Bernie J. Daigle Jr.:
SParSE++: improved event-based stochastic parameter search. 109:1-109:15 - Robert W. Smith, Britta Helwig, Adrie H. Westphal, Eran Pel, Maximilian Hörner, Hannes M. Beyer, Sophia L. Samodelov, Wilfried Weber, Matias D. Zurbriggen, Jan Willem Borst, Christian Fleck:
Unearthing the transition rates between photoreceptor conformers. 110:1-110:15 - Jesse R. Walsh, Mary L. Schaeffer, Peifen Zhang, Seung Yon Rhee, Julie A. Dickerson, Taner Z. Sen:
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. 129:1-129:9 - Miriam Leon, Mae L. Woods, Alex J. H. Fedorec, Chris P. Barnes:
A computational method for the investigation of multistable systems and its application to genetic switches. 130:1-130:12
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