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Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs npj Syst. Biol. Appl. Pub Date : 2020-04-03 Thierry D. G. A. Mondeel; Oleksandr Ivanov; Hans V. Westerhoff; Wolfram Liebermeister; Matteo Barberis
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Publisher Correction: Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae npj Syst. Biol. Appl. Pub Date : 2020-04-02 Bede P. Busby; Eliatan Niktab; Christina A. Roberts; Jeffrey P. Sheridan; Namal V. Coorey; Dinindu S. Senanayake; Lisa M. Connor; Andrew B. Munkacsi; Paul H. Atkinson
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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A hybrid stochastic model of the budding yeast cell cycle npj Syst. Biol. Appl. Pub Date : 2020-03-27 Mansooreh Ahmadian; John J. Tyson; Jean Peccoud; Yang Cao
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Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective npj Syst. Biol. Appl. Pub Date : 2020-03-13 Anne Richelle; Blandine David; Didier Demaegd; Marianne Dewerchin; Romain Kinet; Angelo Morreale; Rui Portela; Quentin Zune; Moritz von Stosch
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Chromosomal origin of replication coordinates logically distinct types of bacterial genetic regulation. npj Syst. Biol. Appl. Pub Date : 2020-02-17 Kosmas Kosmidis,Kim Philipp Jablonski,Georgi Muskhelishvili,Marc-Thorsten Hütt
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An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. npj Syst. Biol. Appl. Pub Date : 2020-01-30 Mohammad Mazharul Islam,Vinai C Thomas,Matthew Van Beek,Jong-Sam Ahn,Abdulelah A Alqarzaee,Chunyi Zhou,Paul D Fey,Kenneth W Bayles,Rajib Saha
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Author Correction: Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models. npj Syst. Biol. Appl. Pub Date : 2020-01-30 Noushin Hadadi,Vikash Pandey,Anush Chiappino-Pepe,Marian Morales,Hector Gallart-Ayala,Florence Mehl,Julijana Ivanisevic,Vladimir Sentchilo,Jan R van der Meer
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models. npj Syst. Biol. Appl. Pub Date : 2020-01-10 Jesper Romers,Sebastian Thieme,Ulrike Münzner,Marcus Krantz
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Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models. npj Syst. Biol. Appl. Pub Date : 2020-01-07 Noushin Hadadi,Vikash Pandey,Anush Chiappino-Pepe,Marian Morales,Hector Gallart-Ayala,Florence Mehl,Julijana Ivanisevic,Vladimir Sentchilo,Jan R van der Meer
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Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds npj Syst. Biol. Appl. Pub Date : 2019-11-26 Vipul Gupta, Alina Crudu, Yukiko Matsuoka, Samik Ghosh, Roger Rozot, Xavier Marat, Sibylle Jäger, Hiroaki Kitano, Lionel Breton
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An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells npj Syst. Biol. Appl. Pub Date : 2019-07-23 Yiqun Chen, Brian O. McConnell, Venkata Gayatri Dhara, Harnish Mukesh Naik, Chien-Ting Li, Maciek R. Antoniewicz, Michael J. Betenbaugh
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Signal integration and information transfer in an allosterically regulated network npj Syst. Biol. Appl. Pub Date : 2019-07-18 Erin M. Shockley, Carol A. Rouzer, Lawrence J. Marnett, Eric J. Deeds, Carlos F. Lopez
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Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants npj Syst. Biol. Appl. Pub Date : 2019-07-18 Michael Vacher, Ian Small
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iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery. npj Syst. Biol. Appl. Pub Date : 2019-07-09 Hiromi W L Koh,Damian Fermin,Christine Vogel,Kwok Pui Choi,Rob M Ewing,Hyungwon Choi
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Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer npj Syst. Biol. Appl. Pub Date : 2019-07-08 Jing Tang, Prson Gautam, Abhishekh Gupta, Liye He, Sanna Timonen, Yevhen Akimov, Wenyu Wang, Agnieszka Szwajda, Alok Jaiswal, Denes Turei, Bhagwan Yadav, Matti Kankainen, Jani Saarela, Julio Saez-Rodriguez, Krister Wennerberg, Tero Aittokallio
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Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition npj Syst. Biol. Appl. Pub Date : 2019-06-14 Kazuhide Watanabe, Nicholas Panchy, Shuhei Noguchi, Harukazu Suzuki, Tian Hong
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Mapping connections in signaling networks with ambiguous modularity npj Syst. Biol. Appl. Pub Date : 2019-05-23 Daniel Lill, Oleksii S. Rukhlenko, Anthony James Mc Elwee, Eugene Kashdan, Jens Timmer, Boris N. Kholodenko
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Identification of an early cell fate regulator by detecting dynamics in transcriptional heterogeneity and co-regulation during astrocyte differentiation npj Syst. Biol. Appl. Pub Date : 2019-05-08 Tatsuya Ando, Ryuji Kato, Hiroyuki Honda
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An in-silico approach for discovery of microRNA-TF regulation of DISC1 interactome mediating neuronal migration npj Syst. Biol. Appl. Pub Date : 2019-05-07 John P. John, Priyadarshini Thirunavukkarasu, Koko Ishizuka, Pravesh Parekh, Akira Sawa
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A yield-cost tradeoff governs Escherichia coli’ s decision between fermentation and respiration in carbon-limited growth npj Syst. Biol. Appl. Pub Date : 2019-05-01 Matteo Mori, Enzo Marinari, Andrea De Martino
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The multiplex network of human diseases npj Syst. Biol. Appl. Pub Date : 2019-04-23 Arda Halu, Manlio De Domenico, Alex Arenas, Amitabh Sharma
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Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli 's ammonium transport and assimilation network npj Syst. Biol. Appl. Pub Date : 2019-04-12 Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, Fred C. Boogerd
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Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer npj Syst. Biol. Appl. Pub Date : 2019-04-11 Matthew A. Care, David R. Westhead, Reuben M. Tooze
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Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics npj Syst. Biol. Appl. Pub Date : 2019-04-04 Renana Sabi, Tamir Tuller
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Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases npj Syst. Biol. Appl. Pub Date : 2019-03-07 Daniel Domingo-Fernández, Charles Tapley Hoyt, Carlos Bobis-Álvarez, Josep Marín-Llaó, Martin Hofmann-Apitius
The original version of this Article had an incorrect Article number of 3, an incorrect Volume of 5 and an incorrect Publication year of 2019. These errors have now been corrected in the PDF and HTML versions of the Article.
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Publisher Correction: Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection npj Syst. Biol. Appl. Pub Date : 2019-03-07 Fabian Fröhlich, Anita Reiser, Laura Fink, Daniel Woschée, Thomas Ligon, Fabian Joachim Theis, Joachim Oskar Rädler, Jan Hasenauer
The original version of this Article had an incorrect Article number of 1, an incorrect Volume of 5 and an incorrect Publication year of 2019. These errors have now been corrected in the PDF and HTML versions of the Article.
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PIMKL: Pathway-Induced Multiple Kernel Learning. npj Syst. Biol. Appl. Pub Date : 2019-03-05 Matteo Manica,Joris Cadow,Roland Mathis,María Rodríguez Martínez
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Erratum: Publisher Correction: Mathematical model of hemodynamic mechanisms and consequences of glomerular hypertension in diabetic mice. npj Syst. Biol. Appl. Pub Date : 2019-03-04 Hari Shankar Mahato,Christine Ahlstrom,Rasmus Jansson-Löfmark,Ulrika Johansson,Gabriel Helmlinger,K Melissa Hallow
[This corrects the article DOI: 10.1038/s41540-018-0077-9.].
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Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. npj Syst. Biol. Appl. Pub Date : 2019-03-01 Cankut Çubuk,Marta R Hidalgo,Alicia Amadoz,Kinza Rian,Francisco Salavert,Miguel A Pujana,Francesca Mateo,Carmen Herranz,Jose Carbonell-Caballero,Joaquín Dopazo
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Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. npj Syst. Biol. Appl. Pub Date : 2019-02-26 Kelly E Regan-Fendt,Jielin Xu,Mallory DiVincenzo,Megan C Duggan,Reena Shakya,Ryejung Na,William E Carson,Philip R O Payne,Fuhai Li
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Defining rules for cancer cell proliferation in TRAIL stimulation. npj Syst. Biol. Appl. Pub Date : 2019-02-15 William Deveaux,Kentaro Hayashi,Kumar Selvarajoo
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Mathematical modeling of diurnal patterns of carbon allocation to shoot and root in Arabidopsis thaliana npj Syst. Biol. Appl. Pub Date : 2019-01-24 Lisa Küstner, Thomas Nägele, Arnd G. Heyer
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ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. npj Syst. Biol. Appl. Pub Date : 2018-12-13 Daniel Domingo-Fernández,Charles Tapley Hoyt,Carlos Bobis-Álvarez,Josep Marín-Llaó,Martin Hofmann-Apitius
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Mathematical model of hemodynamic mechanisms and consequences of glomerular hypertension in diabetic mice. npj Syst. Biol. Appl. Pub Date : 2018-12-10 Hari Shankar Mahato,Christine Ahlstrom,Rasmus Jansson-Löfmark,Ulrika Johansson,Gabriel Helmlinger,K Melissa Hallow
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Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection. npj Syst. Biol. Appl. Pub Date : 2018-12-10 Fabian Fröhlich,Anita Reiser,Laura Fink,Daniel Woschée,Thomas Ligon,Fabian Joachim Theis,Joachim Oskar Rädler,Jan Hasenauer
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Role of noise and parametric variation in the dynamics of gene regulatory circuits npj Syst. Biol. Appl. Pub Date : 2018-11-05 Vivek Kohar, Mingyang Lu
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Systemic network analysis identifies XIAP and IκBα as potential drug targets in TRAIL resistant BRAF mutated melanoma npj Syst. Biol. Appl. Pub Date : 2018-11-05 Greta Del Mistro, Philippe Lucarelli, Ines Müller, Sébastien De Landtsheer, Anna Zinoveva, Meike Hutt, Martin Siegemund, Roland E. Kontermann, Stefan Beissert, Thomas Sauter, Dagmar Kulms
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Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability npj Syst. Biol. Appl. Pub Date : 2018-10-24 Anqi Jing, Frederick S. Vizeacoumar, Sreejit Parameswaran, Bjorn Haave, Chelsea E. Cunningham, Yuliang Wu, Roland Arnold, Keith Bonham, Andrew Freywald, Jie Han, Franco J. Vizeacoumar
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Context-dependent prediction of protein complexes by SiComPre npj Syst. Biol. Appl. Pub Date : 2018-09-17 Simone Rizzetto, Petros Moyseos, Bianca Baldacci, Corrado Priami, Attila Csikász-Nagy
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The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches npj Syst. Biol. Appl. Pub Date : 2018-09-06 Jérémy Gruel, Julia Deichmann, Benoit Landrein, Thomas Hitchcock, Henrik Jönsson
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Prevalence and patterns of higher-order drug interactions in Escherichia coli npj Syst. Biol. Appl. Pub Date : 2018-09-03 Elif Tekin, Cynthia White, Tina Manzhu Kang, Nina Singh, Mauricio Cruz-Loya, Robert Damoiseaux, Van M. Savage, Pamela J. Yeh
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Redefining environmental exposure for disease etiology npj Syst. Biol. Appl. Pub Date : 2018-09-01 Stephen M. Rappaport
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Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence npj Syst. Biol. Appl. Pub Date : 2018-08-31 Bharat Mishra, Yali Sun, TC Howton, Nilesh Kumar, M. Shahid Mukhtar
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A landscape view on the interplay between EMT and cancer metastasis npj Syst. Biol. Appl. Pub Date : 2018-08-23 Chunhe Li, Gabor Balazsi
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A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications npj Syst. Biol. Appl. Pub Date : 2019-11-13 Shuting Jin, Xiangxiang Zeng, Jiansong Fang, Jiawei Lin, Stephen Y. Chan, Serpil C. Erzurum, Feixiong Cheng
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From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL npj Syst. Biol. Appl. Pub Date : 2019-11-11 Anika Liu, Panuwat Trairatphisan, Enio Gjerga, Athanasios Didangelos, Jonathan Barratt, Julio Saez-Rodriguez
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Accelerating systems biology research and its real world deployment. npj Syst. Biol. Appl. Pub Date : 2015-09-28 Hiroaki Kitano
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Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire. npj Syst. Biol. Appl. Pub Date : 2015-01-01 Jason G Lomnitz,Michael A Savageau
BACKGROUND The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here
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A data driven approach reveals disease similarity on a molecular level npj Syst. Biol. Appl. Pub Date : 2019-10-25 Kleanthi Lakiotaki, George Georgakopoulos, Elias Castanas, Oluf Dimitri Røe, Giorgos Borboudakis, Ioannis Tsamardinos
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An omnidirectional visualization model of personalized gene regulatory networks npj Syst. Biol. Appl. Pub Date : 2019-10-11 Chixiang Chen, Libo Jiang, Guifang Fu, Ming Wang, Yaqun Wang, Biyi Shen, Zhenqiu Liu, Zuoheng Wang, Wei Hou, Scott A. Berceli, Rongling Wu
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ModelBricks—modules for reproducible modeling improving model annotation and provenance npj Syst. Biol. Appl. Pub Date : 2019-10-08 Ann E. Cowan, Pedro Mendes, Michael L. Blinov
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Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae npj Syst. Biol. Appl. Pub Date : 2019-10-03 Bede P. Busby, Eliatan Niktab, Christina A. Roberts, Jeffrey P. Sheridan, Namal V. Coorey, Dinindu S. Senanayake, Lisa M. Connor, Andrew B. Munkacsi, Paul H. Atkinson
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Defining subpopulations of differential drug response to reveal novel target populations npj Syst. Biol. Appl. Pub Date : 2019-10-03 Nirmal Keshava, Tzen S. Toh, Haobin Yuan, Bingxun Yang, Michael P. Menden, Dennis Wang
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Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae npj Syst. Biol. Appl. Pub Date : 2019-09-26 Tom Altenburg, Björn Goldenbogen, Jannis Uhlendorf, Edda Klipp
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Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity npj Syst. Biol. Appl. Pub Date : 2019-09-24 Chien-Ting Li, Jacob Yelsky, Yiqun Chen, Cristal Zuñiga, Richard Eng, Liqun Jiang, Alison Shapiro, Kai-Wen Huang, Karsten Zengler, Michael J. Betenbaugh
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Logical design of oral glucose ingestion pattern minimizing blood glucose in humans npj Syst. Biol. Appl. Pub Date : 2019-09-02 Masashi Fujii, Yohei Murakami, Yasuaki Karasawa, Yohei Sumitomo, Suguru Fujita, Masanori Koyama, Shinsuke Uda, Hiroyuki Kubota, Hiroshi Inoue, Katsumi Konishi, Shigeyuki Oba, Shin Ishii, Shinya Kuroda
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Flux sampling is a powerful tool to study metabolism under changing environmental conditions npj Syst. Biol. Appl. Pub Date : 2019-09-02 Helena A. Herrmann, Beth C. Dyson, Lucy Vass, Giles N. Johnson, Jean-Marc Schwartz
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Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma npj Syst. Biol. Appl. Pub Date : 2019-08-16 Mohammad Jafarnejad, Richard J. Sové, Ludmila Danilova, Adam C. Mirando, Yu Zhang, Mark Yarchoan, Phuoc T. Tran, Niranjan B. Pandey, Elana J. Fertig, Aleksander S. Popel
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Publisher Correction: npj Systems Biology and Applications, volume 5 npj Syst. Biol. Appl. Pub Date : 2019-08-13
Publisher Correction
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Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in Arabidopsis thaliana npj Syst. Biol. Appl. Pub Date : 2019-08-12 Zhana Duren, Yaling Wang, Jiguang Wang, Xing-Ming Zhao, Le Lv, Xiaobo Li, Jingdong Liu, Xin-Guang Zhu, Luonan Chen, Yong Wang
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