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A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure

JOURNAL ARTICLE published 24 February 2018 in npj Systems Biology and Applications

Authors: Marc Santolini | Milagros C. Romay | Clara L. Yukhtman | Christoph D. Rau | Shuxun Ren | Jeffrey J. Saucerman | Jessica J. Wang | James N. Weiss | Yibin Wang | Aldons J. Lusis | Alain Karma

https://doi.org/10.1038/s41540-018-0046-3 Actions

A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle

JOURNAL ARTICLE published 6 March 2017 in npj Systems Biology and Applications

Authors: Christian Linke | Anastasia Chasapi | Alberto González-Novo | Istabrak Al Sawad | Silvia Tognetti | Edda Klipp | Mart Loog | Sylvia Krobitsch | Francesc Posas | Ioannis Xenarios | Matteo Barberis

https://doi.org/10.1038/s41540-017-0008-1 Actions

Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients

JOURNAL ARTICLE published 16 June 2016 in npj Systems Biology and Applications

Authors: Marouen Ben Guebila | Ines Thiele

https://doi.org/10.1038/npjsba.2016.13 Actions

The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches

JOURNAL ARTICLE published 6 September 2018 in npj Systems Biology and Applications

Authors: Jérémy Gruel | Julia Deichmann | Benoit Landrein | Thomas Hitchcock | Henrik Jönsson

https://doi.org/10.1038/s41540-018-0072-1 Actions

Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model

JOURNAL ARTICLE published 9 June 2022 in npj Systems Biology and Applications

Authors: Péter Mendik | Márk Kerestély | Sebestyén Kamp | Dávid Deritei | Nina Kunšič | Zsolt Vassy | Péter Csermely | Daniel V. Veres

https://doi.org/10.1038/s41540-022-00228-7 Actions

Peripheral gene interactions define interpretable clusters of core ASD genes in a network-based investigation of the omnigenic theory

JOURNAL ARTICLE published 10 August 2022 in npj Systems Biology and Applications

Authors: Ábel Fóthi | Csaba Pintér | Péter Pollner | András Lőrincz

https://doi.org/10.1038/s41540-022-00240-x Actions

Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs

JOURNAL ARTICLE published 3 April 2020 in npj Systems Biology and Applications

Authors: Thierry D. G. A. Mondeel | Oleksandr Ivanov | Hans V. Westerhoff | Wolfram Liebermeister | Matteo Barberis

https://doi.org/10.1038/s41540-020-0125-0 Actions

Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing

JOURNAL ARTICLE published 18 January 2023 in npj Systems Biology and Applications

Authors: Timur Horn | Alison Gosliga | Congxin Li | Mihaela Enculescu | Stefan Legewie

https://doi.org/10.1038/s41540-022-00264-3 Actions

Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion

JOURNAL ARTICLE published 14 September 2023 in npj Systems Biology and Applications

Research funded by U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM140108,R01GM140108)

Authors: Dhananjay Bhaskar | William Y. Zhang | Alexandria Volkening | Björn Sandstede | Ian Y. Wong

https://doi.org/10.1038/s41540-023-00302-8 Actions

Cross-species gene modules emerge from a systems biology approach to osteoarthritis

JOURNAL ARTICLE published 17 May 2017 in npj Systems Biology and Applications

Authors: Alan James Mueller | Elizabeth G. Canty-Laird | Peter D. Clegg | Simon R. Tew

https://doi.org/10.1038/s41540-017-0014-3 Actions

Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer

JOURNAL ARTICLE published 17 September 2021 in npj Systems Biology and Applications

Research funded by Icelandic Centre for Research (163254-05,163254-05,163254-05,163254-05) | Norges Forskningsråd (71116,239940,190257,239940)

Authors: Sigurdur Trausti Karvelsson | Qiong Wang | Bylgja Hilmarsdottir | Arnar Sigurdsson | Siver Andreas Moestue | Gunhild Mari Mælandsmo | Skarphedinn Halldorsson | Steinn Gudmundsson | Ottar Rolfsson

https://doi.org/10.1038/s41540-021-00195-5 Actions

Regulatory feedback response mechanisms to phosphate starvation in rice

JOURNAL ARTICLE published 8 January 2018 in npj Systems Biology and Applications

Authors: Ishan Ajmera | Jing Shi | Jitender Giri | Ping Wu | Dov J. Stekel | Chungui Lu | T. Charlie Hodgman

https://doi.org/10.1038/s41540-017-0041-0 Actions

Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports

JOURNAL ARTICLE published 25 August 2017 in npj Systems Biology and Applications

Authors: Fumiaki Nin | Takamasa Yoshida | Shingo Murakami | Genki Ogata | Satoru Uetsuka | Samuel Choi | Katsumi Doi | Seishiro Sawamura | Hidenori Inohara | Shizuo Komune | Yoshihisa Kurachi | Hiroshi Hibino

https://doi.org/10.1038/s41540-017-0025-0 Actions

Defining rules for cancer cell proliferation in TRAIL stimulation

JOURNAL ARTICLE published 15 February 2019 in npj Systems Biology and Applications

Research funded by MEXT | Japan Society for the Promotion of Science (FX132008K3) | Agency for Science, Technology and Research (IAF-PP)

Authors: William Deveaux | Kentaro Hayashi | Kumar Selvarajoo

https://doi.org/10.1038/s41540-019-0084-5 Actions

Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol

JOURNAL ARTICLE published 4 November 2022 in npj Systems Biology and Applications

Authors: Shugang Zhang | Weigang Lu | Fei Yang | Zhen Li | Shuang Wang | Mingjian Jiang | Xiaofeng Wang | Zhiqiang Wei

https://doi.org/10.1038/s41540-022-00254-5 Actions

Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types

JOURNAL ARTICLE published 7 August 2019 in npj Systems Biology and Applications

Authors: Jessica Xin Hjaltelin | Jose M. G. Izarzugaza | Lars Juhl Jensen | Francesco Russo | David Westergaard | Søren Brunak

https://doi.org/10.1038/s41540-019-0104-5 Actions

Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections

JOURNAL ARTICLE published 10 April 2023 in npj Systems Biology and Applications

Research funded by Deutsche Forschungsgemeinschaft (FungiNet 210879364) | Bundesministerium für Bildung und Forschung (LPI-BT3 13N15709)

Authors: Christoph Saffer | Sandra Timme | Paul Rudolph | Marc Thilo Figge

https://doi.org/10.1038/s41540-023-00272-x Actions

Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer

JOURNAL ARTICLE published 8 September 2022 in npj Systems Biology and Applications

Authors: Santiago D. Cárdenas | Constance J. Reznik | Ruchira Ranaweera | Feifei Song | Christine H. Chung | Elana J. Fertig | Jana L. Gevertz

https://doi.org/10.1038/s41540-022-00244-7 Actions

Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

JOURNAL ARTICLE published 28 September 2015 in npj Systems Biology and Applications

Authors: Jason G Lomnitz | Michael A Savageau

https://doi.org/10.1038/npjsba.2015.3 Actions

GO2Sum: generating human-readable functional summary of proteins from GO terms

JOURNAL ARTICLE published 15 March 2024 in npj Systems Biology and Applications

Research funded by U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM133840) | National Science Foundation (DBI2003635, DBI2146026, IIS2211598, DMS2151678, CMMI1825941, MCB1925643)

Authors: Swagarika Jaharlal Giri | Nabil Ibtehaz | Daisuke Kihara

https://doi.org/10.1038/s41540-024-00358-0 Actions
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