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Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery

JOURNAL ARTICLE published 21 January 2021 in npj Systems Biology and Applications

Authors: Paola Paci | Giulia Fiscon | Federica Conte | Rui-Sheng Wang | Lorenzo Farina | Joseph Loscalzo

https://doi.org/10.1038/s41540-020-00168-0 Actions

Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology

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

Authors: Takahiro Amemiya | Masashi Honma | Yoshiaki Kariya | Samik Ghosh | Hiroaki Kitano | Yoshihisa Kurachi | Ken-ichi Fujita | Yasutsuna Sasaki | Yukio Homma | Darrel R Abernethy | Haruki Kume | Hiroshi Suzuki

https://doi.org/10.1038/npjsba.2015.5 Actions

Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes

JOURNAL ARTICLE published 15 May 2020 in npj Systems Biology and Applications

Authors: Juan D. Tibocha-Bonilla | Manish Kumar | Anne Richelle | Rubén D. Godoy-Silva | Karsten Zengler | Cristal Zuñiga

https://doi.org/10.1038/s41540-020-0135-y Actions

Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling

JOURNAL ARTICLE published 17 July 2023 in npj Systems Biology and Applications

Research funded by United States Department of Defense | United States Air Force | AFMC | Air Force Office of Scientific Research (FA9550-18-10051,FA9550-18-10051)

Authors: A. Leung | P. Rangamani

https://doi.org/10.1038/s41540-023-00295-4 Actions

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

JOURNAL ARTICLE published 11 November 2019 in npj Systems Biology and Applications

Authors: Anika Liu | Panuwat Trairatphisan | Enio Gjerga | Athanasios Didangelos | Jonathan Barratt | Julio Saez-Rodriguez

https://doi.org/10.1038/s41540-019-0118-z Actions

Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML

JOURNAL ARTICLE published 9 April 2024 in npj Systems Biology and Applications

Research funded by U.S. Department of Health & Human Services | NIH | National Cancer Institute (P30CA034196,P30CA034196,U01CA271830,U01CA271830-03S1) | U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35GM128717,R35GM128717,R35GM133562) | U.S. Department of Health & Human Services | National Institutes of Health (P30CA034196,R35GM128717,P30CA034196) | U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (U01HG013175)

Authors: Ataur Katebi | Xiaowen Chen | Daniel Ramirez | Sheng Li | Mingyang Lu

https://doi.org/10.1038/s41540-024-00366-0 Actions

Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks

JOURNAL ARTICLE published 19 February 2024 in npj Systems Biology and Applications

Research funded by MEXT | JST | Core Research for Evolutional Science and Technology (JPMJCR22N5) | MEXT | Japan Society for the Promotion of Science (JP18H05431)

Authors: Kozo Nishida | Junichi Maruyama | Kazunari Kaizu | Koichi Takahashi | Katsuyuki Yugi

https://doi.org/10.1038/s41540-024-00342-8 Actions

Executable models of immune signaling pathways in HIV-associated atherosclerosis

JOURNAL ARTICLE published 21 September 2022 in npj Systems Biology and Applications

Research funded by U.S. Department of Health & Human Services | National Institutes of Health (UM1 AI069511,P30 AI078498,R01 AI134058,R01 HL160229,R01 AI134058,T32 GM07356,R01 HL123346,R01 HL123346,R01 HL128155,R01 NS066801,R01 HL123346,R01 HL128155,R01 NS066801,R01 HL160229)

Authors: Mukta G. Palshikar | Rohith Palli | Alicia Tyrell | Sanjay Maggirwar | Giovanni Schifitto | Meera V. Singh | Juilee Thakar

https://doi.org/10.1038/s41540-022-00246-5 Actions

Detecting phenotype-driven transitions in regulatory network structure

JOURNAL ARTICLE published 19 April 2018 in npj Systems Biology and Applications

Authors: Megha Padi | John Quackenbush

https://doi.org/10.1038/s41540-018-0052-5 Actions

Network inference from perturbation time course data

JOURNAL ARTICLE published 1 November 2022 in npj Systems Biology and Applications

Authors: Deepraj Sarmah | Gregory R. Smith | Mehdi Bouhaddou | Alan D. Stern | James Erskine | Marc R. Birtwistle

https://doi.org/10.1038/s41540-022-00253-6 Actions

Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients

JOURNAL ARTICLE published 24 August 2020 in npj Systems Biology and Applications

Authors: Niclas Björn | Tejaswi Venkata Satya Badam | Rapolas Spalinskas | Eva Brandén | Hirsh Koyi | Rolf Lewensohn | Luigi De Petris | Zelmina Lubovac-Pilav | Pelin Sahlén | Joakim Lundeberg | Mika Gustafsson | Henrik Gréen

https://doi.org/10.1038/s41540-020-00146-6 Actions

Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121)

JOURNAL ARTICLE published 5 January 2017 in npj Systems Biology and Applications

Authors: Birgit Schoeberl | Art Kudla | Kristina Masson | Ashish Kalra | Michael Curley | Gregory Finn | Emily Pace | Brian Harms | Jaeyeon Kim | Jeff Kearns | Aaron Fulgham | Olga Burenkova | Viara Grantcharova | Defne Yarar | Violette Paragas | Jonathan Fitzgerald | Marisa Wainszelbaum | Kip West | Sara Mathews | Rachel Nering | Bambang Adiwijaya | Gabriela Garcia | Bill Kubasek | Victor Moyo | Akos Czibere | Ulrik B Nielsen | Gavin MacBeath

https://doi.org/10.1038/npjsba.2016.34 Actions

Stochastic system identification without an a priori chosen kinetic model—exploring feasible cell regulation with piecewise linear functions

JOURNAL ARTICLE published 11 April 2018 in npj Systems Biology and Applications

Authors: Martin Hoffmann | Jörg Galle

https://doi.org/10.1038/s41540-018-0049-0 Actions

ROS networks: designs, aging, Parkinson’s disease and precision therapies

JOURNAL ARTICLE published 26 October 2020 in npj Systems Biology and Applications

Research funded by Fonds National de la Recherche Luxembourg (ROSIM,Luxembourg BioTech Initiative,ROSIM) | Ministero dell'Istruzione, dell'Università e della Ricerca (SYSBIO-Italian ROADMAP ESFRI Infrastructures,SYSBIO-Italian ROADMAP ESFRI Infrastructures,SYSBIO-Italian ROADMAP ESFRI Infrastructures) | Fonds De La Recherche Scientifique - FNRS (ROSIM) | EC | EC Seventh Framework Programm | FP7 Health (SYNPOL, EC-MOAN, NUCSYS, UNI-CELLSYS, ITFoM, BioSiM and EPIPredict)

Authors: Alexey N. Kolodkin | Raju Prasad Sharma | Anna Maria Colangelo | Andrew Ignatenko | Francesca Martorana | Danyel Jennen | Jacco J. Briedé | Nathan Brady | Matteo Barberis | Thierry D. G. A. Mondeel | Michele Papa | Vikas Kumar | Bernhard Peters | Alexander Skupin | Lilia Alberghina | Rudi Balling | Hans V. Westerhoff

https://doi.org/10.1038/s41540-020-00150-w Actions

Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes

JOURNAL ARTICLE published 12 May 2022 in npj Systems Biology and Applications

Authors: Deeksha Malhan | Alireza Basti | Angela Relógio

https://doi.org/10.1038/s41540-022-00225-w Actions

Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolytica

JOURNAL ARTICLE published 11 August 2017 in npj Systems Biology and Applications

Authors: Pauline Trébulle | Jean-Marc Nicaud | Christophe Leplat | Mohamed Elati

https://doi.org/10.1038/s41540-017-0024-1 Actions

Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties

JOURNAL ARTICLE published 21 February 2024 in npj Systems Biology and Applications

Authors: Maisa N. G. van Genderen | Jeroen Kneppers | Anniek Zaalberg | Elise M. Bekers | Andries M. Bergman | Wilbert Zwart | Federica Eduati

https://doi.org/10.1038/s41540-024-00344-6 Actions

Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease

JOURNAL ARTICLE published 20 August 2018 in npj Systems Biology and Applications

Research funded by Biotechnology and Biological Sciences Research Council (BB/J014451/1,BB/J014451/1,BB/I008195/1) | Breast Cancer Now (KC4549)

Authors: Elaina M. Maldonado | Ciarán P. Fisher | Dawn J. Mazzatti | Amy L. Barber | Marcus J. Tindall | Nicholas J. Plant | Andrzej M. Kierzek | J. Bernadette Moore

https://doi.org/10.1038/s41540-018-0070-3 Actions

NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding

JOURNAL ARTICLE published 20 October 2021 in npj Systems Biology and Applications

Authors: Kanix Wang | Robert Stevens | Halima Alachram | Yu Li | Larisa Soldatova | Ross King | Sophia Ananiadou | Annika M. Schoene | Maolin Li | Fenia Christopoulou | José Luis Ambite | Joel Matthew | Sahil Garg | Ulf Hermjakob | Daniel Marcu | Emily Sheng | Tim Beißbarth | Edgar Wingender | Aram Galstyan | Xin Gao | Brendan Chambers | Weidi Pan | Bohdan B. Khomtchouk | James A. Evans | Andrey Rzhetsky

https://doi.org/10.1038/s41540-021-00200-x Actions

Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control

JOURNAL ARTICLE published 15 March 2023 in npj Systems Biology and Applications

Research funded by National Science Foundation (1332344,1804733) | U.S. Department of Energy (DE-SC0019388)

Authors: Chien-Ting Li | Richard Eng | Cristal Zuniga | Kai-Wen Huang | Yiqun Chen | Karsten Zengler | Michael J. Betenbaugh

https://doi.org/10.1038/s41540-022-00260-7 Actions
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