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Publisher Correction: Mathematical model of hemodynamic mechanisms and consequences of glomerular hypertension in diabetic mice

JOURNAL ARTICLE published 4 March 2019 in npj Systems Biology and Applications

Authors: Hari Shankar Mahato | Christine Ahlstrom | Rasmus Jansson-Löfmark | Ulrika Johansson | Gabriel Helmlinger | K. Melissa Hallow

https://doi.org/10.1038/s41540-019-0081-8 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

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery

JOURNAL ARTICLE published 9 July 2019 in npj Systems Biology and Applications

Authors: Hiromi W. L. Koh | Damian Fermin | Christine Vogel | Kwok Pui Choi | Rob M. Ewing | Hyungwon Choi

https://doi.org/10.1038/s41540-019-0099-y Actions

Nobel Turing Challenge: creating the engine for scientific discovery

JOURNAL ARTICLE published 18 June 2021 in npj Systems Biology and Applications

Authors: Hiroaki Kitano

https://doi.org/10.1038/s41540-021-00189-3 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

Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery

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

Authors: Frank Emmert-Streib

https://doi.org/10.1038/s41540-022-00251-8 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

Improved prediction of PARP inhibitor response and identification of synergizing agents through use of a novel gene expression signature generation algorithm

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

Authors: Daniel J. McGrail | Curtis Chun-Jen Lin | Jeannine Garnett | Qingxin Liu | Wei Mo | Hui Dai | Yiling Lu | Qinghua Yu | Zhenlin Ju | Jun Yin | Christopher P. Vellano | Bryan Hennessy | Gordon B. Mills | Shiaw-Yih Lin

https://doi.org/10.1038/s41540-017-0011-6 Actions
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