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Systematic integration of experimental data and models in systems biology [PDF]

BMC Bioinformatics, 2010
Background The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions,
Simeonidis Evangelos, Messiha Hanan L, Malys Naglis, Khan Farid, Dunn Warwick, Carroll Kathleen, Swainston Neil, Spasic Irena, Jameson Daniel, Dada Joseph O, Li Peter, Weichart Dieter, Winder Catherine, Wishart Jill, Broomhead David S, Goble Carole A, Gaskell Simon J, Kell Douglas B, Westerhoff Hans V, Mendes Pedro, Paton Norman W   +20 more
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Systems Biology and Experimental Model Systems of Cancer [PDF]

Journal of Personalized Medicine, 2020
Over the past decade, we have witnessed an increasing number of large-scale studies that have provided multi-omics data by high-throughput sequencing approaches. This has particularly helped with identifying key (epi)genetic alterations in cancers. Importantly, aberrations that lead to the activation of signaling networks through the disruption of ...
Gizem Damla Yalcin, Nurseda Danisik, Rana Can Baygin, Ahmet Acar   +3 more
openaire   +5 more sources

Bayesian parameter estimation for dynamical models in systems biology.

PLoS Computational Biology, 2022
Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks.
Nathaniel J Linden, Boris Kramer, Padmini Rangamani   +2 more
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A Bayesian framework for the analysis of systems biology models of the brain.

PLoS Computational Biology, 2019
Systems biology models are used to understand complex biological and physiological systems. Interpretation of these models is an important part of developing this understanding.
Joshua Russell-Buckland, Christopher P Barnes, Ilias Tachtsidis   +2 more
doaj   +2 more sources

A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1

iScience, 2023
Summary: The activation of IKK/NF-κB by genotoxic stress is a crucial process in the DNA damage response. Due to the anti-apoptotic impact of NF-κB, it can affect cell-fate decisions upon DNA damage and therefore interfere with tumor therapy-induced cell
Fabian Konrath, Michael Willenbrock, Dorothea Busse, Claus Scheidereit, Jana Wolf   +4 more
doaj   +1 more source

Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes

iScience, 2021
Summary: Psoriasis is a chronic skin disease, in which immune cells and keratinocytes keep each other in a state of inflammation. It is believed that phospholipase A2 (PLA2)-dependent eicosanoid release plays a key role in this.
Eirini Tsirvouli, Felicity Ashcroft, Berit Johansen, Martin Kuiper   +3 more
doaj   +1 more source

A metabolic regulatory network for the Caenorhabditis elegans intestine

iScience, 2022
Summary: Metabolic perturbations can affect gene expression, for instance to rewire metabolism. While numerous efforts have measured gene expression in response to individual metabolic perturbations, methods that determine all metabolic perturbations ...
Sushila Bhattacharya, Brent B. Horowitz, Jingyan Zhang, Xuhang Li, Hefei Zhang, Gabrielle E. Giese, Amy D. Holdorf, Albertha J.M. Walhout   +7 more
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The cost of bacterial predation via type VI secretion system leads to predator extinction under environmental stress

iScience, 2021
Summary: As a common gut pathogen, Campylobacter jejuni (C. jejuni) harbors the Type VI Secretion System (T6SS) that injects toxic effectors into neighboring cells, modulating microbial competitions in the harsh gut environment.
Subhadeep Gupta, Soumyadipta Ray, Afruja Khan, Arkaprabha China, Dipjyoti Das, Amirul Islam Mallick   +5 more
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Slow waves form expanding, memory-rich mesostates steered by local excitability in fading anesthesia

iScience, 2022
Summary: In the arousal process, the brain restores its integrative activity from the synchronized state of slow wave activity (SWA). The mechanisms underpinning this state transition remain, however, to be elucidated.
Antonio Pazienti, Andrea Galluzzi, Miguel Dasilva, Maria V. Sanchez-Vives, Maurizio Mattia   +4 more
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Patient-derived organoids as personalized avatars and a potential immunotherapy model in cervical cancer

iScience, 2023
Summary: Cervical cancer remains a significant health issue in developing countries. However, finding a preclinical model that accurately reproduces tumor characteristics is challenging.
Hua Huang, Yuwen Pan, Jiaming Huang, Chunyu Zhang, Yuandong Liao, Qiqiao Du, Shuhang Qin, Yili Chen, Hao Tan, Ming Chen, Manman Xu, Meng Xia, Yunyun Liu, Jie Li, Tianyu Liu, Qiaojian Zou, Yijia Zhou, Li Yuan, Wei Wang, Yanchun Liang, Chao yun Pan, Junxiu Liu, Shuzhong Yao   +22 more
doaj   +1 more source