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Mechanistic Models

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Regulating cellular cyclic adenosine monophosphate: “Sources,” “sinks,” and now, “tunable valves”

Focus Article
Michael Getz, Padmini Rangamani, Pradipta Ghosh
Published Online: Apr 23 2020
DOI:10.1002/wsbm.1490

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular networks in Network Medicine: Development and applications

Advanced Review
Jan Baumbach, Kimberly Glass, Gemma Vilahur, Davide Viggiano, Paolo Tieri, John Quackenbush, Manuela Petti, Paola Paci, Claudio Napoli, Cinzia Marchese, Joseph Loscalzo, Michele Gentili, Laurent Gatto, Giulia Fiscon, Lorenzo Farina, Antonella Di Costanzo, Federica Conte, Giovambattista Capasso, Giuditta Benincasa, Jean‐Luc Balligand, Lina Badimon, Marco Angelini, Lucia Altucci, Eleni Anastasiadou, Harald H. H. W. Schmidt, Edwin K. Silverman
Published Online: Apr 19 2020
DOI:10.1002/wsbm.1489

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiscale modeling of vertebrate limb development

Advanced Review
Tilmann Glimm, Ramray Bhat, Stuart A. Newman
Published Online: Mar 24 2020
DOI:10.1002/wsbm.1485

Abstract Full article on Wiley Online Library:   HTML | PDF
Aspirin and the chemoprevention of cancers: A mathematical and evolutionary dynamics perspective

Advanced Review
Natalia L. Komarova, C. Richard Boland, Ajay Goel, Dominik Wodarz
Published Online: Mar 12 2020
DOI:10.1002/wsbm.1487

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling immune cell behavior across scales in cancer

Advanced Review
Sahak Z. Makaryan, Colin G. Cess, Stacey D. Finley
Published Online: Mar 04 2020
DOI:10.1002/wsbm.1484

Abstract Full article on Wiley Online Library:   HTML | PDF
Cholesterol interaction motifs in G protein‐coupled receptors: Slippery hot spots?

Advanced Review
Parijat Sarkar, Amitabha Chattopadhyay
Published Online: Feb 07 2020
DOI:10.1002/wsbm.1481

Abstract Full article on Wiley Online Library:   HTML | PDF
Theory of cell fate

Primer
Michael J. Casey, Patrick S. Stumpf, Ben D. MacArthur
Published Online: Dec 12 2019
DOI:10.1002/wsbm.1471

Abstract Full article on Wiley Online Library:   HTML | PDF
Exploring cardiac form and function: A length‐scale computational biology approach

Advanced Review
William F. Sherman, Anna Grosberg
Published Online: Dec 02 2019
DOI:10.1002/wsbm.1470

Abstract Full article on Wiley Online Library:   HTML | PDF
Stochastic simulation algorithms for computational systems biology: Exact, approximate, and hybrid methods

Advanced Review
Giulia Simoni, Federico Reali, Corrado Priami, Luca Marchetti
Published Online: Jul 01 2019
DOI:10.1002/wsbm.1459

Abstract Full article on Wiley Online Library:   HTML | PDF
Agent‐based models of inflammation in translational systems biology: A decade later

UPDATE
Yoram Vodovotz, Gary An
Published Online: Jul 01 2019
DOI:10.1002/wsbm.1460

Abstract Full article on Wiley Online Library:   HTML | PDF
IL7 receptor signaling in T cells: A mathematical modeling perspective

Overview
Jung‐Hyun Park, Adam T. Waickman, Joseph Reynolds, Mario Castro, Carmen Molina‐París
Published Online: May 28 2019
DOI:10.1002/wsbm.1447

Abstract Full article on Wiley Online Library:   HTML | PDF
Essential contributions of enhancer genomic regulatory elements to microglial cell identity and functions

Focus Article
André Machado Xavier, Sarah Belhocine, David Gosselin
Published Online: Apr 23 2019
DOI:10.1002/wsbm.1449

Abstract Full article on Wiley Online Library:   HTML | PDF
Calcium signals that determine vascular resistance

Focus Article
Matteo Ottolini, Kwangseok Hong, Swapnil K. Sonkusare
Published Online: Mar 18 2019
DOI:10.1002/wsbm.1448

Abstract Full article on Wiley Online Library:   HTML | PDF
Towards multiscale modeling of the CD8+ T cell response to viral infections

Advanced Review
Subhasish Baral, Rubesh Raja, Pramita Sen, Narendra M. Dixit
Published Online: Feb 27 2019
DOI:10.1002/wsbm.1446

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrating molecular networks with genetic variant interpretation for precision medicine

Overview
Emidio Capriotti, Kivilcim Ozturk, Hannah Carter
Published Online: Dec 12 2018
DOI:10.1002/wsbm.1443

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems biology of robustness and homeostatic mechanisms

Overview
H. Frederik Nijhout, Janet A. Best, Michael C. Reed
Published Online: Oct 29 2018
DOI:10.1002/wsbm.1440

Abstract Full article on Wiley Online Library:   HTML | PDF
Context‐dependent regulation of receptor tyrosine kinases: Insights from systems biology approaches

Focus Article
Inez Lam, Christina M. Pickering, Feilim Mac Gabhann
Published Online: Sep 26 2018
DOI:10.1002/wsbm.1437

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational methods for analyzing and modeling genome structure and organization

Focus Article
Dejun Lin, Giancarlo Bonora, Galip Gürkan Yardımcı, William S. Noble
Published Online: Jul 18 2018
DOI:10.1002/wsbm.1435

Abstract Full article on Wiley Online Library:   HTML | PDF
Quantitative systems models illuminate arrhythmia mechanisms in heart failure: Role of the Na+‐Ca2+‐Ca2+/calmodulin‐dependent protein kinase II‐reactive oxygen species feedback

Focus Article
Stefano Morotti, Eleonora Grandi
Published Online: Jul 17 2018
DOI:10.1002/wsbm.1434

Abstract Full article on Wiley Online Library:   HTML | PDF
Kinetic models of hematopoietic differentiation

Advanced Review
Victor Olariu, Carsten Peterson
Published Online: Apr 16 2018
DOI:10.1002/wsbm.1424

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiscale systems biology of trauma‐induced coagulopathy

Focus Article
Scott L. Diamond, Talid Sinno, Carrie Sims, Evan Tsiklidis
Published Online: Feb 27 2018
DOI:10.1002/wsbm.1418

Abstract Full article on Wiley Online Library:   HTML | PDF
Image‐based computational fluid dynamics in the lung: virtual reality or new clinical practice?

Advanced Review
Haribalan Kumar, Jan De Backer, Kelly S. Burrowes
Published Online: Jun 13 2017
DOI:10.1002/wsbm.1392

Abstract Full article on Wiley Online Library:   HTML | PDF
The best models of metabolism

Advanced Review
Eberhard O. Voit
Published Online: May 19 2017
DOI:10.1002/wsbm.1391

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems biology of cellular membranes: a convergence with biophysics

Advanced Review
Morgan Chabanon, Jeanne C. Stachowiak, Padmini Rangamani
Published Online: May 05 2017
DOI:10.1002/wsbm.1386

Abstract Full article on Wiley Online Library:   HTML | PDF
Understanding the mTOR signaling pathway via mathematical modeling

Advanced Review
Nurgazy Sulaimanov, Martin Klose, Hauke Busch, Melanie Boerries
Published Online: Feb 10 2017
DOI:10.1002/wsbm.1379

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiscale modeling methods in biomechanics

Advanced Review
Pinaki Bhattacharya, Marco Viceconti
Published Online: Jan 19 2017
DOI:10.1002/wsbm.1375

Abstract Full article on Wiley Online Library:   HTML | PDF
Mathematical modeling of the female reproductive system: from oocyte to delivery

Overview
Alys R Clark, Jennifer A Kruger
Published Online: Sep 09 2016
DOI:10.1002/wsbm.1353

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems‐level airway models of bronchoconstriction

Focus Article
Graham M. Donovan
Published Online: Jun 27 2016
DOI:10.1002/wsbm.1349

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiscale modeling of brain dynamics: from single neurons and networks to mathematical tools

Advanced Review
Constantinos Siettos, Jens Starke
Published Online: Jun 24 2016
DOI:10.1002/wsbm.1348

Abstract Full article on Wiley Online Library:   HTML | PDF
Mathematical models of breast and ovarian cancers

Advanced Review
Dana‐Adriana Botesteanu, Stanley Lipkowitz, Jung‐Min Lee, Doron Levy
Published Online: Jun 03 2016
DOI:10.1002/wsbm.1343

Abstract Full article on Wiley Online Library:   HTML | PDF
Signaling via the NFκB system

Advanced Review
Simon Mitchell, Jesse Vargas, Alexander Hoffmann
Published Online: Mar 16 2016
DOI:10.1002/wsbm.1331

Abstract Full article on Wiley Online Library:   HTML | PDF
Aging and computational systems biology

Advanced Review
Mark T. Mc Auley, Amy E. Morgan, Kathleen M. Mooney
Published Online: Jan 29 2016
DOI:10.1002/wsbm.1328

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling microcirculatory blood flow: current state and future perspectives

Focus Article
Dmitry A. Fedosov, Gerhard Gompper
Published Online: Dec 22 2015
DOI:10.1002/wsbm.1326

Abstract Full article on Wiley Online Library:   HTML | PDF
Dynamics of the mammalian cell cycle in physiological and pathological conditions

Focus Article
Claude Gérard, Albert Goldbeter
Published Online: Nov 27 2015
DOI:10.1002/wsbm.1325

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling calcium regulation of contraction, energetics, signaling, and transcription in the cardiac myocyte

Advanced Review
Raimond L. Winslow, Mark A. Walker, Joseph L. Greenstein
Published Online: Nov 12 2015
DOI:10.1002/wsbm.1322

Abstract Full article on Wiley Online Library:   HTML | PDF
The macrophage and its role in inflammation and tissue repair: mathematical and systems biology approaches

Focus Article
Joanne L. Dunster
Published Online: Oct 13 2015
DOI:10.1002/wsbm.1320

Abstract Full article on Wiley Online Library:   HTML | PDF
Topology, dynamics, and heterogeneity in immune signaling

Advanced Review
J. Taylor Webb, Marcelo Behar
Published Online: May 27 2015
DOI:10.1002/wsbm.1306

Abstract Full article on Wiley Online Library:   HTML | PDF
The cell as the mechanistic basis for evolution

Advanced Review
J.S. Torday
Published Online: May 25 2015
DOI:10.1002/wsbm.1305

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems biology of host–microbe metabolomics

Advanced Review
Almut Heinken, Ines Thiele
Published Online: Apr 30 2015
DOI:10.1002/wsbm.1301

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrative models of vascular remodeling during tumor growth

Advanced Review
Heiko Rieger, Michael Welter
Published Online: Mar 21 2015
DOI:10.1002/wsbm.1295

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems engineering meets quantitative systems pharmacology: from low‐level targets to engaging the host defenses

Opinion
Ioannis P. Androulakis
Published Online: Mar 16 2015
DOI:10.1002/wsbm.1294

Abstract Full article on Wiley Online Library:   HTML | PDF
Tuneable resolution as a systems biology approach for multi‐scale, multi‐compartment computational models

Advanced Review
Denise E. Kirschner, C. Anthony Hunt, Simeone Marino, Mohammad Fallahi‐Sichani, Jennifer J. Linderman
Published Online: Aug 08 2014
DOI:10.1002/wsbm.1270

Abstract Full article on Wiley Online Library:   HTML | PDF
Cell mechanics: principles, practices, and prospects

Overview
Emad Moeendarbary, Andrew R. Harris
Published Online: Jul 28 2014
DOI:10.1002/wsbm.1275

Abstract Full article on Wiley Online Library:   HTML | PDF
Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

Overview
Réka Albert, Juilee Thakar
Published Online: Jul 15 2014
DOI:10.1002/wsbm.1273

Abstract Full article on Wiley Online Library:   HTML | PDF
Personalizing oncology treatments by predicting drug efficacy, side‐effects, and improved therapy: mathematics, statistics, and their integration

Advanced Review
Zvia Agur, Moran Elishmereni, Yuri Kheifetz
Published Online: Mar 06 2014
DOI:10.1002/wsbm.1263

Abstract Full article on Wiley Online Library:   HTML | PDF
Glass‐like dynamics in the cell and in cellular collectives

Advanced Review
Monirosadat Sadati, Amir Nourhani, Jeffrey J. Fredberg, Nader Taheri Qazvini
Published Online: Jan 15 2014
DOI:10.1002/wsbm.1258

Abstract Full article on Wiley Online Library:   HTML | PDF
The structure of dynamic GPCR signaling networks

Focus Article
Patrick R. O'Neill, Lopamudra Giri, W. K. Ajith Karunarathne, Anilkumar K. Patel, K. V. Venkatesh, N. Gautam
Published Online: Nov 08 2013
DOI:10.1002/wsbm.1249

Abstract Full article on Wiley Online Library:   HTML | PDF
Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

Overview
Lily A. Chylek, Leonard A. Harris, Chang‐Shung Tung, James R. Faeder, Carlos F. Lopez, William S. Hlavacek
Published Online: Sep 30 2013
DOI:10.1002/wsbm.1245

Abstract Full article on Wiley Online Library:   HTML | PDF
Molecular mechanisms underlying neuronal synaptic plasticity: systems biology meets computational neuroscience in the wilds of synaptic plasticity

Advanced Review
Kim T. Blackwell, Joanna Jedrzejewska‐Szmek
Published Online: Sep 09 2013
DOI:10.1002/wsbm.1240

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrative approaches for modeling regulation and function of the respiratory system

Overview
Alona Ben‐Tal, Merryn H. Tawhai
Published Online: Sep 09 2013
DOI:10.1002/wsbm.1244

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational approaches for understanding energy metabolism

Focus Article
Alexander A. Shestov, Brandon Barker, Zhenglong Gu, Jason W. Locasale
Published Online: Jul 29 2013
DOI:10.1002/wsbm.1238

Abstract Full article on Wiley Online Library:   HTML | PDF
Agent‐based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity

Advanced Review
C. Anthony Hunt, Ryan C. Kennedy, Sean H. J. Kim, Glen E. P. Ropella
Published Online: Jun 04 2013
DOI:10.1002/wsbm.1222

Abstract Full article on Wiley Online Library:   HTML | PDF
Mathematical modeling of folate metabolism

Focus Article
John C. Panetta, Steven W. Paugh, William E. Evans
Published Online: May 22 2013
DOI:10.1002/wsbm.1227

Abstract Full article on Wiley Online Library:   HTML | PDF
Toward a quantitative understanding of the Wnt/β‐catenin pathway through simulation and experiment

Overview
Bethan Lloyd‐Lewis, Alexander G. Fletcher, Trevor C. Dale, Helen M. Byrne
Published Online: Mar 29 2013
DOI:10.1002/wsbm.1221

Abstract Full article on Wiley Online Library:   HTML | PDF
Engineered genetic information processing circuits

Overview
Hao Qi, Andrew Blanchard, Ting Lu
Published Online: Feb 26 2013
DOI:10.1002/wsbm.1216

Abstract Full article on Wiley Online Library:   HTML | PDF
β‐Arrestin‐kinase scaffolds: turn them on or turn them off?

Focus Article
Alice Lin, Kathryn A. DeFea
Published Online: Jan 14 2013
DOI:10.1002/wsbm.1203

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems analysis of biological networks in skeletal muscle function

Advanced Review
Lucas R. Smith, Gretchen Meyer, Richard L. Lieber
Published Online: Nov 27 2012
DOI:10.1002/wsbm.1197

Abstract Full article on Wiley Online Library:   HTML | PDF
Accelerating cancer systems biology research through Semantic Web technology

Overview
Zhihui Wang, Jonathan Sagotsky, Thomas Taylor, Patrick Shironoshita, Thomas S. Deisboeck
Published Online: Nov 27 2012
DOI:10.1002/wsbm.1200

Abstract Full article on Wiley Online Library:   HTML | PDF
Post‐translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding

Advanced Review
Sudhakaran Prabakaran, Guy Lippens, Hanno Steen, Jeremy Gunawardena
Published Online: Aug 15 2012
DOI:10.1002/wsbm.1185

Abstract Full article on Wiley Online Library:   HTML | PDF
From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine

Advanced Review
David W. Wright, Shunzhou Wan, Nour Shublaq, Stefan J. Zasada, Peter V. Coveney
Published Online: Aug 15 2012
DOI:10.1002/wsbm.1186

Abstract Full article on Wiley Online Library:   HTML | PDF
Complexity and the reductionism–holism debate in systems biology

Overview
Fulvio Mazzocchi
Published Online: Jul 03 2012
DOI:10.1002/wsbm.1181

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems biology approaches to toll‐like receptor signaling

Focus Article
Alexis Vandenbon, Shunsuke Teraguchi, Shizuo Akira, Kiyoshi Takeda, Daron M. Standley
Published Online: Jun 19 2012
DOI:10.1002/wsbm.1178

Abstract Full article on Wiley Online Library:   HTML | PDF
Theoretical insights into bacterial chemotaxis

Advanced Review
Marcus J. Tindall, Eamonn A. Gaffney, Philip K. Maini, Judith P. Armitage
Published Online: Mar 12 2012
DOI:10.1002/wsbm.1168

Abstract Full article on Wiley Online Library:   HTML | PDF
The virtual liver: a multidisciplinary, multilevel challenge for systems biology

Overview
Hermann‐Georg Holzhütter, Dirk Drasdo, Tobias Preusser, Jörg Lippert, Adriano M. Henney
Published Online: Jan 13 2012
DOI:10.1002/wsbm.1158

Abstract Full article on Wiley Online Library:   HTML | PDF
Virtual Cell: computational tools for modeling in cell biology

Advanced Review
Diana C. Resasco, Fei Gao, Frank Morgan, Igor L. Novak, James C. Schaff, Boris M. Slepchenko
Published Online: Dec 02 2011
DOI:10.1002/wsbm.165

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling of spatially‐restricted intracellular signaling

Focus Article
Susana R. Neves
Published Online: Jul 15 2011
DOI:10.1002/wsbm.155

Abstract Full article on Wiley Online Library:   HTML | PDF
A multifaceted approach to modeling the immune response in tuberculosis

Focus Article
Simeone Marino, Jennifer J. Linderman, Denise E. Kirschner
Published Online: Dec 31 2010
DOI:10.1002/wsbm.131

Abstract Full article on Wiley Online Library:   HTML | PDF
Electrophysiological models of neural processing

Focus Article
Mark E. Nelson
Published Online: Dec 16 2010
DOI:10.1002/wsbm.95

Abstract Full article on Wiley Online Library:   HTML | PDF
Odor representations in the mammalian olfactory bulb

Focus Article
Adil Ghani Khan, K. Parthasarathy, Upinder Singh Bhalla
Published Online: Aug 04 2010
DOI:10.1002/wsbm.85

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling childbirth: elucidating the mechanisms of labor

Focus Article
Xinshan Li, Jennifer A. Kruger, Martyn P. Nash, Poul M.F. Nielsen
Published Online: Jun 15 2010
DOI:10.1002/wsbm.65

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling breast biomechanics for multi‐modal image analysis—successes and challenges

Advanced Review
Vijay Rajagopal, Poul M. F. Nielsen, Martyn P. Nash
Published Online: Apr 09 2010
DOI:10.1002/wsbm.58

Abstract Full article on Wiley Online Library:   HTML | PDF
Spatial regulation of PI3K signaling during chemotaxis

Focus Article
Pablo A. Iglesias
Published Online: Sep 22 2009
DOI:10.1002/wsbm.13

Abstract Full article on Wiley Online Library:   HTML | PDF
Four‐dimensional dynamics of MAPK information‐processing systems

Advanced Review
Boris N. Kholodenko, Marc R. Birtwistle
Published Online: May 05 2009
DOI:10.1002/wsbm.16

Abstract Full article on Wiley Online Library:   HTML | PDF
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