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Analytical and Computational Methods

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Hybrid modeling frameworks of tumor development and treatment

UPDATE
Ibrahim M. Chamseddine, Katarzyna A. Rejniak
Published Online: Jul 17 2019
DOI:10.1002/wsbm.1461

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
Multiscale modeling of the neuromuscular system: Coupling neurophysiology and skeletal muscle mechanics

Advanced Review
Oliver Röhrle, Utku Ş. Yavuz, Thomas Klotz, Francesco Negro, Thomas Heidlauf
Published Online: Jun 24 2019
DOI:10.1002/wsbm.1457

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
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
Recent advancement of light‐based single‐molecule approaches for studying biomolecules

Focus Article
Benjamin Croop, Chenyi Zhang, Youngbin Lim, Ryan M. Gelfand, Kyu Young Han
Published Online: Feb 06 2019
DOI:10.1002/wsbm.1445

Abstract Full article on Wiley Online Library:   HTML | PDF
Models of polymer physics for the architecture of the cell nucleus

Focus Article
Andrea Esposito, Carlo Annunziatella, Simona Bianco, Andrea M. Chiariello, Luca Fiorillo, Mario Nicodemi
Published Online: Dec 19 2018
DOI:10.1002/wsbm.1444

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
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
Computational anatomy and diffeomorphometry: A dynamical systems model of neuroanatomy in the soft condensed matter continuum

Advanced Review
Michael I. Miller, Sylvain Arguillère, Daniel J. Tward, Laurent Younes
Published Online: Jun 04 2018
DOI:10.1002/wsbm.1425

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems approaches to optimizing deep brain stimulation therapies in Parkinson’s disease

Overview
Sabato Santaniello, John T. Gale, Sridevi V. Sarma
Published Online: Mar 20 2018
DOI:10.1002/wsbm.1421

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
Surveying the landscape of optogenetic methods for detection of protein–protein interactions

Advanced Review
Matthew D. Wiens, Robert E. Campbell
Published Online: Jan 15 2018
DOI:10.1002/wsbm.1415

Abstract Full article on Wiley Online Library:   HTML | PDF
Genome‐scale metabolic models applied to human health and disease

Advanced Review
Jens Nielsen, Daniel J Cook
Published Online: Jun 23 2017
DOI:10.1002/wsbm.1393

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
Biomechanics of the human uterus

Focus Article
Kristin M. Myers, David Elad
Published Online: May 12 2017
DOI:10.1002/wsbm.1388

Abstract Full article on Wiley Online Library:   HTML | PDF
Virtual endovascular treatment of intracranial aneurysms: models and uncertainty

Advanced Review
Alejandro F. Frangi, Toni Lassila, Ali Sarrami‐Foroushani
Published Online: May 10 2017
DOI:10.1002/wsbm.1385

Abstract Full article on Wiley Online Library:   HTML | PDF
Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions

Advanced Review
Ying‐Ning Ho, Lin‐Jie Shu, Yu‐Liang Yang
Published Online: May 10 2017
DOI:10.1002/wsbm.1387

Abstract Full article on Wiley Online Library:   HTML | PDF
Trends in high‐throughput and functional neuroimaging in Caenorhabditis elegans

Focus Article
Yongmin Cho, Charles L. Zhao, Hang Lu
Published Online: Feb 21 2017
DOI:10.1002/wsbm.1376

Abstract Full article on Wiley Online Library:   HTML | PDF
Recent lab‐on‐chip developments for novel drug discovery

Opinion
Nauman Khalid, Isao Kobayashi, Mitsutoshi Nakajima
Published Online: Feb 17 2017
DOI:10.1002/wsbm.1381

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
Regulatory elements in molecular networks

Advanced Review
Ashley S. Doane, Olivier Elemento
Published Online: Jan 17 2017
DOI:10.1002/wsbm.1374

Abstract Full article on Wiley Online Library:   HTML | PDF
Traditional and novel tools to probe the mitochondrial metabolism in health and disease

Advanced Review
Yanfei Zhang, José L. Avalos
Published Online: Jan 09 2017
DOI:10.1002/wsbm.1373

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational models of the neural control of breathing

Advanced Review
Yaroslav I. Molkov, Jonathan E. Rubin, Ilya A. Rybak, Jeffrey C. Smith
Published Online: Dec 23 2016
DOI:10.1002/wsbm.1371

Abstract Full article on Wiley Online Library:   HTML | PDF
Toward modeling locomotion using electromyography‐informed 3D models: application to cerebral palsy

Focus Article
M. Sartori, J. W. Fernandez, L. Modenese, C. P. Carty, L. A. Barber, K. Oberhofer, J. Zhang, G. G. Handsfield, N. S. Stott, T. F. Besier, D. Farina, D. G. Lloyd
Published Online: Dec 21 2016
DOI:10.1002/wsbm.1368

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling, signaling and cytoskeleton dynamics: integrated modeling‐experimental frameworks in cell migration

Advanced Review
Meng Sun, Muhammad H. Zaman
Published Online: Nov 15 2016
DOI:10.1002/wsbm.1365

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational approaches for the identification of cancer genes and pathways

Advanced Review
Christos M. Dimitrakopoulos, Niko Beerenwinkel
Published Online: Nov 11 2016
DOI:10.1002/wsbm.1364

Abstract Full article on Wiley Online Library:   HTML | PDF
Network dynamics: quantitative analysis of complex behavior in metabolism, organelles, and cells, from experiments to models and back

Advanced Review
Felix T. Kurz, Jackelyn M. Kembro, Ana G. Flesia, Antonis A. Armoundas, Sonia Cortassa, Miguel A. Aon, David Lloyd
Published Online: Sep 07 2016
DOI:10.1002/wsbm.1352

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico bone mechanobiology: modeling a multifaceted biological system

Advanced Review
Mario Giorgi, Stefaan W. Verbruggen, Damien Lacroix
Published Online: Sep 07 2016
DOI:10.1002/wsbm.1356

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
Systems medicine in colorectal cancer: from a mathematical model toward a new type of clinical trial

Advanced Review
Nicoletta Castagnino, Massimo Maffei, Lorenzo Tortolina, Gabriele Zoppoli, Daniela Piras, Alessio Nencioni, Eva Moran, Alberto Ballestrero, Franco Patrone, Silvio Parodi
Published Online: May 30 2016
DOI:10.1002/wsbm.1342

Abstract Full article on Wiley Online Library:   HTML | PDF
Adaptive resistance to antibiotics in bacteria: a systems biology perspective

Advanced Review
Santiago Sandoval‐Motta, Maximino Aldana
Published Online: Apr 21 2016
DOI:10.1002/wsbm.1335

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico methods for drug repurposing and pharmacology

Overview
Rachel A. Hodos, Brian A. Kidd, Khader Shameer, Ben P. Readhead, Joel T. Dudley
Published Online: Apr 15 2016
DOI:10.1002/wsbm.1337

Abstract Full article on Wiley Online Library:   HTML | PDF
Computational modeling approaches to the dynamics of oncolytic viruses

Advanced Review
Dominik Wodarz
Published Online: Mar 22 2016
DOI:10.1002/wsbm.1332

Abstract Full article on Wiley Online Library:   HTML | PDF
Mathematical modeling of cardiac growth and remodeling

Advanced Review
L.C. Lee, G.S. Kassab, J.M. Guccione
Published Online: Mar 07 2016
DOI:10.1002/wsbm.1330

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

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

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
Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms

Advanced Review
Mary Regina Boland, Alexandra Jacunski, Tal Lorberbaum, Joseph D. Romano, Robert Moskovitch, Nicholas P. Tatonetti
Published Online: Nov 12 2015
DOI:10.1002/wsbm.1323

Abstract Full article on Wiley Online Library:   HTML | PDF
The virtual intestine: in silico modeling of small intestinal electrophysiology and motility and the applications

Advanced Review
Peng Du, Niranchan Paskaranandavadivel, Timothy R. Angeli, Leo K. Cheng, Gregory O'Grady
Published Online: Nov 12 2015
DOI:10.1002/wsbm.1324

Abstract Full article on Wiley Online Library:   HTML | PDF
In search for symmetries in the metabolism of cancer

Advanced Review
Francesco Gatto, Jens Nielsen
Published Online: Nov 05 2015
DOI:10.1002/wsbm.1321

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems biology and mechanics of growth

Advanced Review
Mona Eskandari, Ellen Kuhl
Published Online: Sep 09 2015
DOI:10.1002/wsbm.1312

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrative biomarker discovery in neurodegenerative diseases

Overview
André V. Carreiro, Alexandre Mendonça, Mamede de Carvalho, Sara C. Madeira
Published Online: Jul 02 2015
DOI:10.1002/wsbm.1310

Abstract Full article on Wiley Online Library:   HTML | PDF
Measurement and modeling of coronary blood flow

Overview
Matthew D. Sinclair, Jack Lee, Andrew N. Cookson, Simone Rivolo, Eoin R. Hyde, Nicolas P. Smith
Published Online: Jun 30 2015
DOI:10.1002/wsbm.1309

Abstract Full article on Wiley Online Library:   HTML | PDF
Metabolic network modeling of microbial communities

Advanced Review
Matthew B. Biggs, Gregory L. Medlock, Glynis L. Kolling, Jason A. Papin
Published Online: Jun 24 2015
DOI:10.1002/wsbm.1308

Abstract Full article on Wiley Online Library:   HTML | PDF
Implementation of integral feedback control in biological systems

Advanced Review
Pramod R. Somvanshi, Anilkumar K. Patel, Sharad Bhartiya, K. V. Venkatesh
Published Online: Jun 02 2015
DOI:10.1002/wsbm.1307

Abstract Full article on Wiley Online Library:   HTML | PDF
Genome‐wide association studies in biliary atresia

Advanced Review
Mylarappa Ningappa, Jun Min, Brandon W. Higgs, Chethan Ashokkumar, Sarangarajan Ranganathan, Rakesh Sindhi
Published Online: May 11 2015
DOI:10.1002/wsbm.1303

Abstract Full article on Wiley Online Library:   HTML | PDF
Bringing computational models of bone regeneration to the clinic

Advanced Review
Aurélie Carlier, Liesbet Geris, Johan Lammens, Hans Van Oosterwyck
Published Online: Apr 21 2015
DOI:10.1002/wsbm.1299

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems medicine: evolution of systems biology from bench to bedside

Overview
Rui‐Sheng Wang, Bradley A. Maron, Joseph Loscalzo
Published Online: Apr 17 2015
DOI:10.1002/wsbm.1297

Abstract Full article on Wiley Online Library:   HTML | PDF
Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data

Advanced Review
Gang Liu, Sriram Neelamegham
Published Online: Apr 13 2015
DOI:10.1002/wsbm.1296

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 biology of polycystic kidney disease: a critical review

Focus Article
Luis Fernando Menezes, Gregory G. Germino
Published Online: Feb 02 2015
DOI:10.1002/wsbm.1289

Abstract Full article on Wiley Online Library:   HTML | PDF
Network representations of immune system complexity

Overview
Naeha Subramanian, Parizad Torabi‐Parizi, Rachel A. Gottschalk, Ronald N. Germain, Bhaskar Dutta
Published Online: Jan 27 2015
DOI:10.1002/wsbm.1288

Abstract Full article on Wiley Online Library:   HTML | PDF
Integrating multi‐scale knowledge on cardiac development into a computational model of ventricular trabeculation

Focus Article
Bouke A. de Boer, Jean‐François Le Garrec, Vincent M. Christoffels, Sigolène M. Meilhac, Jan M. Ruijter
Published Online: Oct 06 2014
DOI:10.1002/wsbm.1285

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
Large scale molecular simulations of nanotoxicity

Focus Article
Camilo A. Jimenez‐Cruz, Seung‐gu Kang, Ruhong Zhou
Published Online: Aug 08 2014
DOI:10.1002/wsbm.1271

Abstract Full article on Wiley Online Library:   HTML | PDF
Comparative epigenomics: defining and utilizing epigenomic variations across species, time‐course, and individuals

Opinion
Shu Xiao, Xiaoyi Cao, Sheng Zhong
Published Online: Jul 15 2014
DOI:10.1002/wsbm.1274

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
Recent advances in computational methodology for simulation of mechanical circulatory assist devices

Advanced Review
Alison L. Marsden, Yuri Bazilevs, Christopher C. Long, Marek Behr
Published Online: Jan 21 2014
DOI:10.1002/wsbm.1260

Abstract Full article on Wiley Online Library:   HTML | PDF
Using systems biology approaches to understand cardiac inflammation and extracellular matrix remodeling in the setting of myocardial infarction

Advanced Review
Omid Ghasemi, Yonggang Ma, Merry L. Lindsey, Yu‐Fang Jin
Published Online: Nov 08 2013
DOI:10.1002/wsbm.1248

Abstract Full article on Wiley Online Library:   HTML | PDF
miRNA regulation in the context of functional protein networks: principles and applications

Focus Article
Mohammed Alshalalfa
Published Online: Nov 08 2013
DOI:10.1002/wsbm.1251

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
Systems biology approaches to epidemiological studies of complex diseases

Opinion
Hongzhe Li
Published Online: Sep 09 2013
DOI:10.1002/wsbm.1242

Abstract Full article on Wiley Online Library:   HTML | PDF
Using variability in gene expression as a tool for studying gene regulation

Focus Article
Olivia Padovan‐Merhar, Arjun Raj
Published Online: Aug 29 2013
DOI:10.1002/wsbm.1243

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
Mathematical modeling of kidney transport

Advanced Review
Anita T. Layton
Published Online: Jul 12 2013
DOI:10.1002/wsbm.1232

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiscale image‐based modeling and simulation of gas flow and particle transport in the human lungs

Focus Article
Ching‐Long Lin, Merryn H. Tawhai, Eric A. Hoffman
Published Online: Jul 10 2013
DOI:10.1002/wsbm.1234

Abstract Full article on Wiley Online Library:   HTML | PDF
Excitable behavior in amoeboid chemotaxis

Focus Article
Changji Shi, Pablo A. Iglesias
Published Online: Jun 11 2013
DOI:10.1002/wsbm.1230

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
Modeling cellular compartmentation in one‐carbon metabolism

Advanced Review
Marco Scotti, Lorenzo Stella, Emily J. Shearer, Patrick J. Stover
Published Online: Feb 13 2013
DOI:10.1002/wsbm.1209

Abstract Full article on Wiley Online Library:   HTML | PDF
Bioimage informatics for understanding spatiotemporal dynamics of cellular processes

Advanced Review
Ge Yang
Published Online: Feb 13 2013
DOI:10.1002/wsbm.1214

Abstract Full article on Wiley Online Library:   HTML | PDF
Genomics and epigenomics of colorectal cancer

Advanced Review
Michal‐Ruth Schweiger, Michelle Hussong, Christina Röhr, Hans Lehrach
Published Online: Jan 16 2013
DOI:10.1002/wsbm.1206

Abstract Full article on Wiley Online Library:   HTML | PDF
Model‐based design of experiments for cellular processes

Advanced Review
Ankush Chakrabarty, Gregery T. Buzzard, Ann E. Rundell
Published Online: Jan 04 2013
DOI:10.1002/wsbm.1204

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
Promise of personalized omics to precision medicine

Advanced Review
Rui Chen, Michael Snyder
Published Online: Nov 26 2012
DOI:10.1002/wsbm.1198

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
Mitochondrial network energetics in the heart

Advanced Review
Miguel A. Aon, Sonia Cortassa
Published Online: Aug 15 2012
DOI:10.1002/wsbm.1188

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
Recent approaches to the prioritization of candidate disease genes

Advanced Review
Nadezhda T. Doncheva, Tim Kacprowski, Mario Albrecht
Published Online: Jun 11 2012
DOI:10.1002/wsbm.1177

Abstract Full article on Wiley Online Library:   HTML | PDF
Isotope labeling experiments in metabolomics and fluxomics

Advanced Review
Sebastian Klein, Elmar Heinzle
Published Online: Mar 23 2012
DOI:10.1002/wsbm.1167

Abstract Full article on Wiley Online Library:   HTML | PDF
Linking genome to epigenome

Focus Article
Guo‐Cheng Yuan
Published Online: Feb 17 2012
DOI:10.1002/wsbm.1165

Abstract Full article on Wiley Online Library:   HTML | PDF
Reverse‐engineering human regulatory networks

Advanced Review
Celine Lefebvre, Gabrielle Rieckhof, Andrea Califano
Published Online: Jan 13 2012
DOI:10.1002/wsbm.1159

Abstract Full article on Wiley Online Library:   HTML | PDF
Mass spectrometry‐based proteomics: qualitative identification to activity‐based protein profiling

Advanced Review
Job D. Cardoza, Jignesh R. Parikh, Scott B. Ficarro, Jarrod A. Marto
Published Online: Jan 09 2012
DOI:10.1002/wsbm.166

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
Integrative physical oncology

Opinion
Haralampos Hatzikirou, Arnaud Chauviere, Amy L. Bauer, André Leier, Michael T. Lewis, Paul Macklin, Tatiana T. Marquez‐Lago, Elaine L. Bearer, Vittorio Cristini
Published Online: Aug 18 2011
DOI:10.1002/wsbm.158

Abstract Full article on Wiley Online Library:   HTML | PDF
Mathematical models in biology: from molecules to life

Advanced Review
Yiannis N. Kaznessis
Published Online: Feb 18 2011
DOI:10.1002/wsbm.142

Abstract Full article on Wiley Online Library:   HTML | PDF
Drug repurposing and adverse event prediction using high‐throughput literature analysis

Advanced Review
Spyros N. Deftereos, Christos Andronis, Ellen J. Friedla, Aris Persidis, Andreas Persidis
Published Online: Feb 16 2011
DOI:10.1002/wsbm.147

Abstract Full article on Wiley Online Library:   HTML | PDF
Signaling pathways that control cell migration: models and analysis

Focus Article
Erik S. Welf, Jason M. Haugh
Published Online: Feb 08 2011
DOI:10.1002/wsbm.110

Abstract Full article on Wiley Online Library:   HTML | PDF
Influenza A virus infection kinetics: quantitative data and models

Advanced Review
Amber M. Smith, Alan S. Perelson
Published Online: Dec 31 2010
DOI:10.1002/wsbm.129

Abstract Full article on Wiley Online Library:   HTML | PDF
Synthetic biology: putting synthesis into biology

Advanced Review
Jing Liang, Yunzi Luo, Huimin Zhao
Published Online: Dec 16 2010
DOI:10.1002/wsbm.104

Abstract Full article on Wiley Online Library:   HTML | PDF
Advances in analysis of transcriptional regulatory networks

Advanced Review
Peter J. Park, Tae‐Min Kim
Published Online: Dec 16 2010
DOI:10.1002/wsbm.105

Abstract Full article on Wiley Online Library:   HTML | PDF
An interdisciplinary systems approach to study sperm physiology and evolution

Advanced Review
Linda Z. Shi, Jaclyn Nascimento, Elliot Botvinick, Barbara Durrant, Michael W. Berns
Published Online: Dec 16 2010
DOI:10.1002/wsbm.106

Abstract Full article on Wiley Online Library:   HTML | PDF
Hybrid models of tumor growth

Focus Article
Katarzyna A. Rejniak, Alexander R. A. Anderson
Published Online: Dec 16 2010
DOI:10.1002/wsbm.102

Abstract Full article on Wiley Online Library:   HTML | PDF
An energy systems approach to Parkinson's disease

Opinion
Mathieu Cloutier, Peter Wellstead
Published Online: Dec 16 2010
DOI:10.1002/wsbm.107

Abstract Full article on Wiley Online Library:   HTML | PDF
Role of systems pharmacology in understanding drug adverse events

Opinion
Seth I. Berger, Ravi Iyengar
Published Online: Aug 27 2010
DOI:10.1002/wsbm.114

Abstract Full article on Wiley Online Library:   HTML | PDF
In silico models of bone remodeling from macro to nano—from organ to cell

Focus Article
Duncan Webster, Ralph Müller
Published Online: Aug 25 2010
DOI:10.1002/wsbm.115

Abstract Full article on Wiley Online Library:   HTML | PDF
Modeling of blood flow in arterial trees

Focus Article
Tomer Anor, Leopold Grinberg, Hyoungsu Baek, Joseph R. Madsen, Mahesh V. Jayaraman, George E. Karniadakis
Published Online: Aug 04 2010
DOI:10.1002/wsbm.90

Abstract Full article on Wiley Online Library:   HTML | PDF
Toward failure analyses in systems biology

Opinion
Sanjoy K. Bhattacharya, James Gomes, Colleen M. Cebulla
Published Online: Aug 04 2010
DOI:10.1002/wsbm.83

Abstract Full article on Wiley Online Library:   HTML | PDF
Comparative systems biology: from bacteria to man

Overview
Bas Teusink, Hans V. Westerhoff, Frank J. Bruggeman
Published Online: Aug 04 2010
DOI:10.1002/wsbm.74

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems medicine—viewed through the real and computing lenses

Editorial Commentary
Shankar Subramaniam, Joseph H. Nadeau
Published Online: Jun 15 2010
DOI:10.1002/wsbm.103

Abstract Full article on Wiley Online Library:   HTML | PDF
Image‐based models of cardiac structure in health and disease

Focus Article
Fijoy Vadakkumpadan, Hermenegild Arevalo, Anton J. Prassl, Junjie Chen, Ferdinand Kickinger, Peter Kohl, Gernot Plank, Natalia Trayanova
Published Online: Jun 15 2010
DOI:10.1002/wsbm.76

Abstract Full article on Wiley Online Library:   HTML | PDF
Stochastic approaches in systems biology

Overview
Mukhtar Ullah, Olaf Wolkenhauer
Published Online: Jun 15 2010
DOI:10.1002/wsbm.78

Abstract Full article on Wiley Online Library:   HTML | PDF
The application of flux balance analysis in systems biology

Focus Article
Erwin P. Gianchandani, Arvind K. Chavali, Jason A. Papin
Published Online: Apr 09 2010
DOI:10.1002/wsbm.60

Abstract Full article on Wiley Online Library:   HTML | PDF
Algorithmic and analytical methods in network biology

Overview
Mehmet Koyutürk
Published Online: Apr 09 2010
DOI:10.1002/wsbm.61

Abstract Full article on Wiley Online Library:   HTML | PDF
Systems biology of pro‐angiogenic therapies targeting the VEGF system

Focus Article
Feilim Mac Gabhann, Amina A. Qutub, Brian H. Annex, Aleksander S. Popel
Published Online: Apr 07 2010
DOI:10.1002/wsbm.92

Abstract Full article on Wiley Online Library:   HTML | PDF
Toward a VPH/Physiome ToolKit

Overview
Alan Garny, Jonathan Cooper, Peter J. Hunter
Published Online: Mar 26 2010
DOI:10.1002/wsbm.63

Abstract Full article on Wiley Online Library:   HTML | PDF
Toward a complete in silico, multi‐layered embryonic stem cell regulatory network

Focus Article
Huilei Xu, Christoph Schaniel, Ihor R. Lemischka, Avi Ma'ayan
Published Online: Mar 24 2010
DOI:10.1002/wsbm.93

Abstract Full article on Wiley Online Library:   HTML | PDF
The mammalian phenotype ontology: enabling robust annotation and comparative analysis

Focus Article
Cynthia L. Smith, Janan T. Eppig
Published Online: Nov 13 2009
DOI:10.1002/wsbm.44

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Thermodynamically based constraints for rate coefficients of large biochemical networks

Focus Article
Marcel O. Vlad, John Ross
Published Online: Nov 13 2009
DOI:10.1002/wsbm.50

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Computational modeling of epithelial tissues

Advanced Review
Rod Smallwood
Published Online: Sep 22 2009
DOI:10.1002/wsbm.18

Abstract Full article on Wiley Online Library:   HTML | PDF
Agent‐based models in translational systems biology

Overview
Gary An, Qi Mi, Joyeeta Dutta‐Moscato, Yoram Vodovotz
Published Online: Sep 22 2009
DOI:10.1002/wsbm.45

Abstract Full article on Wiley Online Library:   HTML | PDF
The lung physiome: merging imaging‐based measures with predictive computational models

Advanced Review
Merryn H. Tawhai, Eric A. Hoffman, Ching‐Long Lin
Published Online: May 05 2009
DOI:10.1002/wsbm.17

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Multiscale systems integration in the eye

Advanced Review
Marc D. Jacobs
Published Online: May 05 2009
DOI:10.1002/wsbm.29

Abstract Full article on Wiley Online Library:   HTML | PDF
Multiscale modeling for biologists

Overview
Martin Meier‐Schellersheim, Iain D. C. Fraser, Frederick Klauschen
Published Online: May 05 2009
DOI:10.1002/wsbm.33

Abstract Full article on Wiley Online Library:   HTML | PDF
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