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Intertwined roles for GDF-15, HMGB1, and MIG/CXCL9 in Pediatric Acute Liver Failure.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1470000
By:
- Zamora, Ruben;
- Yin, Jinling;
- Barclay, Derek;
- Squires, James E.;
- Vodovotz, Yoram
Publication type:
Article
Spectral expansion methods for prediction uncertainty quantification in systems biology.
Published in:
Frontiers in Systems Biology, 2024, p. 01
By:
- Deneer, Anna;
- Molenaar, Jaap;
- Fleck, Christian
Publication type:
Article
Accessible Type 2 diabetes medication through stable expression of Exendin-4 in Saccharomyces cerevisiae.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1283371
By:
- Balius, Gia;
- Imani, Kiana;
- Petroff, Zoë;
- Beer, Elizabeth;
- Brasileiro Feitosa, Thiago;
- Mccall, Nathan;
- Paule, Lauren;
- Neo Yixuan Peng;
- Shen, Joanne;
- Singh, Vidhata;
- Strand, Cambell;
- Zau, Jonathan;
- Bernick, D. L.
Publication type:
Article
Building virtual patients using simulation-based inference.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1444912
By:
- Paul, Nathalie;
- Karamitsou, Venetia;
- Giegerich, Clemens;
- Sadeghi, Afshin;
- Lücke, Moritz;
- Wagenhuber, Britta;
- Kister, Alexander;
- Rehberg, Markus
Publication type:
Article
A multi-scale semi-mechanistic CK/PD model for CAR T-cell therapy.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1380018
By:
- Minucci, Sarah;
- Gruver, Scott;
- Subramanian, Kalyanasundaram;
- Renardy, Marissa
Publication type:
Article
Modeling uncertainty: the impact of noise in T cell differentiation.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1412931
By:
- Martínez-Méndez, David;
- Villarreal, Carlos;
- Huerta, Leonor
Publication type:
Article
The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1407994
By:
- Noordijk, Ben;
- Gomez, Monica L. Garcia;
- ten Tusscher, Kirsten H. W. J.;
- de Ridder, Dick;
- van Dijk, Aalt D. J.;
- Smith, Robert W.
Publication type:
Article
Surface-displayed silicatein-α enzyme in bioengineered E. coli enables biocementation and silica mineralization.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1377188
By:
- Vigil, Toriana N.;
- Schwendeman, Nikolas K.;
- Grogger, Melanie L. M.;
- Morrison, Victoria L.;
- Warner, Margaret C.;
- Bone, Nathaniel B.;
- Vance, Morgan T.;
- Morris, David C.;
- McElmurry, Kristi;
- Berger, Bryan W.;
- Steel, J. Jordan
Publication type:
Article
Uncertainty quantified discovery of chemical reaction systems via Bayesian scientific machine learning.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1338518
By:
- Nieves, Emily;
- Dandekar, Raj;
- Rackauckas, Chris
Publication type:
Article
Crosstalking with dendritic cells: a path to engineer advanced T Cell immunotherapy.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1372995
By:
- Schafer, Sogand;
- Kaige Chen;
- Leyuan Ma
Publication type:
Article
First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1375472
By:
- Trego, Anna;
- Palmeiro-Sánchez, Tania;
- Graham, Alison;
- Ijaz, Umer Zeeshan;
- O'Flaherty, Vincent
Publication type:
Article
Pareto task inference analysis reveals cellular trade-offs in diffuse large B-Cell lymphoma transcriptomic data.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1346076
By:
- Blais, Jonatan;
- Jeukens, Julie
Publication type:
Article
Transporter annotations are holding up progress in metabolic modeling.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1394084
By:
- Casey, John;
- Bennion, Brian;
- D’haeseleer, Patrik;
- Kimbrel, Jeffrey;
- Marschmann, Gianna;
- Navid, Ali
Publication type:
Article
Life's building blocks: the modular path to multiscale complexity.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1417800
By:
- Huitzil, Saúl;
- Huepe, Cristián
Publication type:
Article
Coupling quantitative systems pharmacology modelling to machine learning and artificial intelligence for drug development: its pAIns and gAIns.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1380685
By:
- Folguera-Blasco, Núria;
- Boshier, Florencia A. T.;
- Uatay, Aydar;
- Pichardo-Almarza, Cesar;
- Lai, Massimo;
- Biasetti, Jacopo;
- Dearden, Richard;
- Gibbs, Megan;
- Kimko, Holly
Publication type:
Article
Predicting chronic responses to calcium channel blockade with a virtual population of African Americans with hypertensive chronic kidney disease.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1327357
By:
- Clemmer, John S.;
- Pruett, W. Andrew;
- Hester, Robert L.
Publication type:
Article
Specialty grand challenge: how can we use integrative approaches to understand microbial community dynamics?
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1432791
By:
- Ijaz, Umer Zeeshan;
- Ameer, Aqsa;
- Saleem, Farrukh;
- Gul, Farzana;
- Keating, Ciara;
- Javed, Sundus
Publication type:
Article
PdPANA: phagemid display as peptide array for neutralizing antibodies, an engineered in silico vaccine candidate against COVID-19.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1309891
By:
- Uzcátegui, Javier;
- Mullah, Khaleel;
- de Virgini, Daniel Buvat;
- Mendoza, Andrés;
- Urdaneta, Rafael;
- Naranjo, Alejandra
Publication type:
Article
Building an Adverse Outcome Pathway network for COVID-19.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1384481
By:
- Nymark, Penny;
- Clerbaux, Laure-Alix;
- Amorim, Maria-João;
- Andronis, Christos;
- de Bernardi, Francesca;
- Bezemer, Gillina F. G.;
- Coecke, Sandra;
- Gavins, Felicity N. E.;
- Jacobson, Daniel;
- Lekka, Eftychia;
- Margiotta-Casaluci, Luigi;
- Martens, Marvin;
- Mayasich, Sally A.;
- Mortensen, Holly M.;
- Young Jun Kim;
- Sachana, Magdalini;
- Tanabe, Shihori;
- Virvilis, Vassilis;
- Edwards, Stephen W.;
- Halappanavar, Sabina
Publication type:
Article
De novo prediction of functional effects of genetic variants from DNA sequences based on context-specific molecular information.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1402664
By:
- Jiaxin Yang;
- Adhikari, Sikta Das;
- Hao Wang;
- Binbin Huang;
- Wenjie Qi;
- Yuehua Cui;
- Jianrong Wang
Publication type:
Article
Elucidating a genomic signature associated with behavioral and executive function after moderate to severe pediatric TBI: a systems biology informed approach.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1293265
By:
- Kurowski, Brad G.;
- Treble-Barna, Amery;
- Pilipenko, Valentina;
- Martin, Lisa J.;
- Jegga, Anil G.;
- Miley, Aimee E.;
- Nanhua Zhang;
- Fabio, Anthony;
- Chima, Ranjit S.;
- Adlam, Anna-Lynne R.;
- Kaufman, Kenneth;
- Bell, Michael J.;
- Beers, Sue R.;
- Wisniewski, Stephen R.;
- Wade, Shari L.
Publication type:
Article
Forecasting SARS-CoV-2 spike protein evolution from small data by deep learning and regression.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1284668
By:
- King, Samuel;
- Chen, Xinyi E.;
- Ng, Sarah W. S.;
- Rostin, Kimia;
- Hahn, Samuel V.;
- Roberts, Tylo;
- Schwab, Janella C.;
- Sekhon, Parneet;
- Kagieva, Madina;
- Reilly, Taylor;
- Ruo Chen Qi;
- Salman, Paarsa;
- Hong, Ryan J.;
- Ma, Eric J.;
- Hallam, Steven J.
Publication type:
Article
A review of mathematical modeling of bone remodeling from a systems biology perspective.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1368555
By:
- Cook, Carley V.;
- Lighty, Ariel M.;
- Smith, Brenda J.;
- Versypt, Ashlee N. Ford
Publication type:
Article
Context-aware knowledge selection and reliable model recommendation with ACCORDION.
Published in:
2024
By:
- Ahmed, Yasmine;
- Telmer, Cheryl A.;
- Gaoxiang Zhou;
- Miskov-Zivanov, Natasa
Publication type:
Product Review
Is there room in epilepsy for the claustrum?
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1385112
By:
- Watson, Glenn D. R.;
- Meletti, Stefano;
- Mahavadi, Anil K.;
- Besson, Pierre;
- Bandt, S. Kathleen;
- Smith, Jared B.
Publication type:
Article
In silico biomarker analysis of the adverse effects of perfluorooctane sulfonate (PFOS) exposure on the metabolic physiology of embryo-larval zebrafish.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1367562
By:
- Nolen, Rayna M.;
- Petersen, Lene H.;
- Kaiser, Karl;
- Quigg, Antonietta;
- Hala, David
Publication type:
Article
Intein-mediated thyroid hormone biosensors: towards controlled delivery of hormone therapy.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1270071
By:
- Martí-Baena, Quim;
- Pascuet-Fontanet, Andreu;
- Berjaga-Buisan, Tomas;
- Caravaca-Rodríguez, Miriam;
- Puig-Costa-Jussà, Jaume;
- Sanchez-Mejias, Avencia;
- Ivančić, Dimitrije;
- Mogas-Díez, Sira;
- Güell, Marc;
- Macia, Javier
Publication type:
Article
Mathematical modeling of temperature-induced circadian rhythms.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1256398
By:
- Lingjun Lu;
- Yannuo Li;
- Schloss, Rene;
- Androulakis, Ioannis P.
Publication type:
Article
A robust ensemble feature selection approach to prioritize genes associated with survival outcome in high-dimensional gene expression data.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1355595
By:
- Phi Le;
- Xingyue Gong;
- Leah Ung;
- Hai Yang;
- Keenan, Bridget P.;
- Li Zhang;
- Tao He
Publication type:
Article
Calcium oscillations in HEK293 cells lacking SOCE suggest the existence of a balanced regulation of IP<sub>3</sub> production and degradation.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1343006
By:
- Octors, Clara;
- Yoast, Ryan E.;
- Emrich, Scott M.;
- Trebak, Mohamed;
- Sneyd, James
Publication type:
Article
Integrating inverse reinforcement learning into data-driven mechanistic computational models: a novel paradigm to decode cancer cell heterogeneity.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1333760
By:
- Kinnunen, Patrick C.;
- Ho, Kenneth K. Y.;
- Srivastava, Siddhartha;
- Chengyang Huang;
- Wanggang Shen;
- Garikipati, Krishna;
- Luker, Gary D.;
- Banovic, Nikola;
- Xun Huan;
- Linderman, Jennifer J.;
- Luker, Kathryn E.
Publication type:
Article
Computational insights in cell physiology.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1335885
By:
- Dupont, Geneviève;
- Gonze, Didier
Publication type:
Article
Advancing precision medicine therapeutics for Parkinson's utilizing a shared quantitative systems pharmacology model and framework.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1351555
By:
- Denaro, Christopher;
- Stephenson, Diane;
- Müller, Martijn L. T. M.;
- Piccoli, Benedetto;
- Azer, Karim
Publication type:
Article
Computational inference of chemokine-mediated roles for the vagus nerve in modulating intra- and inter-tissue inflammation.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1266279
By:
- Shah, Ashti M.;
- Zamora, Ruben;
- Barclay, Derek;
- Jinling Yin;
- El-Dehaibi, Fayten;
- Addorisio, Meghan;
- Tsaava, Tea;
- Tynan, Aisling;
- Tracey, Kevin;
- Chavan, Sangeeta S.;
- Vodovotz, Yoram
Publication type:
Article
Expanding our thought horizons in systems biology and medicine.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1385458
By:
- Lovejoy, Jennifer C.
Publication type:
Article
Assessing electrogenetic activation via a network model of biological signal propagation.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1291293
By:
- Chun, Kayla;
- VanArsdale, Eric;
- May, Elebeoba;
- Payne, Gregory F.;
- Bentley, William E.
Publication type:
Article
BioModels' Model of the Year 2023.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2024.1363884
By:
- Malik Sheriff, Rahuman S.;
- Hiroki Asari;
- Hermjakob, Henning;
- Huber, Wolfgang;
- Quail, Thomas;
- Santos, Silvia D. M.;
- Smith, Amber M.;
- Uhlmann, Virginie
Publication type:
Article
Editorial: Combining mechanistic modeling with machine learning to study multiscale biological processes.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1367549
By:
- Peirce-Cottler, Shayn;
- Vodovotz, Yoram
Publication type:
Article
Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophile Methylacidiphilum fumariolicum under auto-, hetero-and methanotrophic conditions.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2024.1291612
By:
- Saldivar, Alexis;
- Ruiz-Ruiz, Patricia;
- Revah, Sergio;
- Zuñiga, Cristal
Publication type:
Article
Batch correction and harmonization of -Omics datasets with a tunable median polish of ratio.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2023.1092341
By:
- Dammer, Eric B.;
- Seyfried, Nicholas T.;
- Johnson, Erik C. B.
Publication type:
Article
Maintenance of PKMζ-modulated synaptic efficacies despite protein turnover.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2022.933938
By:
- Aslam, Naveed
Publication type:
Article
A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2023.1283341
By:
- Michael, Christian T.;
- Almohri, Sayed Ahmad;
- Linderman, Jennifer J.;
- Kirschner, Denise E.
Publication type:
Article
A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2023.1283341
By:
- Michael, Christian T.;
- Almohri, Sayed Ahmad;
- Linderman, Jennifer J.;
- Kirschner, Denise E.
Publication type:
Article
Determining the role of advection in patterning by bone morphogenetic proteins through neural network model-based acceleration of a 3D finite element model of the zebrafish embryo.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2022.983372
By:
- Linlin Li;
- Xu Wang;
- Junyi Chai;
- Xiaoqian Wang;
- Buganza-Tepole, Adrian;
- Umulis, David M.
Publication type:
Article
Metabolic perturbation studies using a Nash Equilibrium model of liver machine perfusion: modeling oxidative stress and effect of glutathione supplementation.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2023.1260315
By:
- Lucia, Angelo;
- Uygun, Korkut
Publication type:
Article
Computational design of custom therapeutic cells to correct failing human cardiomyocytes.
Published in:
Frontiers in Systems Biology, 2024, p. 1, doi. 10.3389/fsysb.2023.1102467
By:
- Tieu, Andrew;
- Phillips, Katherine G.;
- Costa, Kevin D.;
- Mayourian, Joshua
Publication type:
Article
A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2022.928159
By:
- Freiesleben, Sherry;
- Unverricht-Yeboah, Marcus;
- Gütebier, Lea;
- Waltemath, Dagmar;
- Kriehuber, Ralf;
- Wolkenhauer, Olaf
Publication type:
Article
From Epidemic to Pandemic Modelling.
Published in:
Frontiers in Systems Biology, 2024, p. 01, doi. 10.3389/fsysb.2022.861562
By:
- Connolly, Shannon;
- Gilbert, David;
- Heiner, Monika
Publication type:
Article

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