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Search life-sciences literature (45,104,206 articles, preprints and more)

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PhysiMeSS - a new physiCell addon for extracellular matrix modelling.
Noël V, Ruscone M, Shuttleworth R, Macnamara CK
GigaByte, 2024:gigabyte136, 16 Oct 2024
Cited by: 0 articles | PMID: 39449986 | PMCID: PMC11500100
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Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies.
Mongeon B, Hébert-Doutreloux J, Surendran A, Karimi E, Fiset B, Quail DF, Walsh LA, Jenner AL, Craig M
NPJ Syst Biol Appl, 10(1):91, 18 Aug 2024
Cited by: 0 articles | PMID: 39155294 | PMCID: PMC11330976
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Building multiscale models with PhysiBoSS, an agent-based modeling tool.
Ruscone M, Checcoli A, Heiland R, Barillot E, Macklin P, Calzone L, Noël V
Brief Bioinform, 25(6):bbae509, 01 Sep 2024
Cited by: 0 articles | PMID: 39425527 | PMCID: PMC11489466
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A comprehensive review of computational cell cycle models in guiding cancer treatment strategies.
Ma C, Gurkan-Cavusoglu E
NPJ Syst Biol Appl, 10(1):71, 05 Jul 2024
Cited by: 0 articles | PMID: 38969664 | PMCID: PMC11226463
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Agent-based modeling in cancer biomedicine: applications and tools for calibration and validation.
Cogno N, Axenie C, Bauer R, Vavourakis V
Cancer Biol Ther, 25(1):2344600, 28 Apr 2024
Cited by: 0 articles | PMID: 38678381 | PMCID: PMC11057625
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Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study.
Jayathilake PG, Victori P, Pavillet CE, Lee CH, Voukantsis D, Miar A, Arora A, Harris AL, Morten KJ, Buffa FM
PLoS Comput Biol, 20(3):e1011944, 15 Mar 2024
Cited by: 1 article | PMID: 38489376 | PMCID: PMC10971686
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Modeling the extracellular matrix in cell migration and morphogenesis: a guide for the curious biologist.
Crossley RM, Johnson S, Tsingos E, Bell Z, Berardi M, Botticelli M, Braat QJS, Metzcar J, Ruscone M, Yin Y, Shuttleworth R
Front Cell Dev Biol, 12:1354132, 01 Mar 2024
Cited by: 10 articles | PMID: 38495620 | PMCID: PMC10940354
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Dynamic Boolean modeling of molecular and cellular interactions in psoriasis predicts drug target candidates.
Tsirvouli E, Noël V, Flobak Å, Calzone L, Kuiper M
iScience, 27(2):108859, 11 Jan 2024
Cited by: 0 articles | PMID: 38303723 | PMCID: PMC10831929
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PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks.
Ponce-de-Leon M, Montagud A, Noël V, Meert A, Pradas G, Barillot E, Calzone L, Valencia A
NPJ Syst Biol Appl, 9(1):54, 30 Oct 2023
Cited by: 14 articles | PMID: 37903760 | PMCID: PMC10616087
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Closing the loop on morphogenesis: a mathematical model of morphogenesis by closed-loop reaction-diffusion.
Grodstein J, McMillen P, Levin M
Front Cell Dev Biol, 11:1087650, 14 Aug 2023
Cited by: 0 articles | PMID: 37645245 | PMCID: PMC10461482
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From time-series transcriptomics to gene regulatory networks: A review on inference methods.
Marku M, Pancaldi V
PLoS Comput Biol, 19(8):e1011254, 10 Aug 2023
Cited by: 4 articles | PMID: 37561790 | PMCID: PMC10414591
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Multiscale model of the different modes of cancer cell invasion.
Ruscone M, Montagud A, Chavrier P, Destaing O, Bonnet I, Zinovyev A, Barillot E, Noël V, Calzone L
Bioinformatics, 39(6):btad374, 01 Jun 2023
Cited by: 8 articles | PMID: 37289551 | PMCID: PMC10293590
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Predicting anti-cancer drug combination responses with a temporal cell state network model.
Sarmah D, Meredith WO, Weber IK, Price MR, Birtwistle MR
PLoS Comput Biol, 19(5):e1011082, 01 May 2023
Cited by: 1 article | PMID: 37126527 | PMCID: PMC10174488
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An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia.
Verstraete N, Marku M, Domagala M, Arduin H, Bordenave J, Fournié JJ, Ysebaert L, Poupot M, Pancaldi V
iScience, 26(6):106897, 19 May 2023
Cited by: 1 article | PMID: 37332613 | PMCID: PMC10275988
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PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects.
Gonçalves IG, Hormuth DA, Prabhakaran S, Phillips CM, García-Aznar JM
GigaByte, 2023:gigabyte77, 28 Feb 2023
Cited by: 3 articles | PMID: 36949818 | PMCID: PMC10027115
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A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion.
Sivakumar N, Warner HV, Peirce SM, Lazzara MJ
PLoS Comput Biol, 18(11):e1010701, 28 Nov 2022
Cited by: 3 articles | PMID: 36441822 | PMCID: PMC9747056
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PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell.
Bergman D, Marazzi L, Chowkwale M, Maheshvare M D, Bidanta S, Mapder T, Li J
GigaByte, 2022:gigabyte72, 30 Nov 2022
Cited by: 7 articles | PMID: 36950142 | PMCID: PMC10027063
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Multiscale modeling in the framework of biological systems and its potential for spaceflight biology studies.
Millar-Wilson A, Ward Ó, Duffy E, Hardiman G
iScience, 25(11):105421, 26 Oct 2022
Cited by: 2 articles | PMID: 36388986 | PMCID: PMC9663911
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Unravelling cell migration: defining movement from the cell surface.
Merino-Casallo F, Gomez-Benito MJ, Hervas-Raluy S, Garcia-Aznar JM
Cell Adh Migr, 16(1):25-64, 01 Dec 2022
Cited by: 22 articles | PMID: 35499121 | PMCID: PMC9067518
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Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells.
Calzone L, Noël V, Barillot E, Kroemer G, Stoll G
Comput Struct Biotechnol J, 20:5661-5671, 07 Oct 2022
Cited by: 3 articles | PMID: 36284705 | PMCID: PMC9582792
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Cytoplasmic forces functionally reorganize nuclear condensates in oocytes.
Al Jord A, Letort G, Chanet S, Tsai FC, Antoniewski C, Eichmuller A, Da Silva C, Huynh JR, Gov NS, Voituriez R, Terret MÉ, Verlhac MH
Nat Commun, 13(1):5070, 29 Aug 2022
Cited by: 14 articles | PMID: 36038550 | PMCID: PMC9424315
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Explicit Calculation of Structural Commutation Relations for Stochastic and Dynamical Graph Grammar Rule Operators in Biological Morphodynamics.
Mjolsness E
Front Syst Biol, 2:898858, 09 Sep 2022
Cited by: 2 articles | PMID: 36712785 | PMCID: PMC9879069
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The Art of Reprogramming for Regenerative Medicine.
Kuang J, Huang T, Pei D
Front Cell Dev Biol, 10:927555, 30 Jun 2022
Cited by: 2 articles | PMID: 35846373 | PMCID: PMC9280648
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Computational framework for single-cell spatiotemporal dynamics of optogenetic membrane recruitment.
Kuznetsov IA, Berlew EE, Glantz ST, Hannanta-Anan P, Chow BY
Cell Rep Methods, 2(7):100245, 06 Jul 2022
Cited by: 0 articles | PMID: 35880018 | PMCID: PMC9308134
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Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth.
Ponce-de-Leon M, Montagud A, Akasiadis C, Schreiber J, Ntiniakou T, Valencia A
Front Mol Biosci, 9:836794, 06 Apr 2022
Cited by: 3 articles | PMID: 35463947 | PMCID: PMC9019571
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