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For: Boehm ME, Adlung L, Schilling M, Roth S, Klingmüller U, Lehmann WD. Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent STAT5 Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling. J Proteome Res 2014;13:5685-94. [DOI: 10.1021/pr5006923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Number Cited by Other Article(s)
1
Dorešić D, Grein S, Hasenauer J. Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data. Bioinformatics 2024;40:i558-i566. [PMID: 38940161 PMCID: PMC11211815 DOI: 10.1093/bioinformatics/btae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]  Open
2
Raimúndez E, Fedders M, Hasenauer J. Posterior marginalization accelerates Bayesian inference for dynamical models of biological processes. iScience 2023;26:108083. [PMID: 37867942 PMCID: PMC10589897 DOI: 10.1016/j.isci.2023.108083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/16/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023]  Open
3
Tönsing C, Steiert B, Timmer J, Kreutz C. Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models. PLoS Comput Biol 2023;19:e1011417. [PMID: 37738254 PMCID: PMC10550180 DOI: 10.1371/journal.pcbi.1011417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/04/2023] [Accepted: 08/08/2023] [Indexed: 09/24/2023]  Open
4
Faida P, Attiogbe MKI, Majeed U, Zhao J, Qu L, Fan D. Lung cancer treatment potential and limits associated with the STAT family of transcription factors. Cell Signal 2023:110797. [PMID: 37423343 DOI: 10.1016/j.cellsig.2023.110797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
5
Egert J, Kreutz C. Realistic simulation of time-course measurements in systems biology. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:10570-10589. [PMID: 37322949 DOI: 10.3934/mbe.2023467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
6
Chakraborty S, Andrieux G, Kastl P, Adlung L, Altamura S, Boehm ME, Schwarzmüller LE, Abdullah Y, Wagner MC, Helm B, Gröne HJ, Lehmann WD, Boerries M, Busch H, Muckenthaler MU, Schilling M, Klingmüller U. Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo. Cell Rep 2022;40:111360. [PMID: 36130519 DOI: 10.1016/j.celrep.2022.111360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]  Open
7
Fleury M, Vazquez-Mateo C, Hernandez-Escalante J, Dooms H. Partial STAT5 signaling is sufficient for CD4+ T cell priming but not memory formation. Cytokine 2022;150:155770. [PMID: 34839177 PMCID: PMC8761165 DOI: 10.1016/j.cyto.2021.155770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/06/2021] [Indexed: 02/03/2023]
8
Schmiester L, Weindl D, Hasenauer J. Efficient gradient-based parameter estimation for dynamic models using qualitative data. BIOINFORMATICS (OXFORD, ENGLAND) 2021. [PMID: 34260697 DOI: 10.1101/2021.02.06.430039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
9
Adlung L, Stapor P, Tönsing C, Schmiester L, Schwarzmüller LE, Postawa L, Wang D, Timmer J, Klingmüller U, Hasenauer J, Schilling M. Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells. Cell Rep 2021;36:109507. [PMID: 34380040 DOI: 10.1016/j.celrep.2021.109507] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/01/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022]  Open
10
Schmiester L, Weindl D, Hasenauer J. Efficient gradient-based parameter estimation for dynamic models using qualitative data. Bioinformatics 2021;37:4493-4500. [PMID: 34260697 PMCID: PMC8652033 DOI: 10.1093/bioinformatics/btab512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022]  Open
11
Borisov I, Metelkin E. Confidence intervals by constrained optimization-An algorithm and software package for practical identifiability analysis in systems biology. PLoS Comput Biol 2020;16:e1008495. [PMID: 33347435 PMCID: PMC7785248 DOI: 10.1371/journal.pcbi.1008495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/05/2021] [Accepted: 11/06/2020] [Indexed: 11/30/2022]  Open
12
Schmiester L, Weindl D, Hasenauer J. Parameterization of mechanistic models from qualitative data using an efficient optimal scaling approach. J Math Biol 2020;81:603-623. [PMID: 32696085 PMCID: PMC7427713 DOI: 10.1007/s00285-020-01522-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/28/2020] [Indexed: 12/21/2022]
13
Schälte Y, Hasenauer J. Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. Bioinformatics 2020;36:i551-i559. [PMID: 32657404 PMCID: PMC7355286 DOI: 10.1093/bioinformatics/btaa397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
14
Hass H, Loos C, Raimúndez-Álvarez E, Timmer J, Hasenauer J, Kreutz C. Benchmark problems for dynamic modeling of intracellular processes. Bioinformatics 2020;35:3073-3082. [PMID: 30624608 PMCID: PMC6735869 DOI: 10.1093/bioinformatics/btz020] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/19/2018] [Accepted: 01/06/2019] [Indexed: 12/19/2022]  Open
15
Maurer B, Kollmann S, Pickem J, Hoelbl-Kovacic A, Sexl V. STAT5A and STAT5B-Twins with Different Personalities in Hematopoiesis and Leukemia. Cancers (Basel) 2019;11:E1726. [PMID: 31690038 PMCID: PMC6895831 DOI: 10.3390/cancers11111726] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022]  Open
16
Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS. PyBioNetFit and the Biological Property Specification Language. iScience 2019;19:1012-1036. [PMID: 31522114 PMCID: PMC6744527 DOI: 10.1016/j.isci.2019.08.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/21/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023]  Open
17
Kreutz C. An easy and efficient approach for testing identifiability. Bioinformatics 2019;34:1913-1921. [PMID: 29365095 DOI: 10.1093/bioinformatics/bty035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/19/2018] [Indexed: 11/12/2022]  Open
18
Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, Klingmüller U. Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression. Cell Syst 2018;6:75-89.e11. [DOI: 10.1016/j.cels.2017.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 06/23/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022]
19
Adlung L, Kar S, Wagner MC, She B, Chakraborty S, Bao J, Lattermann S, Boerries M, Busch H, Wuchter P, Ho AD, Timmer J, Schilling M, Höfer T, Klingmüller U. Protein abundance of AKT and ERK pathway components governs cell type-specific regulation of proliferation. Mol Syst Biol 2017;13:904. [PMID: 28123004 PMCID: PMC5293153 DOI: 10.15252/msb.20167258] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
20
Lehmann WD. A timeline of stable isotopes and mass spectrometry in the life sciences. MASS SPECTROMETRY REVIEWS 2017;36:58-85. [PMID: 26919394 DOI: 10.1002/mas.21497] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
21
Merkle R, Steiert B, Salopiata F, Depner S, Raue A, Iwamoto N, Schelker M, Hass H, Wäsch M, Böhm ME, Mücke O, Lipka DB, Plass C, Lehmann WD, Kreutz C, Timmer J, Schilling M, Klingmüller U. Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells. PLoS Comput Biol 2016;12:e1005049. [PMID: 27494133 PMCID: PMC4975441 DOI: 10.1371/journal.pcbi.1005049] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/05/2016] [Indexed: 01/23/2023]  Open
22
Verma R, Green JM, Schatz PJ, Wojchowski DM. A dimeric peptide with erythropoiesis-stimulating activity uniquely affects erythropoietin receptor ligation and cell surface expression. Exp Hematol 2016;44:765-769.e1. [PMID: 27174804 DOI: 10.1016/j.exphem.2016.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/14/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
23
Kreutz C. New Concepts for Evaluating the Performance of Computational Methods * *The author acknowledge financial support by the by the German Ministry of Education and Research (BMBF) via e:Bio Grant No. 031L0080. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ifacol.2016.12.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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