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For: Jetka T, Nienałtowski K, Winarski T, Błoński S, Komorowski M. Information-theoretic analysis of multivariate single-cell signaling responses. PLoS Comput Biol 2019;15:e1007132. [PMID: 31299056 DOI: 10.1371/journal.pcbi.1007132] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 07/24/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]  Open

Supplementary Information

The online version contains supplementary material available at 10.1186/s12964-021-00770-7.

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Number Cited by Other Article(s)
1
Tkačik G, Wolde PRT. Information Processing in Biochemical Networks. Annu Rev Biophys 2025;54:249-274. [PMID: 39929539 DOI: 10.1146/annurev-biophys-060524-102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2025]
2
Wang AG, Son M, Gorin A, Kenna E, Padhi A, Keisham B, Schauer A, Hoffmann A, Tay S. Macrophage memory emerges from coordinated transcription factor and chromatin dynamics. Cell Syst 2025;16:101171. [PMID: 39938520 DOI: 10.1016/j.cels.2025.101171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 09/18/2024] [Accepted: 01/09/2025] [Indexed: 02/14/2025]
3
Madsen RR, Le Marois A, Mruk ON, Voliotis M, Yin S, Sufi J, Qin X, Zhao SJ, Gorczynska J, Morelli D, Davidson L, Sahai E, Korolchuk VI, Tape CJ, Vanhaesebroeck B. Oncogenic PIK3CA corrupts growth factor signaling specificity. Mol Syst Biol 2025;21:126-157. [PMID: 39706867 PMCID: PMC11791070 DOI: 10.1038/s44320-024-00078-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 11/06/2024] [Accepted: 11/11/2024] [Indexed: 12/23/2024]  Open
4
Marković A, Briscoe J, Page KM. Dynamics of positional information in the vertebrate neural tube. J R Soc Interface 2024;21:20240414. [PMID: 39657793 PMCID: PMC11631457 DOI: 10.1098/rsif.2024.0414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 09/06/2024] [Accepted: 10/23/2024] [Indexed: 12/12/2024]  Open
5
Sheu KM, Pimplaskar A, Hoffmann A. Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages. Mol Cell 2024;84:4095-4110.e6. [PMID: 39413794 PMCID: PMC11560543 DOI: 10.1016/j.molcel.2024.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 07/05/2024] [Accepted: 09/19/2024] [Indexed: 10/18/2024]
6
Tserunyan V, Finley S. Information-Theoretic Analysis of a Model of CAR-4-1BB-Mediated NFκB Activation. Bull Math Biol 2023;86:5. [PMID: 38038772 PMCID: PMC10691998 DOI: 10.1007/s11538-023-01232-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
7
Stano P, Gentili PL, Damiano L, Magarini M. A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things? Molecules 2023;28:5564. [PMID: 37513436 PMCID: PMC10385758 DOI: 10.3390/molecules28145564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]  Open
8
Tserunyan V, Finley S. Information-theoretic analysis of a model of CAR-4-1BB-mediated NFκB activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544433. [PMID: 37333129 PMCID: PMC10274880 DOI: 10.1101/2023.06.09.544433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
9
Kirby D, Zilman A. Proofreading does not result in more reliable ligand discrimination in receptor signaling due to its inherent stochasticity. Proc Natl Acad Sci U S A 2023;120:e2212795120. [PMID: 37192165 PMCID: PMC10214210 DOI: 10.1073/pnas.2212795120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/05/2023] [Indexed: 05/18/2023]  Open
10
Sheu KM, Guru AA, Hoffmann A. Quantifying stimulus-response specificity to probe the functional state of macrophages. Cell Syst 2023;14:180-195.e5. [PMID: 36657439 PMCID: PMC10023480 DOI: 10.1016/j.cels.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/05/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023]
11
Rammohan J, Sarkar S, Ross D. Single-cell measurement quality in bits. PLoS One 2022;17:e0269272. [PMID: 35951522 PMCID: PMC9371318 DOI: 10.1371/journal.pone.0269272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/17/2022] [Indexed: 11/18/2022]  Open
12
Ying T, Alexander H. Quantifying information of intracellular signaling: progress with machine learning. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022;85:10.1088/1361-6633/ac7a4a. [PMID: 35724636 PMCID: PMC9507437 DOI: 10.1088/1361-6633/ac7a4a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
13
Introduction to Genomic Network Reconstruction for Cancer Research. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2486:197-214. [PMID: 35437724 DOI: 10.1007/978-1-0716-2265-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
14
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression. Cell Syst 2022;13:353-364.e6. [PMID: 35298924 DOI: 10.1016/j.cels.2022.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/18/2021] [Accepted: 02/17/2022] [Indexed: 12/27/2022]
15
Coggan JS, Keller D, Markram H, Schürmann F, Magistretti PJ. Representing Stimulus Information in an Energy Metabolism Pathway. J Theor Biol 2022;540:111090. [PMID: 35271865 DOI: 10.1016/j.jtbi.2022.111090] [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: 04/06/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
16
Topolewski P, Zakrzewska KE, Walczak J, Nienałtowski K, Müller-Newen G, Singh A, Komorowski M. Phenotypic variability, not noise, accounts for most of the cell-to-cell heterogeneity in IFN-γ and oncostatin M signaling responses. Sci Signal 2022;15:eabd9303. [PMID: 35167339 DOI: 10.1126/scisignal.abd9303] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
17
Lee JB, Caywood LM, Lo JY, Levering N, Keung AJ. Mapping the dynamic transfer functions of eukaryotic gene regulation. Cell Syst 2021;12:1079-1093.e6. [PMID: 34469745 DOI: 10.1016/j.cels.2021.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/26/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022]
18
Wen Y, Zhao J, He H, Zhao Q, Liu Z. Multiplexed Single-Cell Plasmonic Immunoassay of Intracellular Signaling Proteins Enables Non-Destructive Monitoring of Cell Fate. Anal Chem 2021;93:14204-14213. [PMID: 34648273 DOI: 10.1021/acs.analchem.1c03062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
19
Kirby D, Parmar B, Fathi S, Marwah S, Nayak CR, Cherepanov V, MacParland S, Feld JJ, Altan-Bonnet G, Zilman A. Determinants of Ligand Specificity and Functional Plasticity in Type I Interferon Signaling. Front Immunol 2021;12:748423. [PMID: 34691060 PMCID: PMC8529159 DOI: 10.3389/fimmu.2021.748423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022]  Open
20
Fiebelkow J, Guendel A, Guendel B, Mehwald N, Jetka T, Komorowski M, Waldherr S, Schaper F, Dittrich A. The tyrosine phosphatase SHP2 increases robustness and information transfer within IL-6-induced JAK/STAT signalling. Cell Commun Signal 2021;19:94. [PMID: 34530865 PMCID: PMC8444181 DOI: 10.1186/s12964-021-00770-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/28/2021] [Indexed: 11/21/2022]  Open

Video Abstract

  • Jessica Fiebelkow
    • Institute of Biology, Department of Systems Biology, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
  • André Guendel
    • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
  • Beate Guendel
    • Institute of Biology, Department of Systems Biology, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany.,Karolinska Institutet, Clintec, Huddinge, Sweden
  • Nora Mehwald
    • Institute of Biology, Department of Systems Biology, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
  • Tomasz Jetka
    • Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, Hong Kong
  • Michal Komorowski
    • Institute of Fundamental Technological Research, Polish Academy of Sciences, Warszawa, Poland
  • Fred Schaper
    • Institute of Biology, Department of Systems Biology, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany.,Center for Dynamic Systems: Systems Engineering (CDS), Otto-von-Guericke University, Magdeburg, Germany.,Magdeburg Center for Systems Biology (MACS), Otto-von-Guericke University, Magdeburg, Germany
  • Anna Dittrich
    • Institute of Biology, Department of Systems Biology, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany. .,Center for Dynamic Systems: Systems Engineering (CDS), Otto-von-Guericke University, Magdeburg, Germany. .,Magdeburg Center for Systems Biology (MACS), Otto-von-Guericke University, Magdeburg, Germany.
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21
Nienałtowski K, Rigby RE, Walczak J, Zakrzewska KE, Głów E, Rehwinkel J, Komorowski M. Fractional response analysis reveals logarithmic cytokine responses in cellular populations. Nat Commun 2021;12:4175. [PMID: 34234126 PMCID: PMC8263596 DOI: 10.1038/s41467-021-24449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 06/17/2021] [Indexed: 01/10/2023]  Open
22
Kinnunen PC, Luker KE, Luker GD, Linderman JJ. Computational methods for characterizing and learning from heterogeneous cell signaling data. CURRENT OPINION IN SYSTEMS BIOLOGY 2021;26:98-108. [PMID: 35647414 DOI: 10.1016/j.coisb.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
23
Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity 2021;54:916-930.e7. [PMID: 33979588 PMCID: PMC8184127 DOI: 10.1016/j.immuni.2021.04.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/21/2020] [Accepted: 04/13/2021] [Indexed: 12/12/2022]
24
Karolak A, Branciamore S, McCune JS, Lee PP, Rodin AS, Rockne RC. Concepts and Applications of Information Theory to Immuno-Oncology. Trends Cancer 2021;7:335-346. [PMID: 33618998 PMCID: PMC8156485 DOI: 10.1016/j.trecan.2020.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/27/2023]
25
Tang Y, Adelaja A, Ye FXF, Deeds E, Wollman R, Hoffmann A. Quantifying information accumulation encoded in the dynamics of biochemical signaling. Nat Commun 2021;12:1272. [PMID: 33627672 PMCID: PMC7904837 DOI: 10.1038/s41467-021-21562-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023]  Open
26
Biswas D, Iglesias PA. Sensitivity minimization, biological homeostasis and information theory. BIOLOGICAL CYBERNETICS 2021;115:103-113. [PMID: 33475834 PMCID: PMC7818071 DOI: 10.1007/s00422-021-00860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/06/2021] [Indexed: 06/01/2023]
27
Pope RJ, Garner KL, Voliotis M, Lay AC, Betin VM, Tsaneva-Atanasova K, Welsh GI, Coward RJ, McArdle CA. An information theoretic approach to insulin sensing by human kidney podocytes. Mol Cell Endocrinol 2020;518:110976. [PMID: 32750396 DOI: 10.1016/j.mce.2020.110976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 12/16/2022]
28
Liuweidihuang Pill Alleviates Inflammation of the Testis via AMPK/SIRT1/NF-κB Pathway in Aging Rats. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020;2020:2792738. [PMID: 32565851 PMCID: PMC7267858 DOI: 10.1155/2020/2792738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/28/2020] [Indexed: 12/29/2022]
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