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For: Shivanandan A, Unnikrishnan J, Radenovic A. On characterizing protein spatial clusters with correlation approaches. Sci Rep 2016;6:31164. [PMID: 27507257 PMCID: PMC4979030 DOI: 10.1038/srep31164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/15/2016] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Adler J, Bernhem K, Parmryd I. Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy - identification and correction. Commun Biol 2024;7:791. [PMID: 38951588 PMCID: PMC11217499 DOI: 10.1038/s42003-024-06472-3] [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: 01/16/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]  Open
2
Ray S, Hewitt K. Sticky, Adaptable, and Many-sided: SAM protein versatility in normal and pathological hematopoietic states. Bioessays 2023;45:e2300022. [PMID: 37318311 PMCID: PMC10527593 DOI: 10.1002/bies.202300022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
3
Feher K, Graus MS, Coelho S, Farrell MV, Goyette J, Gaus K. K-Neighbourhood Analysis: A Method for Understanding SMLM Images as Compositions of Local Neighbourhoods. FRONTIERS IN BIOINFORMATICS 2021;1:724127. [PMID: 36303786 PMCID: PMC9581049 DOI: 10.3389/fbinf.2021.724127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/04/2021] [Indexed: 11/30/2022]  Open
4
Haas KT, Peaucelle A. Protocol for multicolor three-dimensional dSTORM data analysis using MATLAB-based script package Grafeo. STAR Protoc 2021;2:100808. [PMID: 34541556 PMCID: PMC8437824 DOI: 10.1016/j.xpro.2021.100808] [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] [Indexed: 11/30/2022]  Open
5
Neguembor MV, Martin L, Castells-García Á, Gómez-García PA, Vicario C, Carnevali D, AlHaj Abed J, Granados A, Sebastian-Perez R, Sottile F, Solon J, Wu CT, Lakadamyali M, Cosma MP. Transcription-mediated supercoiling regulates genome folding and loop formation. Mol Cell 2021;81:3065-3081.e12. [PMID: 34297911 PMCID: PMC9482096 DOI: 10.1016/j.molcel.2021.06.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 03/27/2021] [Accepted: 06/08/2021] [Indexed: 12/21/2022]
6
Peaucelle A, Wightman R, Haas KT. Multicolor 3D-dSTORM Reveals Native-State Ultrastructure of Polysaccharides' Network during Plant Cell Wall Assembly. iScience 2020;23:101862. [PMID: 33336161 PMCID: PMC7733027 DOI: 10.1016/j.isci.2020.101862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/07/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]  Open
7
Vincent GB, Proudian AP, Zimmerman JD. Three dimensional cluster analysis for atom probe tomography using Ripley's K-function and machine learning. Ultramicroscopy 2020;220:113151. [PMID: 33152650 DOI: 10.1016/j.ultramic.2020.113151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/25/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
8
Wu YL, Tschanz A, Krupnik L, Ries J. Quantitative Data Analysis in Single-Molecule Localization Microscopy. Trends Cell Biol 2020;30:837-851. [PMID: 32830013 DOI: 10.1016/j.tcb.2020.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
9
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CSO, Aparicio S, Baaijens J, Balvert M, Barbanson BD, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowska A, Reinders M, Ridder JD, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Eleven grand challenges in single-cell data science. Genome Biol 2020;21:31. [PMID: 32033589 PMCID: PMC7007675 DOI: 10.1186/s13059-020-1926-6] [Citation(s) in RCA: 688] [Impact Index Per Article: 137.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/02/2020] [Indexed: 02/08/2023]  Open
10
Can single molecule localization microscopy detect nanoclusters in T cells? Curr Opin Chem Biol 2019;51:130-137. [DOI: 10.1016/j.cbpa.2019.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/10/2019] [Accepted: 05/21/2019] [Indexed: 11/21/2022]
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