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Publications

 Complete List of Published Work:

  1. Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. “Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast”. Methods Molecular Biology. 2019;2038. doi: 10.1007/978-1-4939-9674-2_9. PMID: 31407282; NIHMS:1608774; PMCID: PMC7392168.
  2. Ma H, Tu LC, Chung YC, Naseri A,  Grunwald D, Zhang S, Pederson T. ”Cell Cycle- and Genomic Distance-Dependent Dynamics of a Discrete Chromosomal Region”. The Journal of Cell Biology. 2019 May 6;218(5). doi: 10.1083/JCB.201807162. PMID: 30846483; PMCID: PMC6504907.
  3. Smith CS, Jouravleva K, Huisman M, Jolly SM, Zamore PD, Grunwald D. “An automated Bayesian pipeline for rapid analysis of single-molecule binding data”. Nature Communication. 2019 Jan 17;10(1):272. doi: 10.1038/s41467-018-08045-5. PMID: 30655518; PMCID: PMC6336789.
  4. Tu LC, Huisman M, Chung YC, Smith CS, Grunwald D.  "Deconstructing transport-distribution reconstruction in the nuclear-pore complex”. Nature Structural and Molecular Biology. 2018 Dec;25(12):1061-1062. doi: 10.1038/s41594-018-0161-2. Epub 2018 Dec 5. PMID: 30518848; PMCID: PMC6481291.
  5. Thorsen RØ, Hulleman CN, Hammer M, Grunwald D, Stallinga S, Rieger B. “Impact of optical aberrations on axial position determination by photometry”. Nature Methods. 2018 Dec;15(12):989-990. doi: 10.1038/s41592-018-0227-4. PMID: 30504865; PMCID: PMC6588158.
  6. Ma H, Tu LC, Naseri A, Chung YC, Grunwald D, Zhang S, Pederson T. “CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging”. Nature Methods. 2018 Nov;15(11):928-931. doi: 10.1038/s41592-018-0174-0. Epub 2018 Oct 30. PMID: 30377374; PMCID: PMC6252086.
  7. Huisman M, Hammer M, Smith C, Grunwald D. “Introducing a data-standard for fluorescence microscopy: increasing data quality and fidelity for biological measurements”. Proceedings Volume 10726, Nanoimaging and Nanospectroscopy VI; 107260A (2018) https://doi.org/10.1117/12.232366.
  8. Noma A, Smith CS, Huisman M, Martin RM, Moore M, Grunwald D.  "Advanced 3D Analysis and Optimization of Single-Molecule FSH in Drosophila Muscle". Small Methods. 2018, 1700324; DOI:10.1002/smtd.201700324. PubMed PMID: 32158910. PMCID: PMC7063683. BioRxiv 156091 [Preprint]. Available from: http://doi.org/10.110
  9. Hulleman CN, Huisman M, Moerland RJ, Grunwald D, Stallinga S, Rieger B. ”Fluorescence Polarization Control for On–Off Switching of Single Molecules at Cryogenic Temperatures”. Small Methods. April. 2018, 1700323, doi:10.1002/smtd.201700323. PMID: 31240238; PMCID: PMC6592266.
  10. Vallotton P, van Oijen AM, Whitchurch CB, Gelfand V, Yeo L, Tsiavaliaris G, Heinrich S, Dultz E, Weis K and Grunwald D. “Diatrack object tracking software for dynamic imaging: review of applications and performance evaluation”. Traffic 2017; 18:840-852, doi: 10.1111/tra.12530. PMID: 28945316; PMCID: PMC5677553.
  11. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T.  “CRISPR-Cas9 nuclear dynamics and target recognition in living cells”. The Journal of Cell Biology. 2016; 214(5):529-37. doi: 10.1038/JCB.2016041115; PMID: 27551060; PMCID: PMC5004447.
  12. Musser SM, Grunwald D. “Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches”. Journal of Molecular Biology. 2016; 428(10 Pt A):2091-119. doi: 10.1016/j.jmb.2016.02.023; PMID: 26944195; PMCID: PMC4909493.
  13. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. “Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow”. Nature Biotechnology. 2016; 34(5):528-30. doi: 10.1038/not.3526; PMID: 27088723 PMCID: PMC4864854.
  14. Chen J, Rahman SA, Nikolaitchik OA, Grunwald D, Sardo L, Burdick RC, Plisov S, Liang E, Tai S, Pathak VK, Hu WS*. “HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein”. Proceedings of the National Academy of Sciences of the United States of America. 2016; 113(2):E201-8. doi: 10.1073/Pena’s.1518572113; PMID: 26712001; PMCID: PMC4720333.
  15. Smith C, Huisman M, Siemons M, Grunwald D, Stallinga S. “Simultaneous measurement of emission color and 3D position of single molecules”. Optics Express. 2016 Mar 7;24(5):4996-5013. doi: 10.1364/OE.24.004996. PMID: 29092328. PMCID: PMC5499633.
  16. Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grunwald D, Montpetit B. “In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstratn essential role for Mex67p”. The Journal of Cell Biology. 2015; 211(6):1121-30. doi: 10.1083/JCB.201503135; PMID: 26694837; PMCID: PMC4687877.
  17. Smith CS, Stallinga S, Lidke KA, Rieger B, Grunwald D. “Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking”. Mol Biol Cell. 2015; 26(22):4057-62. doi: 10.1091/mbc.E15-06-0448; PMID: 26424801; PMCID: PMC4710236.
  18. Smith CS, Preibisch S, Joseph A, Abrahamsson S, Rieger B, Myers E, Singer RH, Grunwald D. “Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking”. The Journal of Cell Biology. 2015; 209(4):609-19. doi: 10.1083/JCB.201411032; PMID: 26008747; PMCID: PMC4442804.
  19. Chen D, Lockett S, Larson DR, Pathak VK, Hu WS. “Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein”. Proc Natl Acad Sci USA. 2014; 111(48):E5205-13. doi: 10.1073/pans.1413169111; PMID: 25404326; PMCID: PMC4260538.
  20. Nieuwenhuizen RP, Lidke KA, Bates M, Puig DL, Grunwald D, Stallinga S, Rieger B. ”Measuring image resolution in optical nanoscopy”. Nature Methods. 2013; 10(6):557-62. doi: 10.1038/nmeth.2448; PMID: 23624665; PMCID: PMC4149789.
  21. Grunwald D, Singer, R.H., “Multiscale dynamics in nucleocytoplasmic transport”. Curr Opin Cell Biol. 2012 Feb. doi.org/10.1016/j.ceb.2011.11.011. PMID: 30. PMCID: PMC3294057.
  22. Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker HJ, Singer RH, Schirmacher P, Prives C. “Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes”. Molecular Cell. 2012; 48(5):799-810. DOI: 10.1016/j.molcel.2012.09.020. PMID: 23102701; PMCID: PMC3525737.
  23. Grunwald D. and Singer, R.H. “Multiscale dynamics in nucleocytoplasmic transport”. Current Opinion in Cell Biology, 1: 100-106 (2012) Feb; 24(1):100-6. doi: 10.1016/j.ceb.2011.11.011. PMID: 22196930; PMICD: PMC3294057.
  24. Grunwald D., Singer, R.H., and Rout, M. “Nuclear Export Dynamics of RNA-Protein Complexes”. Nature, 475: 333-341 (2011). doi: 10.1038/nature10318. PMID: 21776079; PMCID: PMC3154952.
  25. Grunwald D, Singer RH. “In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport”. Nature. 2010; 467(7315):604-7. doi: 10.1038/nature09438. PubMed PMID: 20844488 PMCID: PMC3005609.
  26. Dange T, Grunwald D, Grünwald A, Peters R, Kubitscheck U. “Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study”. The Journal of Cell Biology. 2008; 183(1):77-86. doi: 10.1083/jcb.200806173. PMID: 18824568; PMCID: PMC2557044.
  27. Grunwald D, Martin RM, Buschmann V, Bazett-Jones DP, Leonhardt H, Kubitscheck U, Cardoso MC. “Probing intranuclear environments at the single-molecule level”. Biophysical Journal. 2008; 94(7):2847-58. doi: 10.1529/biophysj.107.115014. PMID: 18065482; PMCID: PMC2267134.
  28. Grunwald D, Shenoy SM, Burke S, Singer RH. “Calibrating excitation light fluxes for quantitative light microscopy in cell biology”. Nature Protocols. 2008; 3(11):1809-14. doi: 10.1038/nprot.2008.180. PMID: 18974739; PMCID: PMC3109976.
  29. Siebrasse, JP., Grunwald D. and Kubitscheck, U. “Single-molecule tracking in eukaryotic cell nuclei”. Anal. Bioanal. Chem., 387(1): 41-44 (2007). doi: 10.1007/s00216-006-0763-0. PMID: 17033772; PMICD: Not shown.
  30. Grunwald D, Spottke B, Buschmann V, Kubitscheck U. “Intranuclear binding kinetics and mobility of single native U1 snRNP particles in living cells”. Molecular Biology of the Cell. 2006; 17(12):5017-27. doi: 10.1091/mbc.e06-06-0559. PubMed PMID: 16987963; PMCID: PMC1679670.
  31. Grunwald D, Hoekstra A, Dange T, Buschmann V, Kubitscheck U. ”Direct observation of single protein molecules in aqueous solution”. Chemphyschem. 2006; 7(4):812-5. doi: 10.1002/cphc.200500632. PMID: 16528778; PMCID: Not shown.
  32. Grunwald D, Cardoso MC, Leonhardt H, Buschmann V. “Diffusion and binding properties investigated by Fluorescence Correlation Spectroscopy (FCS)”. Current Pharmaceutical Biotechnology. 2005; 6(5):381-6. doi : 10.2174/138920105774370616. PMID: 16248811; PMCID: Not Shown.
  33. Kubitscheck U, Grunwald D, Hoekstra A, Rohleder D, Kues T, Siebrasse JP, Peters R*. ”Nuclear transport of single molecules: dwell times at the nuclear pore complex”. The Journal of Cell Biology. 2005; 168(2):233-43. doi: 10.1083/jcb.200411005. PMID: 15657394; PMCID: PMC2171583.

 Books and Chapters:

  1. 4D Nuclome Network. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. "The 4D Nucleome project". Nature 2017; 549(7671):219-226, doi:10.1038/nature23884. PMID: 28905911; PMCID: PMC5617335.
  2. Dange, T., Joseph, A. and Grunwald D. “A perspective of the dynamic structure of the nucleus explored at the single-molecule level”. Chromosome Research, (Editor: J. McNally), (1): 117-129. (2011). doi: 10.1007/s10577-010-9156-5, PMID: 20842420; PMCID: PMC3040321.
  3. Hocine, S., Singer, R.H. and Grunwald D. “RNA Processing and Export”. The Nucleus, (Editors: T. Misteli and D. Spector) pp. 697-712, (2010). PMID: 20961978; PMCID: PMC2982171.
  4. Lionnet T, Wu B, Grunwald D, Singer RH, Larson DR. ”Nuclear physics: quantitative single-cell approaches to nuclear organization and gene expression”. Cold Spring Harbor symposia on quantitative biology. (2010); 75:113-26;. doi: 0.1101/cshperspect.a000752. PMID: 21502409; PMCID: PMC3145213.
  5. Grunwald D, Singer RH, Czaplinski K, Maquat L.E., Kiledjian M., “Cell Biology of mRNA Decay. Imaging individual mRNAs in single cells". Methods in Enzymology (Eds: L.E. Maquat and M. Kiledjian), 448: 553-577 Elsevier (2008). doi: 10.1016/S0076-6879(08)02627-X. PMID: 19111194; PMCID: PMC3152983. 

Preprints and Other Interim Research Products:

  1. Huisman M, Hammer M, Rigano A, Gopinathan R, Smith C, Grunwald D, Strambio-De-Castillia, C., “Minimum Information guidelines for fluorescence microscopy: increasing the value, quality and fidelity of image data”. https://arxiv.org/abs/1910.11370.
  2. Grunwald D, Tu LC, Huisman M, Chung Y, Smith C. “Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images — How Reliable Is It?” BioRxiv 145110 [Preprint]. Available from: https://doi.org/10.1101/145110.