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Cells Undergo Major Changes in the Quantity of Cytoplasmic Organelles after Uptake of Gold Nanoparticles with Biologically Relevant Surface Coatings.

Kepsutlu B, Wycisk V, Achazi K, Kapishnikov S, Pérez-Berná AJ, Guttmann P, Cossmer A, Pereiro E, Ewers H, Ballauff M, Schneider G, McNally JG.

ACS Nano. 2020 Jan 17. doi: 10.1021/acsnano.9b09264. [Epub ahead of print]


Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast.

Mehta GD, Ball DA, Eriksson PR, Chereji RV, Clark DJ, McNally JG, Karpova TS.

Mol Cell. 2018 Dec 6;72(5):875-887.e9. doi: 10.1016/j.molcel.2018.09.009. Epub 2018 Oct 11.


Unraveling heme detoxification in the malaria parasite by in situ correlative X-ray fluorescence microscopy and soft X-ray tomography.

Kapishnikov S, Grolimund D, Schneider G, Pereiro E, McNally JG, Als-Nielsen J, Leiserowitz L.

Sci Rep. 2017 Aug 8;7(1):7610. doi: 10.1038/s41598-017-06650-w.


Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin.

Ball DA, Mehta GD, Salomon-Kent R, Mazza D, Morisaki T, Mueller F, McNally JG, Karpova TS.

Nucleic Acids Res. 2016 Dec 1;44(21):e160. Epub 2016 Aug 26.


Fluorescence recovery after photobleaching in material and life sciences: putting theory into practice.

Lorén N, Hagman J, Jonasson JK, Deschout H, Bernin D, Cella-Zanacchi F, Diaspro A, McNally JG, Ameloot M, Smisdom N, Nydén M, Hermansson AM, Rudemo M, Braeckmans K.

Q Rev Biophys. 2015 Aug;48(3):323-87. doi: 10.1017/S0033583515000013.


Regulation of RNA polymerase II activation by histone acetylation in single living cells.

Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, Kimura H.

Nature. 2014 Dec 11;516(7530):272-5. doi: 10.1038/nature13714. Epub 2014 Sep 21.


Photoswitching-free FRAP analysis with a genetically encoded fluorescent tag.

Morisaki T, McNally JG.

PLoS One. 2014 Sep 18;9(9):e107730. doi: 10.1371/journal.pone.0107730. eCollection 2014.


Stress-dependent proteolytic processing of the actin assembly protein Lsb1 modulates a yeast prion.

Ali M, Chernova TA, Newnam GP, Yin L, Shanks J, Karpova TS, Lee A, Laur O, Subramanian S, Kim D, McNally JG, Seyfried NT, Chernoff YO, Wilkinson KD.

J Biol Chem. 2014 Oct 3;289(40):27625-39. doi: 10.1074/jbc.M114.582429. Epub 2014 Aug 20.


Single-molecule analysis of transcription factor binding at transcription sites in live cells.

Morisaki T, Müller WG, Golob N, Mazza D, McNally JG.

Nat Commun. 2014 Jul 18;5:4456. doi: 10.1038/ncomms5456.


Now you see it, now you don't: a biochemist's primer for advances in high-resolution microscopy: comment on "Biomolecular dynamics and binding studies in the living cell" by Stephan Diekmann and Christian Hoischen.

Dalal Y, McNally JG.

Phys Life Rev. 2014 Mar;11(1):36-7; discussion 38. doi: 10.1016/j.plrev.2013.11.007. Epub 2013 Nov 22. No abstract available.


Measuring chromatin interaction dynamics on the second time scale at single-copy genes.

Poorey K, Viswanathan R, Carver MN, Karpova TS, Cirimotich SM, McNally JG, Bekiranov S, Auble DT.

Science. 2013 Oct 18;342(6156):369-72. doi: 10.1126/science.1242369. Epub 2013 Oct 3.


Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories.

Rieder D, Ploner C, Krogsdam AM, Stocker G, Fischer M, Scheideler M, Dani C, Amri EZ, Müller WG, McNally JG, Trajanoski Z.

Cell Mol Life Sci. 2014 May;71(9):1741-59. doi: 10.1007/s00018-013-1465-3. Epub 2013 Sep 12.


Quantifying transcription factor kinetics: at work or at play?

Mueller F, Stasevich TJ, Mazza D, McNally JG.

Crit Rev Biochem Mol Biol. 2013 Sep-Oct;48(5):492-514. doi: 10.3109/10409238.2013.833891. Epub 2013 Sep 11. Review. Erratum in: Crit Rev Biochem Mol Biol. 2014 Nov-Dec;49(6):533.


Monitoring dynamic binding of chromatin proteins in vivo by single-molecule tracking.

Mazza D, Ganguly S, McNally JG.

Methods Mol Biol. 2013;1042:117-37. doi: 10.1007/978-1-62703-526-2_9.


Convergence of chromatin binding estimates in live cells.

Mazza D, Mueller F, Stasevich TJ, McNally JG.

Nat Methods. 2013 Aug;10(8):691-2. doi: 10.1038/nmeth.2573. No abstract available.


Genome-wide haploinsufficiency screen reveals a novel role for γ-TuSC in spindle organization and genome stability.

Choy JS, O'Toole E, Schuster BM, Crisp MJ, Karpova TS, McNally JG, Winey M, Gardner MK, Basrai MA.

Mol Biol Cell. 2013 Sep;24(17):2753-63. doi: 10.1091/mbc.E12-12-0902. Epub 2013 Jul 3.


CKAP2 ensures chromosomal stability by maintaining the integrity of microtubule nucleation sites.

Case CM, Sackett DL, Wangsa D, Karpova T, McNally JG, Ried T, Camps J.

PLoS One. 2013 May 30;8(5):e64575. doi: 10.1371/journal.pone.0064575. Print 2013.


Transcription factories.

Rieder D, Trajanoski Z, McNally JG.

Front Genet. 2012 Oct 23;3:221. doi: 10.3389/fgene.2012.00221. eCollection 2012.


Through thick and thin: the conundrum of chromatin fibre folding in vivo.

Quénet D, McNally JG, Dalal Y.

EMBO Rep. 2012 Nov 6;13(11):943-4. doi: 10.1038/embor.2012.143. Epub 2012 Oct 5. No abstract available.


A benchmark for chromatin binding measurements in live cells.

Mazza D, Abernathy A, Golob N, Morisaki T, McNally JG.

Nucleic Acids Res. 2012 Aug;40(15):e119. doi: 10.1093/nar/gks701. Epub 2012 Jul 25.


Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis.

Mueller F, Morisaki T, Mazza D, McNally JG.

Biophys J. 2012 Apr 4;102(7):1656-65. doi: 10.1016/j.bpj.2012.02.029. Epub 2012 Apr 3.


Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.

Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD.

Nature. 2012 Apr 11;484(7393):251-5. doi: 10.1038/nature10985.


Monitoring dynamic binding of chromatin proteins in vivo by fluorescence correlation spectroscopy and temporal image correlation spectroscopy.

Mazza D, Stasevich TJ, Karpova TS, McNally JG.

Methods Mol Biol. 2012;833:177-200. doi: 10.1007/978-1-61779-477-3_12.


Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching.

Mueller F, Karpova TS, Mazza D, McNally JG.

Methods Mol Biol. 2012;833:153-76. doi: 10.1007/978-1-61779-477-3_11.


Towards an atlas of mammalian cell ultrastructure by cryo soft X-ray tomography.

Müller WG, Heymann JB, Nagashima K, Guttmann P, Werner S, Rehbein S, Schneider G, McNally JG.

J Struct Biol. 2012 Feb;177(2):179-92. doi: 10.1016/j.jsb.2011.11.025. Epub 2011 Dec 2.


Assembly of the transcription machinery: ordered and stable, random and dynamic, or both?

Stasevich TJ, McNally JG.

Chromosoma. 2011 Dec;120(6):533-45. doi: 10.1007/s00412-011-0340-y. Epub 2011 Nov 3. Review.


Fast transcription rates of RNA polymerase II in human cells.

Maiuri P, Knezevich A, De Marco A, Mazza D, Kula A, McNally JG, Marcello A.

EMBO Rep. 2011 Dec 1;12(12):1280-5. doi: 10.1038/embor.2011.196.


Prion induction by the short-lived, stress-induced protein Lsb2 is regulated by ubiquitination and association with the actin cytoskeleton.

Chernova TA, Romanyuk AV, Karpova TS, Shanks JR, Ali M, Moffatt N, Howie RL, O'Dell A, McNally JG, Liebman SW, Chernoff YO, Wilkinson KD.

Mol Cell. 2011 Jul 22;43(2):242-52. doi: 10.1016/j.molcel.2011.07.001.


Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload.

Kuipers MA, Stasevich TJ, Sasaki T, Wilson KA, Hazelwood KL, McNally JG, Davidson MW, Gilbert DM.

J Cell Biol. 2011 Jan 10;192(1):29-41. doi: 10.1083/jcb.201007111.


Foreword. Biophysics in chromatin structure and nuclear dynamics.

McNally JG.

Chromosome Res. 2011 Jan;19(1):1-3. doi: 10.1007/s10577-010-9173-4. No abstract available.


Three-dimensional cellular ultrastructure resolved by X-ray microscopy.

Schneider G, Guttmann P, Heim S, Rehbein S, Mueller F, Nagashima K, Heymann JB, Müller WG, McNally JG.

Nat Methods. 2010 Dec;7(12):985-7. doi: 10.1038/nmeth.1533. Epub 2010 Nov 14.


Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates.

Stasevich TJ, Mueller F, Michelman-Ribeiro A, Rosales T, Knutson JR, McNally JG.

Biophys J. 2010 Nov 3;99(9):3093-101. doi: 10.1016/j.bpj.2010.08.059.


Live cell imaging and systems biology.

Sung MH, McNally JG.

Wiley Interdiscip Rev Syst Biol Med. 2011 Mar-Apr;3(2):167-82. doi: 10.1002/wsbm.108. Epub 2010 Aug 20. Review.


FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

Mueller F, Mazza D, Stasevich TJ, McNally JG.

Curr Opin Cell Biol. 2010 Jun;22(3):403-11. doi: 10.1016/ Epub 2010 Apr 21. Review.


Core histone hyperacetylation impacts cooperative behavior and high-affinity binding of histone H1 to chromatin.

Raghuram N, Carrero G, Stasevich TJ, McNally JG, Th'ng J, Hendzel MJ.

Biochemistry. 2010 Jun 1;49(21):4420-31. doi: 10.1021/bi100296z.


The arylstibonic acid compound NSC13746 disrupts B-ZIP binding to DNA in living cells.

Heyerdahl SL, Rozenberg J, Jamtgaard L, Rishi V, Varticovski L, Akah K, Scudiero D, Shoemaker RH, Karpova TS, Day RN, McNally JG, Vinson C.

Eur J Cell Biol. 2010 Jul;89(7):564-73. doi: 10.1016/j.ejcb.2009.11.029. Epub 2010 Apr 1.


Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis.

Stasevich TJ, Mueller F, Brown DT, McNally JG.

EMBO J. 2010 Apr 7;29(7):1225-34. doi: 10.1038/emboj.2010.24. Epub 2010 Mar 11.


Fractal geometry in the nucleus.

McNally JG, Mazza D.

EMBO J. 2010 Jan 6;29(1):2-3. doi: 10.1038/emboj.2009.375. No abstract available.


iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis.

Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M, McNally JG, Trajanoski Z.

BMC Bioinformatics. 2009 Nov 26;10:390. doi: 10.1186/1471-2105-10-390.


Transcription dynamics.

Hager GL, McNally JG, Misteli T.

Mol Cell. 2009 Sep 24;35(6):741-53. doi: 10.1016/j.molcel.2009.09.005. Review.


The interaction of NSBP1/HMGN5 with nucleosomes in euchromatin counteracts linker histone-mediated chromatin compaction and modulates transcription.

Rochman M, Postnikov Y, Correll S, Malicet C, Wincovitch S, Karpova TS, McNally JG, Wu X, Bubunenko NA, Grigoryev S, Bustin M.

Mol Cell. 2009 Sep 11;35(5):642-56. doi: 10.1016/j.molcel.2009.07.002.


Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy.

Michelman-Ribeiro A, Mazza D, Rosales T, Stasevich TJ, Boukari H, Rishi V, Vinson C, Knutson JR, McNally JG.

Biophys J. 2009 Jul 8;97(1):337-46. doi: 10.1016/j.bpj.2009.04.027.


Not choosing nursing: work experience and career choice of high academic achieving school leavers.

Neilson GR, McNally JG.

Nurse Educ Today. 2010 Jan;30(1):9-14. doi: 10.1016/j.nedt.2009.05.007.


Transcription, chromatin condensation, and gene migration.

McNally JG.

J Cell Biol. 2009 Apr 6;185(1):7-9. doi: 10.1083/jcb.200903056.


Detecting protein-protein interactions with CFP-YFP FRET by acceptor photobleaching.

Karpova T, McNally JG.

Curr Protoc Cytom. 2006 Feb;Chapter 12:Unit12.7. doi: 10.1002/0471142956.cy1207s35.


Regulation of TATA-binding protein dynamics in living yeast cells.

Sprouse RO, Karpova TS, Mueller F, Dasgupta A, McNally JG, Auble DT.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13304-8. doi: 10.1073/pnas.0801901105. Epub 2008 Sep 2.


Dynamic effect of bortezomib on nuclear factor-kappaB activity and gene expression in tumor cells.

Sung MH, Bagain L, Chen Z, Karpova T, Yang X, Silvin C, Voss TC, McNally JG, Van Waes C, Hager GL.

Mol Pharmacol. 2008 Nov;74(5):1215-22. doi: 10.1124/mol.108.049114. Epub 2008 Aug 6.


Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression.

Nishiyama A, Mochizuki K, Mueller F, Karpova T, McNally JG, Ozato K.

FEBS Lett. 2008 Apr 30;582(10):1501-7. doi: 10.1016/j.febslet.2008.03.044. Epub 2008 Apr 7.


Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter.

Karpova TS, Kim MJ, Spriet C, Nalley K, Stasevich TJ, Kherrouche Z, Heliot L, McNally JG.

Science. 2008 Jan 25;319(5862):466-9. doi: 10.1126/science.1150559.


Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching.

Mueller F, Wach P, McNally JG.

Biophys J. 2008 Apr 15;94(8):3323-39. doi: 10.1529/biophysj.107.123182. Epub 2008 Jan 16.

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