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Publications

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2024

Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules

Nucleic Acids Res. In press

Nucleic acid hybridization-based detection of pathogenic RNA using microscale thermophoresis

J Biol Chem. 2024 Jan 24:105676.

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2023

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Mol Cell. 2023 Aug 3;83(15):2624-2640

Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins

Cytometry A. 2023 Aug;103(8):664-669

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2022

A seven-transmembrane protein-TM7SF3, resides in nuclear speckles and regulates alternative splicing

iScience. 2022 Oct 4;25(11):105270

RNA export through the nuclear pore complex is directional

Nat Commun. 2022 Oct 6;13(1):5881

Nuclear speckles - a driving force in gene expression

J Cell Sci. 2022 Jul 1;135(13):jcs259594

The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells

Cells. 2022 Jun 16;11(12):1942

Glucocorticoids enhance chemotherapy-driven stress granule assembly and impair granule dynamics, leading to cell death

J Cell Sci. 2022 Jul 15;135(14):jcs259629

Gene architecture directs splicing outcome in separate nuclear spatial regions

Mol Cell. 2022 Mar 3;82(5):1021-1034.e8

Peroxisome function relies on organelle-associated mRNA translation

Mol Cell. 2022 Mar 3;82(5):1021-1034.e8

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2021

The Portal Vertex of KSHV Promotes Docking of Capsids at the Nuclear Pores

Viruses. 2021 Mar 31;13(4):597

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2020

The Sub-Nuclear Localization of RNA-Binding Proteins in KSHV-Infected Cells

Cells. 2020 Aug 25;9(9):1958

Speculating on the Roles of Nuclear Speckles: How RNA-Protein Nuclear Assemblies Affect Gene Expression

Bioessays. 2020 Oct;42(10):e2000104

Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State

Front Genet. 2020 May 15:11:409

Specific, Sensitive, and Quantitative Detection of HER-2 mRNA Breast Cancer Marker by Fluorescent Light-Up Hybridization Probes

Bioconjug Chem. 2020 Apr 15;31(4):1188-1198

Into the basket and beyond: the journey of mRNA through the nuclear pore complex

Biochem J. 2020 Jan 17;477(1):23-44

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2019

Availability of splicing factors in the nucleoplasm can regulate the release of mRNA from the gene after transcription

PLoS Genet. 2019 Nov 25;15(11):e1008459

Detection of mRNAs Anchored to the Nuclear Envelope During Export Inhibition in Living Cells

Methods Mol Biol. 2019:2038:151-163

Imaging within single NPCs reveals NXF1's role in mRNA export on the cytoplasmic side of the pore

J Cell Biol. 2019 Sep 2;218(9):2962-2981

Cytoplasmic DNA can be detected by RNA fluorescence in situ hybridization

Nucleic Acids Res. 2019 Oct 10;47(18):e109

An oligonucleotide probe incorporating the chromophore of green fluorescent protein is useful for the detection of HER-2 mRNA breast cancer marker

Eur J Med Chem. 2019 Jul 1:173:99-106

Active RNA polymerase II curbs chromatin movement

J Cell Biol. 2019 May 6;218(5):1427-1428

The dynamic lifecycle of mRNA in the nucleus

Curr Opin Cell Biol. 2019 Jun:58:69-75

Uncoupling of nucleo-cytoplasmic RNA export and localization during stress

Nucleic Acids Res. 2019 May 21;47(9):4778-4797

Phospho-Tau Impairs Nuclear-Cytoplasmic Transport

ACS Chem Neurosci. 2019 Jan 16;10(1):36-38

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2018

S-phase transcriptional buffering quantified on two different promoters

Life Sci Alliance. 2018 Sep 19;1(5):e201800086

Yeast and Human Nuclear Pore Complexes: Not So Similar After All

Trends Cell Biol. 2018 Aug;28(8):589-591

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2017

Visualizing nuclear RNAi activity in single living human cells

Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):E8837-E8846

Visualizing Nuclear RNA Editing

Trends Biochem Sci. 2017 Nov;42(11):845-847

mRNPs meet stress granules

FEBS Lett. 2017 Sep;591(17):2534-2542

Mutations in S-adenosylhomocysteine hydrolase (AHCY) affect its nucleocytoplasmic distribution and capability to interact with S-adenosylhomocysteine hydrolase-like 1 protein

Eur J Cell Biol. 2017 Sep;96(6):579-590

CD-tagging-MS2: detecting allelic expression of endogenous mRNAs and their protein products in single cells

Biol Methods Protoc. 2017 May 12;2(1):bpx004

Measuring transcription dynamics in living cells using a photobleaching approach

Methods. 2017 May 1:120:58-64

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2016

Quantifying β-catenin subcellular dynamics and cyclin D1 mRNA transcription during Wnt signaling in single living cells

Elife. 2016 Nov 23:5:e16748

De-novo protein function prediction using DNA binding and RNA binding proteins as a test case

Nat Commun. 2016 Nov 21:7:13424

FRET energy transfer via Pdots improves the efficiency of photodynamic therapy and leads to rapid cell death

J Photochem Photobiol B. 2016 Nov:164:123-131

The stress-inducible transcription factor ATF4 accumulates at specific rRNA-processing nucleolar regions after proteasome inhibition

Eur J Cell Biol. 2016 Oct;95(10):389-400

Dynamic Encounters of Genes and Transcripts with the Nuclear Pore

Trends Genet. 2016 Jul;32(7):419-431

A hydrothermal reaction of an aqueous solution of BSA yields highly fluorescent N doped C-dots used for imaging of live mammalian cells

J Mater Chem B. 2016 May 7;4(17):2913-2920

Methods for visualizing RNA in cells, tissues and whole organisms

Methods. 2016 Apr 1:98:1-3

Exploring chromatin organization mechanisms through its dynamic properties

Nucleus. 2016;7(1):27-33

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2015

Design (and) principles of nuclear dynamics in Stockholm

Nucleus. 2015;6(6):425-9

Single-site transcription rates through fitting of ensemble-averaged data from fluorescence recovery after photobleaching: a fat-tailed distribution

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 ;92(3):032715

Loss of lamin A function increases chromatin dynamics in the nuclear interior

Nat Commun. 2015 Aug 24:6:8044

The proteolysis adaptor, NblA, is essential for degradation of the core pigment of the cyanobacterial light-harvesting complex

Plant J. 2015 Sep;83(5):845-52

Cellular Levels of Signaling Factors Are Sensed by β-actin Alleles to Modulate Transcriptional Pulse Intensity

Cell Rep. 2015 Apr 21;11(3):419-32

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2014

Quantifying mRNA targeting to P-bodies in living human cells reveals their dual role in mRNA decay and storage

J Cell Sci. 2014 Oct 15;127(Pt 20):4443-56

The proteolysis adaptor, NblA, initiates protein pigment degradation by interacting with the cyanobacterial light-harvesting complexes

Plant J. 2014 Jul;79(1):118-26

Development of fluorescent double-strand probes labeled with 8-(p-CF3-cinnamyl)-adenosine for the detection of cyclin D1 breast cancer marker

Eur J Med Chem. 2014 May 22:79:77-88

Detection of cyclin D1 mRNA by hybridization sensitive NIC-oligonucleotide probe

Bioorg Med Chem. 2014 May 1;22(9):2613-21

Quantifying the ratio of spliceosome components assembled on pre-mRNA

Methods Mol Biol. 2014:1126:257-69

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2013

Resolving the spatial relationship between intracellular components by dual color super resolution optical fluctuations imaging (SOFI)

Opt Nanoscopy. 2013 Feb 25:2:10.1186/2192-2853-2-2

Single mRNP tracking in living mammalian cells

Methods Mol Biol. 2013:1042:87-99

The nuclear cap-binding complex interacts with the U4/U6·U5 tri-snRNP and promotes spliceosome assembly in mammalian cells

RNA. 2013 Aug;19(8):1054-63

Zooming in on single active genes in living mammalian cells

Histochem Cell Biol. 2013 Jul;140(1):71-9

Detection of mRNA of the cyclin D1 breast cancer marker by a novel duplex-DNA probe

J Med Chem. 2013 Jun 27;56(12):4860-9

The dynamic pathway of nuclear RNA in eukaryotes

Nucleus. 2013 May-Jun;4(3):195-205

Quantifying the transcriptional output of single alleles in single living mammalian cells

Nat Protoc. 2013 Feb;8(2):393-408

Acting on impulse: dissecting the dynamics of the NFAT transcriptional response

Genome Biol. 2013 Jan 24;14(1):102

Nek7 kinase accelerates microtubule dynamic instability

Biochim Biophys Acta. 2013 May;1833(5):1104-13

The P body protein Dcp1a is hyper-phosphorylated during mitosis

PLoS One. 2013;8(1):e49783

Proteinaceous microspheres for targeted RNA delivery prepared by an ultrasonic emulsification method

J Mater Chem B. 2013 Jan 7;1(1):82-90

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2011

Transcription and splicing: when the twain meet

Transcription. 2011 Sep-Oct;2(5):216-20

Measuring the kinetics of mRNA transcription in single living cells

J Vis Exp. 2011 Aug 25:(54):e2898

The dynamics of the alternatively spliced NOL7 gene products and role in nucleolar architecture

Nucleus. 2011 May-Jun;2(3):229-45

Sonochemical synthesis of DNA nanospheres

Chembiochem. 2011 Jul 25;12(11):1678-81

The Dbp5 cycle at the nuclear pore complex during mRNA export I: dbp5 mutants with defects in RNA binding and ATP hydrolysis define key steps for Nup159 and Gle1

Genes Dev. 2011 May 15;25(10):1052-64

Imaging mRNAs in living mammalian cells

Methods Mol Biol. 2011:714:249-63

The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing

PLoS Biol 2011 Jan 11;9(1):e1000573

A transgenic mouse for in vivo detection of endogenous labeled mRNA

Nat Methods 2011 Feb;8(2):165-70.

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2010

Dynamics and kinetics of nucleo-cytoplasmic mRNA export

Wiley Interdiscip Rev R. 2010 Nov-Dec;1(3):388-401

On the right track: following the nucleo-cytoplasmic path of an mRNA

Nucleus. 2010 Nov-Dec;1(6):492-8

Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20

Nucleus 2010 Sep-Oct;1(5):412-21

The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells

J Cell Biol 2010 Oct 4;191(1):75-86

Single-allele analysis of transcription kinetics in living mammalian cells

Nat Methods 2010 Aug;7(8):631-3

Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells

Nat Cell Biol 2010 Jun;12(6):543-52

The life of an mRNA in space and time

J Cell Sci 2010 May 15;123(Pt 10):1761-74

Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells

Nat Cell Biol 2010 Jun;12(6):543-52

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2009

Transient anomalous diffusion of telomeres in the nucleus of mammalian cells

Phys Rev Lett 2009 Jul 3;103(1):018102

Single-molecule dynamics of nuclear mRNA

F1000 Biol Rep 2009 Apr 29:1:29

Incomplete T-cell receptor-beta peptides target the mitochondrion and induce apoptosis

Blood 2009 Apr 9;113(15):3530-41

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2008

Intracellular trafficking and dynamics of P bodies

Prion 2008 Oct-Dec;2(4):131-4

The dynamics of mammalian P body transport, assembly, and disassembly in vivo

Prion 2008 Oct-Dec;2(4):131-4

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2007

In vivo dynamics of RNA polymerase II transcription

Nat Struct Mol Biol 2007 Sep;14(9):796-806

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2006

Gene expression within a dynamic nuclear landscape

EMBO J 2006 Aug 9;25(15):3469-79

Stepwise RNP assembly at the site of H/ACA RNA transcription in human cells

J Cell Biol 2006 Apr 24;173(2):207-18

The living test-tube: imaging of real-time gene expression

Soft Matter 2006 Apr 18;2(5):361-370

Assembling an intermediate filament network by dynamic cotranslation

J Cell Biol 2006 Feb 27;172(5):747-58

2005

RNA localization

J Cell Sci 2005 Sep 15;118(Pt 18):4077-81

Dynamics of transcription and mRNA export

Curr Opin Cell Biol 2005 Jun;17(3):332-9

Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition

Mol Biol Cell 2005 May;16(5):2395-413

2004

Imaging gene expression in single living cells

Nat Rev Mol Cell Biol 2004 Oct;5(10):855-61

Dynamics of single mRNPs in nuclei of living cells

Science 2004 Jun 18;304(5678):1797-800

From silencing to gene expression: real-time analysis in single cells

Cell 2004 Mar 5;116(5):683-98

2003

The mesenchymal stroma negatively regulates B cell lymphopoiesis through the expression of activin A

Ann N Y Acad Sci 2003 May:996:245-60

2002

The role of activin a in regulation of hemopoiesis

Stem Cells 2002;20(6):493-500

PSF and p54(nrb)/NonO--multi-functional nuclear proteins

FEBS Lett 2002 Nov 6;531(2):109-14

The mesenchyme expresses T cell receptor mRNAs: relevance to cell growth control

Oncogene 2002 Mar 27;21(13):2029-36

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2001

Nuclear relocalization of the pre-mRNA splicing factor PSF during apoptosis involves hyperphosphorylation, masking of antigenic epitopes, and changes in protein interactions

Mol Biol Cell 2001 Aug;12(8):2328-40

Reorganization of nuclear factors during myeloid differentiation

J Cell Biochem 2001;81(3):379-92.

2000

Enhanced proteolysis of pre-mRNA splicing factors in myeloid cells

Exp Hematol 2000 Sep;28(9):1029-38

1999

Adhesion molecules involved in the interactions between early T cells and mesenchymal bone marrow stromal cells

Exp Hematol1999 May;27(5):834-44

1997

SA-1, a nuclear protein encoded by one member of a novel gene family: molecular cloning and detection in hemopoietic organs

Gene 1997 Aug 22;195(2):151-9

Nuclear antigen expressed by proliferating cells

Hybridoma 1997 Aug;16(4):325-34

1996

A hematopoietic organ-specific 49-kD nuclear antigen: predominance in immature normal and tumor granulocytes and detection in hematopoietic precursor cells

Blood 1996 Mar 15;87(6):2283-91

1995

The plasmacytoma growth inhibitor restrictin-P is an antagonist of interleukin 6 and interleukin 11. Identification as a stroma-derived activin A

J Biol Chem 1995 Dec 8;270(49):29594-600

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