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papers @ Université de Montréal


35. Rahman S, Zorca C, Traboulsi T, Noutahi E, Krause M, Mader S and Zenklusen D. Single-cell profiling reveals that eRNA accumulation at enhancer-promoter loops is not required to sustain transcription. Nucleic Acid Research. link

34. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 016 Nov 17;167(5):1215-1228.e25 link

33. Bensidoun P, Raymond P, Oeffinger M, Zenklusen D. Imaging single mRNAs to study dynamics of mRNA export in the yeast Saccharomyces cerevisiae. Methods 2016 Jan 16;S1046-2023(16) link

32. Saroufim MA, Bensidoun P, Raymond P, Rahman S, Krause MR, Oeffinger M, Zenklusen D. The nuclear basket mediates perinuclear mRNA scanning in budding yeast. Journal of Cell Biology 2015 Dec 21;211(6):1131-40 link

31. 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 demonstrates an essential role for Mex67p. Journal of Cell Biology 2015, Dec 21;211(6):1121-30 link

30. Hocine S, Vera M, Zenklusen D, Singer RH Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH. Sci Rep. 2015 May 28;5:9934. link

29. Zorca CE, Kim LK, Kim YJ, Krause MR, Zenklusen D, Spilianakis CG, and Flavell RA. Myosin VI regulates gene pairing and transcriptional pause release in T cells. PNAS 2015, published ahead of print March 13. link

28. Rahman S and Zenklusen D. Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae. Methods Mol Biol. 2013;1042:33-46. link

27. Castelnuovo M, Rahman S, Guffanti E, Infantino V, Stutz F and Zenklusen D. Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat Struct Mol Biol. 2013 Jul;20(7):851-8. link

26. Messier, V, Zenklusen D, Mishnick S. A nutrient responsive pathway that determines M-phase timing through control of B cyclin mRNA stability. Cell. 2013 May 23;153(5):1080-93. link

25. Hocine S, Raymond P, Zenklusen D, Chao JA and Singer RH. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nature Methods 2013 Feb;10(2):119-21 link

24. Oeffinger M, Zenklusen D. To the pore and through the pore: A story of mRNA export kinetics. Biochim Biophys Acta. 2012 Jun;1819(6):494-506. PDF

23. Trcek T, Chao J, Larson DR, Park HY, Zenklusen D, Shenoy S, Singer RH. Single-mRNA counting using fluorescent in situ hybridization in budding yeast. Nature Protocols. 2011 Feb 2;(7), 408419. PDF

22. Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene. Science. 2011 Apr 22;332(6028):475-478. Evaluated by the Faculty of 1000. PDF

21. Powrie EA, Zenklusen D, Singer RH. A nucleoporin, Nup60p affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiae. RNA. 2011 Jan;17(1):134-44. Evaluated by the Faculty of 1000. PDF

papers @ Albert Einstein College of Medicine


20. Gandhi S, Zenklusen D, Lionnet T, Singer RH. Transcription of functionally related constitutive genes is not coordinated. Nat Struct Mol Biol. 2011 Jan;18(1):27-34. PDF

19. Zenklusen D and Singer RH. Analyzing mRNA expression using single mRNA resolution fluorescent in situ hybridization. Methods Enzymol. 2010, 470:641-659. PDF

18. Sanford JS, Pettia A, Slavova N, Parsonsa L, Briehof R, Thibergea SY, Zenklusen D, Gandhi S, Larson D, Singer RH and Botstein D. Metabolic Cycling in Single Yeast Cells from Unsynchronized Steady-State Populations Limited on Glucose or Phosphate. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6946-51. Evaluated by the Faculty of 1000. PDF

17. Larson D, Singer RH, Zenklusen D. A Single Molecule View of Gene Expression. Trends Cell Biol. 2009 Nov;19(11):630-7. PDF

16. Oeffinger M, Zenklusen D, Wei KE, Ferguson A, El Hage A, Tollervey D, Singer RH, Chait BT and Rout MP. Rrp17p is a eukaryotic exonuclease required for 5' end processing of pre-60S ribosomal RNA. Mol Cell. 2009 Dec 11; 36 (5): 768-81. PDF

15. Darzacq X, Yao J, Larson D, Bosnac L, deTurris V, Ruda V, Lionnet T, Zenklusen D, Causse S, Tjian R, Singer RH (Janelia Farm Research Consortium on Imaging Transcription). Imaging Transcription in Living Cells. Annual review of biophysics. 2009;38:173-96. PDF

14. Zenklusen D, Larson DR, Singer RH. Single RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol. 2008 Dec;15(12):1263-71. Evaluated by the Faculty of 1000. PDF

13. Wells AL, Condeelis JS, Singer RH, Zenklusen D. Imaging Real-Time Gene Expression in Living Systems. Laboratory Manual for Single Molecule Studies. Cold Spring Harbor Laboratory Press. 2008. ISBN  978-087969775-4.

12. Dong S, Li C, Zenklusen D, Singer RH, Jacobson A, He F. YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA. Mol Cell. 2007 Feb 23;25(4):559-73. PDF

11. Huttelmaier S, Zenklusen D, Lederer M, Dictenberg J, Lorenz M, Meng X, Bassell GJ, Condeelis J, Singer RH. Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1. Nature. 2005;438(7067):512-515. Evaluated by the Faculty of 1000. PDF

10. Niessing D, Huttelmaier S, Zenklusen D, Singer RH, Burley SK. She2p is a novel RNA binding protein with a basic helical hairpin motif. Cell 2004;119(4):491-502. PDF

9. Gu W, Deng Y, Zenklusen D, Singer RH. A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization. Genes Dev. 2004;18(12):1452-65. Evaluated by the Faculty of 1000. PDF

8. Darzacq X, Powrie E, Gu W, Singer RH, Zenklusen D. RNA asymmetric distribution and daughter/mother differentiation in yeast. Curr Opin Microbiol. 2003; 6(6):614-20. PDF

papers @ Université de Lausanne


7. Vinciguerra P, Iglesias N, Camblong J, Zenklusen D, Stutz F. Perinuclear Mlp proteins downregulate gene expression in response to a defect in mRNA export. EMBO J. 2005; 24(4):813-23. PDF

6. Zenklusen D, Vinciguerra P, Wyss J-C, Stutz F. Stable mRNP formation and export requires co-transcriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol Cell Biol. 2002;22(23):8241-53. PDF

5. Hammell C.M, Gross S, Zenklusen D, Heath C.V, Stutz F, Moore C, Cole CN. Coupling of termination, 3' processing and mRNA export. Mol Cell Biol. 2002;22(18):6441-57. PDF

4. Zenklusen D, Stutz F. Nuclear export of mRNA. FEBS Lett. 2001; 498(2-3):150-6. PDF

3. Zenklusen D, Vinciguerra P, Strahm Y, Stutz F. The yeast hnRNP-Like proteins Yra1p and Yra2p participate in mRNA export through interaction with Mex67p. Mol Cell Biol 2001; 21(13):4219-32. PDF

2. Strahm Y, Fahrenkrog B, Zenklusen D, Rychner E, Kantor J, Rosbach M, Stutz F. The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p. EMBO J. 1999; 18(20):5761-77. PDF

papers @ Universität Bern


1. Martin F, Michel F, Zenklusen D, Muller B, Schumperli D. Positive and negative mutant selection in the human histone hairpin-binding protein using the yeast three-hybrid system. Nucleic Acids Res. 2000; 28(7):1594-603. PDF