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Items: 1 to 50 of 52

1.

Long-term expanding human airway organoids for disease modeling.

Sachs N, Papaspyropoulos A, Zomer-van Ommen DD, Heo I, Böttinger L, Klay D, Weeber F, Huelsz-Prince G, Iakobachvili N, Amatngalim GD, de Ligt J, van Hoeck A, Proost N, Viveen MC, Lyubimova A, Teeven L, Derakhshan S, Korving J, Begthel H, Dekkers JF, Kumawat K, Ramos E, van Oosterhout MF, Offerhaus GJ, Wiener DJ, Olimpio EP, Dijkstra KK, Smit EF, van der Linden M, Jaksani S, van de Ven M, Jonkers J, Rios AC, Voest EE, van Moorsel CH, van der Ent CK, Cuppen E, van Oudenaarden A, Coenjaerts FE, Meyaard L, Bont LJ, Peters PJ, Tans SJ, van Zon JS, Boj SF, Vries RG, Beekman JM, Clevers H.

EMBO J. 2019 Feb 15;38(4). pii: e100300. doi: 10.15252/embj.2018100300. Epub 2019 Jan 14.

2.

Sign epistasis caused by hierarchy within signalling cascades.

Nghe P, Kogenaru M, Tans SJ.

Nat Commun. 2018 Apr 13;9(1):1451. doi: 10.1038/s41467-018-03644-8.

3.

Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells.

Wehrens M, Ershov D, Rozendaal R, Walker N, Schultz D, Kishony R, Levin PA, Tans SJ.

Curr Biol. 2018 Mar 19;28(6):972-979.e5. doi: 10.1016/j.cub.2018.02.006. Epub 2018 Mar 1.

PMID:
29502951
4.

Information-theoretic analysis of the directional influence between cellular processes.

Lahiri S, Nghe P, Tans SJ, Rosinberg ML, Lacoste D.

PLoS One. 2017 Nov 9;12(11):e0187431. doi: 10.1371/journal.pone.0187431. eCollection 2017.

5.

Protein Tethering for Folding Studies.

Moayed F, van Wijk RJ, Minde DP, Tans SJ.

Methods Mol Biol. 2018;1665:43-51. doi: 10.1007/978-1-4939-7271-5_3.

PMID:
28940063
6.

Protein Folding Mediated by Trigger Factor and Hsp70: New Insights from Single-Molecule Approaches.

Wruck F, Avellaneda MJ, Koers EJ, Minde DP, Mayer MP, Kramer G, Mashaghi A, Tans SJ.

J Mol Biol. 2018 Feb 16;430(4):438-449. doi: 10.1016/j.jmb.2017.09.004. Epub 2017 Sep 11. Review.

PMID:
28911846
7.

Topology of polymer chains under nanoscale confinement.

Satarifard V, Heidari M, Mashaghi S, Tans SJ, Ejtehadi MR, Mashaghi A.

Nanoscale. 2017 Aug 24;9(33):12170-12177. doi: 10.1039/c7nr04220e.

PMID:
28805849
8.

Topology of internally constrained polymer chains.

Heidari M, Satarifard V, Tans SJ, Ejtehadi MR, Mashaghi S, Mashaghi A.

Phys Chem Chem Phys. 2017 Jul 19;19(28):18389-18393. doi: 10.1039/c7cp02145c.

PMID:
28678226
9.

The chaperone toolbox at the single-molecule level: From clamping to confining.

Avellaneda MJ, Koers EJ, Naqvi MM, Tans SJ.

Protein Sci. 2017 Jul;26(7):1291-1302. doi: 10.1002/pro.3161. Epub 2017 Apr 20. Review.

10.

Step by Step, Cell by Cell: Quantification of the Bacterial Cell Cycle.

Osella M, Tans SJ, Cosentino Lagomarsino M.

Trends Microbiol. 2017 Apr;25(4):250-256. doi: 10.1016/j.tim.2016.12.005. Epub 2017 Jan 13. Review.

PMID:
28094092
11.

Alternative modes of client binding enable functional plasticity of Hsp70.

Mashaghi A, Bezrukavnikov S, Minde DP, Wentink AS, Kityk R, Zachmann-Brand B, Mayer MP, Kramer G, Bukau B, Tans SJ.

Nature. 2016 Nov 17;539(7629):448-451. doi: 10.1038/nature20137. Epub 2016 Oct 26.

PMID:
27783598
12.

Single-Cell Analysis of the Dps Response to Oxidative Stress.

De Martino M, Ershov D, van den Berg PJ, Tans SJ, Meyer AS.

J Bacteriol. 2016 May 13;198(11):1662-1674. doi: 10.1128/JB.00239-16. Print 2016 Jun 1.

13.

Individuality and universality in the growth-division laws of single E. coli cells.

Kennard AS, Osella M, Javer A, Grilli J, Nghe P, Tans SJ, Cicuta P, Cosentino Lagomarsino M.

Phys Rev E. 2016 Jan;93(1):012408. doi: 10.1103/PhysRevE.93.012408. Epub 2016 Jan 19.

PMID:
26871102
14.

Generation and filtering of gene expression noise by the bacterial cell cycle.

Walker N, Nghe P, Tans SJ.

BMC Biol. 2016 Feb 11;14:11. doi: 10.1186/s12915-016-0231-z.

15.

Stochasticity and homeostasis in the E. coli replication and division cycle.

Adiciptaningrum A, Osella M, Moolman MC, Cosentino Lagomarsino M, Tans SJ.

Sci Rep. 2015 Dec 16;5:18261. doi: 10.1038/srep18261.

16.

Breaking evolutionary constraint with a tradeoff ratchet.

de Vos MG, Dawid A, Sunderlikova V, Tans SJ.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14906-11. doi: 10.1073/pnas.1510282112. Epub 2015 Nov 13.

17.

High-throughput 3D tracking of bacteria on a standard phase contrast microscope.

Taute KM, Gude S, Tans SJ, Shimizu TS.

Nat Commun. 2015 Nov 2;6:8776. doi: 10.1038/ncomms9776.

18.

The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins.

Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG.

PLoS Comput Biol. 2015 Oct 29;11(10):e1004444. doi: 10.1371/journal.pcbi.1004444. eCollection 2015 Oct.

19.

Non-monotonic dynamics and crosstalk in signaling pathways and their implications for pharmacology.

van Wijk R, Tans SJ, ten Wolde PR, Mashaghi A.

Sci Rep. 2015 Jun 18;5:11376. doi: 10.1038/srep11376.

20.

[Random fluctuations, metabolism and growth at the single-cell level].

Nghe P, Boulineau S, Tans SJ.

Med Sci (Paris). 2015 Mar;31(3):233-5. doi: 10.1051/medsci/20153103002. Epub 2015 Apr 8. French. No abstract available.

21.

Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

Mugler A, Tans SJ, Mashaghi A.

Phys Chem Chem Phys. 2014 Nov 7;16(41):22537-44. doi: 10.1039/c4cp03402c.

PMID:
25228051
22.

Stochasticity of metabolism and growth at the single-cell level.

Kiviet DJ, Nghe P, Walker N, Boulineau S, Sunderlikova V, Tans SJ.

Nature. 2014 Oct 16;514(7522):376-9. doi: 10.1038/nature13582. Epub 2014 Sep 3.

PMID:
25186725
23.

Circuit topology of proteins and nucleic acids.

Mashaghi A, van Wijk RJ, Tans SJ.

Structure. 2014 Sep 2;22(9):1227-1237. doi: 10.1016/j.str.2014.06.015. Epub 2014 Aug 7. Review.

24.

Misfolding of luciferase at the single-molecule level.

Mashaghi A, Mashaghi S, Tans SJ.

Angew Chem Int Ed Engl. 2014 Sep 22;53(39):10390-3. doi: 10.1002/anie.201405566. Epub 2014 Aug 14.

PMID:
25124399
25.

Trehalose facilitates DNA melting: a single-molecule optical tweezers study.

Bezrukavnikov S, Mashaghi A, van Wijk RJ, Gu C, Yang LJ, Gao YQ, Tans SJ.

Soft Matter. 2014 Oct 7;10(37):7269-77. doi: 10.1039/c4sm01532k.

PMID:
25096217
26.

Evolutionary constraints in variable environments, from proteins to networks.

Taute KM, Gude S, Nghe P, Tans SJ.

Trends Genet. 2014 May;30(5):192-8. doi: 10.1016/j.tig.2014.04.003. Epub 2014 Apr 26. Review.

PMID:
24780086
27.
28.

Microfabricated polyacrylamide devices for the controlled culture of growing cells and developing organisms.

Nghe P, Boulineau S, Gude S, Recouvreux P, van Zon JS, Tans SJ.

PLoS One. 2013 Sep 24;8(9):e75537. doi: 10.1371/journal.pone.0075537. eCollection 2013.

29.

Chaperone action at the single-molecule level.

Mashaghi A, Kramer G, Lamb DC, Mayer MP, Tans SJ.

Chem Rev. 2014 Jan 8;114(1):660-76. doi: 10.1021/cr400326k. Epub 2013 Sep 3. Review. No abstract available.

PMID:
24001118
30.

Reshaping of the conformational search of a protein by the chaperone trigger factor.

Mashaghi A, Kramer G, Bechtluft P, Zachmann-Brand B, Driessen AJ, Bukau B, Tans SJ.

Nature. 2013 Aug 1;500(7460):98-101. doi: 10.1038/nature12293. Epub 2013 Jul 7.

PMID:
23831649
31.

Environmental dependence of genetic constraint.

de Vos MG, Poelwijk FJ, Battich N, Ndika JD, Tans SJ.

PLoS Genet. 2013 Jun;9(6):e1003580. doi: 10.1371/journal.pgen.1003580. Epub 2013 Jun 27.

32.

Optimality in evolution: new insights from synthetic biology.

de Vos MG, Poelwijk FJ, Tans SJ.

Curr Opin Biotechnol. 2013 Aug;24(4):797-802. doi: 10.1016/j.copbio.2013.04.008. Epub 2013 May 16. Review.

PMID:
23684729
33.

Single-cell dynamics reveals sustained growth during diauxic shifts.

Boulineau S, Tostevin F, Kiviet DJ, ten Wolde PR, Nghe P, Tans SJ.

PLoS One. 2013 Apr 30;8(4):e61686. doi: 10.1371/journal.pone.0061686. Print 2013.

34.

Hydrophobic collapse of trigger factor monomer in solution.

Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG.

PLoS One. 2013;8(4):e59683. doi: 10.1371/journal.pone.0059683. Epub 2013 Apr 2.

35.

A polypeptide-DNA hybrid with selective linking capability applied to single molecule nano-mechanical measurements using optical tweezers.

Moayed F, Mashaghi A, Tans SJ.

PLoS One. 2013;8(1):e54440. doi: 10.1371/journal.pone.0054440. Epub 2013 Jan 15.

36.

Noise reduction by signal combination in Fourier space applied to drift correction in optical tweezers.

Mashaghi A, Vach PJ, Tans SJ.

Rev Sci Instrum. 2011 Nov;82(11):115103. doi: 10.1063/1.3658825.

PMID:
22129009
37.

Optimality and evolution of transcriptionally regulated gene expression.

Poelwijk FJ, Heyning PD, de Vos MG, Kiviet DJ, Tans SJ.

BMC Syst Biol. 2011 Aug 16;5:128. doi: 10.1186/1752-0509-5-128.

38.

Tradeoffs and optimality in the evolution of gene regulation.

Poelwijk FJ, de Vos MG, Tans SJ.

Cell. 2011 Aug 5;146(3):462-70. doi: 10.1016/j.cell.2011.06.035. Epub 2011 Jul 28.

39.

Calcium modulates force sensing by the von Willebrand factor A2 domain.

Jakobi AJ, Mashaghi A, Tans SJ, Huizinga EG.

Nat Commun. 2011 Jul 12;2:385. doi: 10.1038/ncomms1385.

40.

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes.

Poelwijk FJ, Tănase-Nicola S, Kiviet DJ, Tans SJ.

J Theor Biol. 2011 Mar 7;272(1):141-4. doi: 10.1016/j.jtbi.2010.12.015. Epub 2010 Dec 16.

PMID:
21167837
41.

Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape.

Dawid A, Kiviet DJ, Kogenaru M, de Vos M, Tans SJ.

Chaos. 2010 Jun;20(2):026105. doi: 10.1063/1.3453602.

PMID:
20590334
42.

SecB--a chaperone dedicated to protein translocation.

Bechtluft P, Nouwen N, Tans SJ, Driessen AJ.

Mol Biosyst. 2010 Apr;6(4):620-7. doi: 10.1039/b915435c. Epub 2009 Oct 19. Review.

PMID:
20237639
43.

Tight hydrophobic contacts with the SecB chaperone prevent folding of substrate proteins.

Bechtluft P, Kedrov A, Slotboom DJ, Nouwen N, Tans SJ, Driessen AJ.

Biochemistry. 2010 Mar 23;49(11):2380-8. doi: 10.1021/bi902051e.

PMID:
20146530
44.

Revealing evolutionary pathways by fitness landscape reconstruction.

Kogenaru M, de Vos MG, Tans SJ.

Crit Rev Biochem Mol Biol. 2009 Jul-Aug;44(4):169-74. doi: 10.1080/10409230903039658. Review.

PMID:
19552615
45.

Internal dynamics of supercoiled DNA molecules.

Kalkbrenner T, Arnold A, Tans SJ.

Biophys J. 2009 Jun 17;96(12):4951-5. doi: 10.1016/j.bpj.2009.03.056.

46.

Direct observation of type 1 fimbrial switching.

Adiciptaningrum AM, Blomfield IC, Tans SJ.

EMBO Rep. 2009 May;10(5):527-32. doi: 10.1038/embor.2009.25. Epub 2009 Mar 27.

47.

Direct observation of chaperone-induced changes in a protein folding pathway.

Bechtluft P, van Leeuwen RG, Tyreman M, Tomkiewicz D, Nouwen N, Tepper HL, Driessen AJ, Tans SJ.

Science. 2007 Nov 30;318(5855):1458-61.

48.

Empirical fitness landscapes reveal accessible evolutionary paths.

Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ.

Nature. 2007 Jan 25;445(7126):383-6.

PMID:
17251971
49.

Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutation data.

Poelwijk FJ, Kiviet DJ, Tans SJ.

PLoS Comput Biol. 2006 May;2(5):e58. Epub 2006 May 26.

50.

The bacteriophage straight phi29 portal motor can package DNA against a large internal force.

Smith DE, Tans SJ, Smith SB, Grimes S, Anderson DL, Bustamante C.

Nature. 2001 Oct 18;413(6857):748-52.

PMID:
11607035

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