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Items: 1 to 50 of 69

1.

The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity.

Andrade JM, Dos Santos RF, Chelysheva I, Ignatova Z, Arraiano CM.

EMBO J. 2018 Apr 18. pii: e97631. doi: 10.15252/embj.201797631. [Epub ahead of print]

PMID:
29669858
2.

Examining tRNA 3'-ends in Escherichia coli: teamwork between CCA-adding enzyme, RNase T, and RNase R.

Wellner K, Czech A, Ignatova Z, Betat H, Mörl M.

RNA. 2018 Mar;24(3):361-370. doi: 10.1261/rna.064436.117. Epub 2017 Nov 27.

PMID:
29180590
3.

Growth-Rate Dependent Regulation of tRNA Level and Charging in Bacillus licheniformis.

Ferro I, Liebeton K, Ignatova Z.

J Mol Biol. 2017 Oct 13;429(20):3102-3112. doi: 10.1016/j.jmb.2017.09.010. Epub 2017 Sep 14.

PMID:
28918092
4.

Alteration of protein function by a silent polymorphism linked to tRNA abundance.

Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN, Ignatova Z.

PLoS Biol. 2017 May 16;15(5):e2000779. doi: 10.1371/journal.pbio.2000779. eCollection 2017 May.

5.

Competition for amino acid flux among translation, growth and detoxification in bacteria.

Ferro I, Chelysheva I, Ignatova Z.

RNA Biol. 2017 Mar 15:1-4. doi: 10.1080/15476286.2017.1306174. [Epub ahead of print]

PMID:
28296576
6.

Systematic probing of the bacterial RNA structurome to reveal new functions.

Ignatova Z, Narberhaus F.

Curr Opin Microbiol. 2017 Apr;36:14-19. doi: 10.1016/j.mib.2017.01.003. Epub 2017 Feb 1. Review.

PMID:
28160611
7.
8.

Rewiring host activities for synthetic circuit production: a translation view.

Avcilar-Kucukgoze I, Ignatova Z.

Biotechnol Lett. 2017 Jan;39(1):25-31. doi: 10.1007/s10529-016-2229-6. Epub 2016 Oct 4. Review.

PMID:
27704283
9.

Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli.

Avcilar-Kucukgoze I, Bartholomäus A, Cordero Varela JA, Kaml RF, Neubauer P, Budisa N, Ignatova Z.

Nucleic Acids Res. 2016 Sep 30;44(17):8324-34. doi: 10.1093/nar/gkw697. Epub 2016 Aug 9.

10.

An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting.

Saffert P, Adamla F, Schieweck R, Atkins JF, Ignatova Z.

J Biol Chem. 2016 Aug 26;291(35):18505-13. doi: 10.1074/jbc.M116.744326. Epub 2016 Jul 5.

11.

A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes.

Gorochowski TE, Avcilar-Kucukgoze I, Bovenberg RA, Roubos JA, Ignatova Z.

ACS Synth Biol. 2016 Jul 15;5(7):710-20. doi: 10.1021/acssynbio.6b00040. Epub 2016 May 3.

12.

Bacteria differently regulate mRNA abundance to specifically respond to various stresses.

Bartholomäus A, Fedyunin I, Feist P, Sin C, Zhang G, Valleriani A, Ignatova Z.

Philos Trans A Math Phys Eng Sci. 2016 Mar 13;374(2063). pii: 20150069. doi: 10.1098/rsta.2015.0069.

13.

Probing dimensionality beyond the linear sequence of mRNA.

Del Campo C, Ignatova Z.

Curr Genet. 2016 May;62(2):331-4. doi: 10.1007/s00294-015-0551-5. Epub 2015 Dec 9. Review.

PMID:
26650615
14.

Tuning innate immunity by translation.

Rauscher R, Ignatova Z.

Biochem Soc Trans. 2015 Dec;43(6):1247-52. doi: 10.1042/BST20150166. Review.

PMID:
26614668
15.

Quantifying the 'escapers' among RNA species.

Ferro I, Ignatova Z.

Biochem Soc Trans. 2015 Dec;43(6):1215-20. doi: 10.1042/BST20150158. Review.

PMID:
26614663
16.

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.

Del Campo C, Bartholomäus A, Fedyunin I, Ignatova Z.

PLoS Genet. 2015 Oct 23;11(10):e1005613. doi: 10.1371/journal.pgen.1005613. eCollection 2015 Oct.

17.

Mapping the non-standardized biases of ribosome profiling.

Bartholomäus A, Del Campo C, Ignatova Z.

Biol Chem. 2016 Jan;397(1):23-35. doi: 10.1515/hsz-2015-0197. Review.

PMID:
26351919
19.

Optimization of translation profiles enhances protein expression and solubility.

Hess AK, Saffert P, Liebeton K, Ignatova Z.

PLoS One. 2015 May 12;10(5):e0127039. doi: 10.1371/journal.pone.0127039. eCollection 2015.

20.

A flexible approach to assess fluorescence decay functions in complex energy transfer systems.

Roethlein C, Miettinen MS, Ignatova Z.

BMC Biophys. 2015 Apr 3;8:5. doi: 10.1186/s13628-015-0020-z. eCollection 2015.

21.

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate.

Gorochowski TE, Ignatova Z, Bovenberg RA, Roubos JA.

Nucleic Acids Res. 2015 Mar 31;43(6):3022-32. doi: 10.1093/nar/gkv199. Epub 2015 Mar 12.

22.

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease.

Kirchner S, Ignatova Z.

Nat Rev Genet. 2015 Feb;16(2):98-112. doi: 10.1038/nrg3861. Epub 2014 Dec 23. Review.

PMID:
25534324
23.

Architecture of polyglutamine-containing fibrils from time-resolved fluorescence decay.

Röthlein C, Miettinen MS, Borwankar T, Bürger J, Mielke T, Kumke MU, Ignatova Z.

J Biol Chem. 2014 Sep 26;289(39):26817-28. doi: 10.1074/jbc.M114.581991. Epub 2014 Aug 4.

24.

Systematic identification of tRNAome and its dynamics in Lactococcus lactis.

Puri P, Wetzel C, Saffert P, Gaston KW, Russell SP, Cordero Varela JA, van der Vlies P, Zhang G, Limbach PA, Ignatova Z, Poolman B.

Mol Microbiol. 2014 Sep;93(5):944-56. doi: 10.1111/mmi.12710. Epub 2014 Aug 6.

25.

Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains-but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers.

Miettinen MS, Monticelli L, Nedumpully-Govindan P, Knecht V, Ignatova Z.

Biophys J. 2014 Apr 15;106(8):1721-8. doi: 10.1016/j.bpj.2014.02.027.

26.

GPER functions as a tumor suppressor in triple-negative breast cancer cells.

Weißenborn C, Ignatov T, Ochel HJ, Costa SD, Zenclussen AC, Ignatova Z, Ignatov A.

J Cancer Res Clin Oncol. 2014 May;140(5):713-23. doi: 10.1007/s00432-014-1620-8. Epub 2014 Feb 20.

PMID:
24553912
27.

Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes.

Lukoszek R, Mueller-Roeber B, Ignatova Z.

FEBS Lett. 2013 Nov 15;587(22):3692-5. doi: 10.1016/j.febslet.2013.09.033. Epub 2013 Oct 7.

28.

Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress.

Czech A, Wende S, Mörl M, Pan T, Ignatova Z.

PLoS Genet. 2013 Aug;9(8):e1003767. doi: 10.1371/journal.pgen.1003767. Epub 2013 Aug 29.

29.

Efficient translation initiation dictates codon usage at gene start.

Bentele K, Saffert P, Rauscher R, Ignatova Z, Blüthgen N.

Mol Syst Biol. 2013 Jun 18;9:675. doi: 10.1038/msb.2013.32.

30.

Depletion of cognate charged transfer RNA causes translational frameshifting within the expanded CAG stretch in huntingtin.

Girstmair H, Saffert P, Rode S, Czech A, Holland G, Bannert N, Ignatova Z.

Cell Rep. 2013 Jan 31;3(1):148-59. doi: 10.1016/j.celrep.2012.12.019. Epub 2013 Jan 24.

31.

tRNA concentration fine tunes protein solubility.

Fedyunin I, Lehnhardt L, Böhmer N, Kaufmann P, Zhang G, Ignatova Z.

FEBS Lett. 2012 Sep 21;586(19):3336-40. doi: 10.1016/j.febslet.2012.07.012. Epub 2012 Jul 20.

32.

Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations.

Miettinen MS, Knecht V, Monticelli L, Ignatova Z.

J Phys Chem B. 2012 Aug 30;116(34):10259-65. doi: 10.1021/jp305065c. Epub 2012 Aug 16.

PMID:
22770401
33.

Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis.

Varshney NK, Kumar RS, Ignatova Z, Prabhune A, Pundle A, Dodson E, Suresh CG.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Mar 1;68(Pt 3):273-7. doi: 10.1107/S1744309111053930. Epub 2012 Feb 15.

34.

FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.

Zhang G, Fedyunin I, Kirchner S, Xiao C, Valleriani A, Ignatova Z.

Nucleic Acids Res. 2012 Jun;40(11):e83. doi: 10.1093/nar/gks196. Epub 2012 Feb 29.

35.

Polyglutamine expansion alters the dynamics and molecular architecture of aggregates in dentatorubropallidoluysian atrophy.

Hinz J, Lehnhardt L, Zakrzewski S, Zhang G, Ignatova Z.

J Biol Chem. 2012 Jan 13;287(3):2068-78. doi: 10.1074/jbc.M111.318915. Epub 2011 Dec 1.

36.

Length-dependent translation of messenger RNA by ribosomes.

Valleriani A, Zhang G, Nagar A, Ignatova Z, Lipowsky R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Apr;83(4 Pt 1):042903. Epub 2011 Apr 21.

PMID:
21599226
37.

Natural osmolytes remodel the aggregation pathway of mutant huntingtin exon 1.

Borwankar T, Röthlein C, Zhang G, Techen A, Dosche C, Ignatova Z.

Biochemistry. 2011 Mar 29;50(12):2048-60. doi: 10.1021/bi1018368. Epub 2011 Feb 20.

PMID:
21332223
38.

Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

Zhang G, Lukoszek R, Mueller-Roeber B, Ignatova Z.

Nucleic Acids Res. 2011 Apr;39(8):3331-9. doi: 10.1093/nar/gkq1257. Epub 2010 Dec 7.

39.

Folding at the birth of the nascent chain: coordinating translation with co-translational folding.

Zhang G, Ignatova Z.

Curr Opin Struct Biol. 2011 Feb;21(1):25-31. doi: 10.1016/j.sbi.2010.10.008. Epub 2010 Nov 24. Review.

PMID:
21111607
40.

Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations.

Czech A, Fedyunin I, Zhang G, Ignatova Z.

Mol Biosyst. 2010 Oct;6(10):1767-72. doi: 10.1039/c004796c. Epub 2010 Jul 9. Review.

PMID:
20617253
41.

Global and local depletion of ternary complex limits translational elongation.

Zhang G, Fedyunin I, Miekley O, Valleriani A, Moura A, Ignatova Z.

Nucleic Acids Res. 2010 Aug;38(14):4778-87. doi: 10.1093/nar/gkq196. Epub 2010 Mar 31.

42.

Improved A. faecalis penicillin amidase mutant retains the thermodynamic and pH stability of the wild type enzyme.

Yuryev R, Kasche V, Ignatova Z, Galunsky B.

Protein J. 2010 Apr;29(3):181-7. doi: 10.1007/s10930-010-9238-4.

PMID:
20224955
43.

Exploiting the features of the finite state automata for biomolecular computing.

Martínez-Pérez IM, Ignatova Z, Zimmermann KH.

Recent Pat DNA Gene Seq. 2009;3(2):130-8. Review.

PMID:
19519583
44.

Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis.

Zhang G, Ignatova Z.

PLoS One. 2009;4(4):e5036. doi: 10.1371/journal.pone.0005036. Epub 2009 Apr 3.

45.

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.

Zhang G, Hubalewska M, Ignatova Z.

Nat Struct Mol Biol. 2009 Mar;16(3):274-80. doi: 10.1038/nsmb.1554. Epub 2009 Feb 8.

PMID:
19198590
46.

A method for direct measurement of protein stability in vivo.

Ignatova Z, Gierasch LM.

Methods Mol Biol. 2009;490:165-78. doi: 10.1007/978-1-59745-367-7_7.

47.

An autonomous DNA model for finite state automata.

Martinez-Perez IM, Zimmermann KH, Ignatova Z.

Int J Bioinform Res Appl. 2009;5(1):81-96.

PMID:
19136366
48.

Chapter 3: A fluorescent window into protein folding and aggregation in cells.

Ignatova Z, Gierasch LM.

Methods Cell Biol. 2008;89:59-70. doi: 10.1016/S0091-679X(08)00603-1.

49.

Orthogonal cross-seeding: an approach to explore protein aggregates in living cells.

Hinz J, Gierasch LM, Ignatova Z.

Biochemistry. 2008 Apr 8;47(14):4196-200. doi: 10.1021/bi800002j. Epub 2008 Mar 11.

50.

Biomolecular autonomous solution of the Hamiltonian path problem via hairpin formation.

Martinez-Perez IM, Zhang G, Ignatova Z, Zimmermann KH.

Int J Bioinform Res Appl. 2005;1(4):389-98.

PMID:
18048143

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