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Items: 26

1.

Discovering Yersinia-Host Interactions by Tissue Dual RNA-Seq.

Kusmierek M, Heroven AK, Beckstette M, Nuss AM, Dersch P.

Methods Mol Biol. 2019;2010:99-116. doi: 10.1007/978-1-4939-9541-7_8.

PMID:
31177434
2.

Comparative Transcriptomic Profiling of Yersinia enterocolitica O:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation.

Schmühl C, Beckstette M, Heroven AK, Bunk B, Spröer C, McNally A, Overmann J, Dersch P.

mSystems. 2019 Apr 23;4(2). pii: e00239-18. doi: 10.1128/mSystems.00239-18. eCollection 2019 Mar-Apr.

3.

Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli.

Berndt V, Beckstette M, Volk M, Dersch P, Brönstrup M.

Sci Rep. 2019 Jan 15;9(1):138. doi: 10.1038/s41598-018-36932-w.

4.

Iron Regulation in Clostridioides difficile.

Berges M, Michel AM, Lassek C, Nuss AM, Beckstette M, Dersch P, Riedel K, Sievers S, Becher D, Otto A, Maaß S, Rohde M, Eckweiler D, Borrero-de Acuña JM, Jahn M, Neumann-Schaal M, Jahn D.

Front Microbiol. 2018 Dec 24;9:3183. doi: 10.3389/fmicb.2018.03183. eCollection 2018.

5.

Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes.

Pezoldt J, Pasztoi M, Zou M, Wiechers C, Beckstette M, Thierry GR, Vafadarnejad E, Floess S, Arampatzi P, Buettner M, Schweer J, Fleissner D, Vital M, Pieper DH, Basic M, Dersch P, Strowig T, Hornef M, Bleich A, Bode U, Pabst O, Bajénoff M, Saliba AE, Huehn J.

Nat Commun. 2018 Sep 25;9(1):3903. doi: 10.1038/s41467-018-06423-7.

6.

Tracking gene expression and oxidative damage of O2-stressed Clostridioides difficile by a multi-omics approach.

Neumann-Schaal M, Metzendorf NG, Troitzsch D, Nuss AM, Hofmann JD, Beckstette M, Dersch P, Otto A, Sievers S.

Anaerobe. 2018 Oct;53:94-107. doi: 10.1016/j.anaerobe.2018.05.018. Epub 2018 May 31.

PMID:
29859941
7.

Intact interleukin-10 receptor signaling protects from hippocampal damage elicited by experimental neurotropic virus infection of SJL mice.

Uhde AK, Ciurkiewicz M, Herder V, Khan MA, Hensel N, Claus P, Beckstette M, Teich R, Floess S, Baumgärtner W, Jung K, Huehn J, Beineke A.

Sci Rep. 2018 Apr 17;8(1):6106. doi: 10.1038/s41598-018-24378-z.

8.

Loss of CNFY toxin-induced inflammation drives Yersinia pseudotuberculosis into persistency.

Heine W, Beckstette M, Heroven AK, Thiemann S, Heise U, Nuss AM, Pisano F, Strowig T, Dersch P.

PLoS Pathog. 2018 Feb 1;14(2):e1006858. doi: 10.1371/journal.ppat.1006858. eCollection 2018 Feb.

9.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

10.

Mesenteric lymph node stromal cell-derived extracellular vesicles contribute to peripheral de novo induction of Foxp3+ regulatory T cells.

Pasztoi M, Pezoldt J, Beckstette M, Lipps C, Wirth D, Rohde M, Paloczi K, Buzas EI, Huehn J.

Eur J Immunol. 2017 Dec;47(12):2142-2152. doi: 10.1002/eji.201746960. Epub 2017 Sep 15.

11.

Alloantigen-Induced Regulatory T Cells Generated in Presence of Vitamin C Display Enhanced Stability of Foxp3 Expression and Promote Skin Allograft Acceptance.

Nikolouli E, Hardtke-Wolenski M, Hapke M, Beckstette M, Geffers R, Floess S, Jaeckel E, Huehn J.

Front Immunol. 2017 Jun 28;8:748. doi: 10.3389/fimmu.2017.00748. eCollection 2017.

12.

Unique properties of thymic antigen-presenting cells promote epigenetic imprinting of alloantigen-specific regulatory T cells.

Garg G, Nikolouli E, Hardtke-Wolenski M, Toker A, Ohkura N, Beckstette M, Miyao T, Geffers R, Floess S, Gerdes N, Lutgens E, Osterloh A, Hori S, Sakaguchi S, Jaeckel E, Huehn J.

Oncotarget. 2017 May 30;8(22):35542-35557. doi: 10.18632/oncotarget.16221.

13.

Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes.

Nuss AM, Beckstette M, Pimenova M, Schmühl C, Opitz W, Pisano F, Heroven AK, Dersch P.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E791-E800. doi: 10.1073/pnas.1613405114. Epub 2017 Jan 17.

14.

Transcriptomic and Phenotypic Analysis Reveals New Functions for the Tat Pathway in Yersinia pseudotuberculosis.

Avican U, Beckstette M, Heroven AK, Lavander M, Dersch P, Forsberg Å.

J Bacteriol. 2016 Sep 22;198(20):2876-86. doi: 10.1128/JB.00352-16. Print 2016 Oct 15.

15.

Foxp3(+) T cells expressing RORγt represent a stable regulatory T-cell effector lineage with enhanced suppressive capacity during intestinal inflammation.

Yang BH, Hagemann S, Mamareli P, Lauer U, Hoffmann U, Beckstette M, Föhse L, Prinz I, Pezoldt J, Suerbaum S, Sparwasser T, Hamann A, Floess S, Huehn J, Lochner M.

Mucosal Immunol. 2016 Mar;9(2):444-57. doi: 10.1038/mi.2015.74. Epub 2015 Aug 26.

PMID:
26307665
16.

Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs.

Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M, Dersch P.

PLoS Genet. 2015 Mar 27;11(3):e1005087. doi: 10.1371/journal.pgen.1005087. eCollection 2015 Mar.

17.

Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.

Avican K, Fahlgren A, Huss M, Heroven AK, Beckstette M, Dersch P, Fällman M.

PLoS Pathog. 2015 Jan 15;11(1):e1004600. doi: 10.1371/journal.ppat.1004600. eCollection 2015 Jan. Erratum in: PLoS Pathog. 2015 Mar;11(3):e1004769.

18.

An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome.

Abdollahpour H, Alawi M, Kortüm F, Beckstette M, Seemanova E, Komárek V, Rosenberger G, Kutsche K.

Eur J Hum Genet. 2015 Feb;23(2):256-9. doi: 10.1038/ejhg.2014.73. Epub 2014 Apr 30.

19.

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.

Meyer F, Kurtz S, Beckstette M.

BMC Bioinformatics. 2013 Jul 17;14:226. doi: 10.1186/1471-2105-14-226.

20.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.

Alawi M, Kurtz S, Beckstette M.

J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.

PMID:
21690655
21.

Structator: fast index-based search for RNA sequence-structure patterns.

Meyer F, Kurtz S, Backofen R, Will S, Beckstette M.

BMC Bioinformatics. 2011 May 27;12:214. doi: 10.1186/1471-2105-12-214.

22.

Significant speedup of database searches with HMMs by search space reduction with PSSM family models.

Beckstette M, Homann R, Giegerich R, Kurtz S.

Bioinformatics. 2009 Dec 15;25(24):3251-8. doi: 10.1093/bioinformatics/btp593. Epub 2009 Oct 14.

23.

Lightweight comparison of RNAs based on exact sequence-structure matches.

Heyne S, Will S, Beckstette M, Backofen R.

Bioinformatics. 2009 Aug 15;25(16):2095-102. doi: 10.1093/bioinformatics/btp065. Epub 2009 Feb 2.

24.

Fast index based algorithms and software for matching position specific scoring matrices.

Beckstette M, Homann R, Giegerich R, Kurtz S.

BMC Bioinformatics. 2006 Aug 24;7:389.

25.

XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis.

Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR.

BMC Genomics. 2005 Sep 14;6:123.

26.

The maize Single myb histone 1 gene, Smh1, belongs to a novel gene family and encodes a protein that binds telomere DNA repeats in vitro.

Marian CO, Bordoli SJ, Goltz M, Santarella RA, Jackson LP, Danilevskaya O, Beckstette M, Meeley R, Bass HW.

Plant Physiol. 2003 Nov;133(3):1336-50. Epub 2003 Oct 23.

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