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The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification.

Miess H, Arlt P, Apel AK, Weber T, Nieselt K, Hanssen F, Czemmel S, Nahnsen S, Gross H.

Microbiol Resour Announc. 2019 Nov 7;8(45). pii: e01120-19. doi: 10.1128/MRA.01120-19.


Efficient merging of genome profile alignments.

Hennig A, Nieselt K.

Bioinformatics. 2019 Jul 15;35(14):i71-i80. doi: 10.1093/bioinformatics/btz377.


Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds.

Bufe T, Hennig A, Klumpp J, Weiss A, Nieselt K, Schmidt H.

BMC Microbiol. 2019 Sep 5;19(1):212. doi: 10.1186/s12866-019-1578-4.


MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO2 levels.

Fan SH, Ebner P, Reichert S, Hertlein T, Zabel S, Lankapalli AK, Nieselt K, Ohlsen K, Götz F.

Nat Commun. 2019 Aug 9;10(1):3627. doi: 10.1038/s41467-019-11547-5.


Exploiting orthology and de novo transcriptome assembly to refine target sequence information.

Söllner JF, Leparc G, Zwick M, Schönberger T, Hildebrandt T, Nieselt K, Simon E.

BMC Med Genomics. 2019 May 23;12(1):69. doi: 10.1186/s12920-019-0524-5.


Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing.

Denyer T, Ma X, Klesen S, Scacchi E, Nieselt K, Timmermans MCP.

Dev Cell. 2019 Mar 25;48(6):840-852.e5. doi: 10.1016/j.devcel.2019.02.022.


Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient.

Schön ME, Nieselt K, Garnica S.

PLoS One. 2018 Dec 5;13(12):e0208493. doi: 10.1371/journal.pone.0208493. eCollection 2018.


Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue.

Knauf S, Gogarten JF, Schuenemann VJ, De Nys HM, Düx A, Strouhal M, Mikalová L, Bos KI, Armstrong R, Batamuzi EK, Chuma IS, Davoust B, Diatta G, Fyumagwa RD, Kazwala RR, Keyyu JD, Lejora IAV, Levasseur A, Liu H, Mayhew MA, Mediannikov O, Raoult D, Wittig RM, Roos C, Leendertz FH, Šmajs D, Nieselt K, Krause J, Calvignac-Spencer S.

Emerg Microbes Infect. 2018 Sep 19;7(1):157. doi: 10.1038/s41426-018-0156-4. No abstract available.


Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme.

Grillová L, Bawa T, Mikalová L, Gayet-Ageron A, Nieselt K, Strouhal M, Sednaoui P, Ferry T, Cavassini M, Lautenschlager S, Dutly F, Pla-Díaz M, Krützen M, González-Candelas F, Bagheri HC, Šmajs D, Arora N, Bosshard PP.

PLoS One. 2018 Jul 30;13(7):e0200773. doi: 10.1371/journal.pone.0200773. eCollection 2018.


DACCOR-Detection, characterization, and reconstruction of repetitive regions in bacterial genomes.

Seitz A, Hanssen F, Nieselt K.

PeerJ. 2018 May 29;6:e4742. doi: 10.7717/peerj.4742. eCollection 2018.


Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Schuenemann VJ, Avanzi C, Krause-Kyora B, Seitz A, Herbig A, Inskip S, Bonazzi M, Reiter E, Urban C, Dangvard Pedersen D, Taylor GM, Singh P, Stewart GR, Velemínský P, Likovsky J, Marcsik A, Molnár E, Pálfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K, Cole ST, Krause J.

PLoS Pathog. 2018 May 10;14(5):e1006997. doi: 10.1371/journal.ppat.1006997. eCollection 2018 May.


Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche.

Peltzer A, Mittnik A, Wang CC, Begg T, Posth C, Nieselt K, Krause J.

Sci Rep. 2018 Feb 1;8(1):2115. doi: 10.1038/s41598-018-20180-z.


Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes.

Strouhal M, Oppelt J, Mikalová L, Arora N, Nieselt K, González-Candelas F, Šmajs D.

BMC Res Notes. 2018 Jan 11;11(1):16. doi: 10.1186/s13104-017-3106-7.


AureoWiki ̵ The repository of the Staphylococcus aureus research and annotation community.

Fuchs S, Mehlan H, Bernhardt J, Hennig A, Michalik S, Surmann K, Pané-Farré J, Giese A, Weiss S, Backert L, Herbig A, Nieselt K, Hecker M, Völker U, Mäder U.

Int J Med Microbiol. 2018 Aug;308(6):558-568. doi: 10.1016/j.ijmm.2017.11.011. Epub 2017 Nov 24.


A15 Rapid radiation of treponema pallidum pertenue in wild non-human primates.

Düx A, Schuenemann VJ, Gogarten JF, De Nys HM, Nieselt K, Mayhew MA, Leendertz FH, Calvignac-Spencer S, Krause J.

Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.014. doi: 10.1093/ve/vew036.014. eCollection 2017 Mar. No abstract available.


dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome.

Bauer JS, Fillinger S, Förstner K, Herbig A, Jones AC, Flinspach K, Sharma C, Gross H, Nieselt K, Apel AK.

RNA Biol. 2017 Nov 2;14(11):1617-1626. doi: 10.1080/15476286.2017.1341020. Epub 2017 Jul 31.


Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods.

Schuenemann VJ, Peltzer A, Welte B, van Pelt WP, Molak M, Wang CC, Furtwängler A, Urban C, Reiter E, Nieselt K, Teßmann B, Francken M, Harvati K, Haak W, Schiffels S, Krause J.

Nat Commun. 2017 May 30;8:15694. doi: 10.1038/ncomms15694.


Improving ancient DNA genome assembly.

Seitz A, Nieselt K.

PeerJ. 2017 Apr 5;5:e3126. doi: 10.7717/peerj.3126. eCollection 2017.


Expression of Desmoglein 2, Desmocollin 3 and Plakophilin 2 in Placenta and Bone Marrow-Derived Mesenchymal Stromal Cells.

Hart ML, Rusch E, Kaupp M, Nieselt K, Aicher WK.

Stem Cell Rev Rep. 2017 Apr;13(2):258-266. doi: 10.1007/s12015-016-9710-4.


Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R.

Microbiome. 2017 Jan 25;5(1):11. doi: 10.1186/s40168-017-0233-2.


Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster.

Arora N, Schuenemann VJ, Jäger G, Peltzer A, Seitz A, Herbig A, Strouhal M, Grillová L, Sánchez-Busó L, Kühnert D, Bos KI, Davis LR, Mikalová L, Bruisten S, Komericki P, French P, Grant PR, Pando MA, Vaulet LG, Fermepin MR, Martinez A, Centurion Lara A, Giacani L, Norris SJ, Šmajs D, Bosshard PP, González-Candelas F, Nieselt K, Krause J, Bagheri HC.

Nat Microbiol. 2016 Dec 5;2:16245. doi: 10.1038/nmicrobiol.2016.245.


EAGER: efficient ancient genome reconstruction.

Peltzer A, Jäger G, Herbig A, Seitz A, Kniep C, Krause J, Nieselt K.

Genome Biol. 2016 Mar 31;17:60. doi: 10.1186/s13059-016-0918-z.


Bone marrow-derived mesenchymal stromal cells differ in their attachment to fibronectin-derived peptides from term placenta-derived mesenchymal stromal cells.

Maerz JK, Roncoroni LP, Goldeck D, Abruzzese T, Kalbacher H, Rolauffs B, DeZwart P, Nieselt K, Hart ML, Klein G, Aicher WK.

Stem Cell Res Ther. 2016 Feb 11;7:29. doi: 10.1186/s13287-015-0243-6.


Highlights from the 5th Symposium on Biological Data Visualization: Part 2.

Aerts J, Marai GE, Nieselt K, Nielsen C, Streit M, Weiskopf D.

BMC Proc. 2015 Aug 13;9(Suppl 6 Proceedings of the 5th Symposium on Biological Data):S1. doi: 10.1186/1753-6561-9-S6-S1. eCollection 2015. No abstract available.


Highlights from the 5th Symposium on Biological Data Visualization: Part 1.

Aerts J, Marai GE, Nieselt K, Nielsen C, Streit M, Weiskopf D.

BMC Bioinformatics. 2015;16 Suppl 11:S1. doi: 10.1186/1471-2105-16-S11-S1. Epub 2015 Aug 13. No abstract available.


Pan-Tetris: an interactive visualisation for Pan-genomes.

Hennig A, Bernhardt J, Nieselt K.

BMC Bioinformatics. 2015;16 Suppl 11:S3. doi: 10.1186/1471-2105-16-S11-S3. Epub 2015 Aug 13.


A novel point mutation promotes growth phase-dependent daptomycin tolerance in Staphylococcus aureus.

Mechler L, Herbig A, Paprotka K, Fraunholz M, Nieselt K, Bertram R.

Antimicrob Agents Chemother. 2015 Sep;59(9):5366-76. doi: 10.1128/AAC.00643-15. Epub 2015 Jun 22.


Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.

Bischler T, Tan HS, Nieselt K, Sharma CM.

Methods. 2015 Sep 15;86:89-101. doi: 10.1016/j.ymeth.2015.06.012. Epub 2015 Jun 16.


Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis.

Singh P, Benjak A, Schuenemann VJ, Herbig A, Avanzi C, Busso P, Nieselt K, Krause J, Vera-Cabrera L, Cole ST.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4459-64. doi: 10.1073/pnas.1421504112. Epub 2015 Mar 23.


Emergence of coding and its specificity as a physico-informatic problem.

Wills PR, Nieselt K, McCaskill JS.

Orig Life Evol Biosph. 2015 Jun;45(1-2):249-55. doi: 10.1007/s11084-015-9434-5.


A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8.

Fengler S, Spirer I, Neef M, Ecke M, Nieselt K, Hampp R.

Biomed Res Int. 2015;2015:547495. doi: 10.1155/2015/547495. Epub 2015 Jan 13.


Parallel detection of ancient pathogens via array-based DNA capture.

Bos KI, Jäger G, Schuenemann VJ, Vågene ÅJ, Spyrou MA, Herbig A, Nieselt K, Krause J.

Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130375. doi: 10.1098/rstb.2013.0375.


Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.

Thomason MK, Bischler T, Eisenbart SK, Förstner KU, Zhang A, Herbig A, Nieselt K, Sharma CM, Storz G.

J Bacteriol. 2015 Jan 1;197(1):18-28. doi: 10.1128/JB.02096-14. Epub 2014 Sep 29.


Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J.

Nature. 2014 Oct 23;514(7523):494-7. doi: 10.1038/nature13591. Epub 2014 Aug 20.


inPHAP: interactive visualization of genotype and phased haplotype data.

Jäger G, Peltzer A, Nieselt K.

BMC Bioinformatics. 2014 Jul 10;15:200. doi: 10.1186/1471-2105-15-200.


Metabolic and transcriptional activities of Staphylococcus aureus challenged with high-doses of daptomycin.

Lechner S, Prax M, Lange B, Huber C, Eisenreich W, Herbig A, Nieselt K, Bertram R.

Int J Med Microbiol. 2014 Nov;304(8):931-40. doi: 10.1016/j.ijmm.2014.05.008. Epub 2014 May 28.


Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus.

Schröder W, Bernhardt J, Marincola G, Klein-Hitpass L, Herbig A, Krupp G, Nieselt K, Wolz C.

BMC Genomics. 2014 Apr 16;15:291. doi: 10.1186/1471-2164-15-291.


Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic.

Mendum TA, Schuenemann VJ, Roffey S, Taylor GM, Wu H, Singh P, Tucker K, Hinds J, Cole ST, Kierzek AM, Nieselt K, Krause J, Stewart GR.

BMC Genomics. 2014 Apr 8;15:270. doi: 10.1186/1471-2164-15-270.


Genome-wide comparison of medieval and modern Mycobacterium leprae.

Schuenemann VJ, Singh P, Mendum TA, Krause-Kyora B, Jäger G, Bos KI, Herbig A, Economou C, Benjak A, Busso P, Nebel A, Boldsen JL, Kjellström A, Wu H, Stewart GR, Taylor GM, Bauer P, Lee OY, Wu HH, Minnikin DE, Besra GS, Tucker K, Roffey S, Sow SO, Cole ST, Nieselt K, Krause J.

Science. 2013 Jul 12;341(6142):179-83. doi: 10.1126/science.1238286. Epub 2013 Jun 13.


Low osteogenic differentiation potential of placenta-derived mesenchymal stromal cells correlates with low expression of the transcription factors Runx2 and Twist2.

Ulrich C, Rolauffs B, Abele H, Bonin M, Nieselt K, Hart ML, Aicher WK.

Stem Cells Dev. 2013 Nov 1;22(21):2859-72. doi: 10.1089/scd.2012.0693. Epub 2013 Jul 20.


High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates.

Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM.

PLoS Genet. 2013 May;9(5):e1003495. doi: 10.1371/journal.pgen.1003495. Epub 2013 May 16.


Yersinia pestis: new evidence for an old infection.

Bos KI, Stevens P, Nieselt K, Poinar HN, Dewitte SN, Krause J.

PLoS One. 2012;7(11):e49803. doi: 10.1371/journal.pone.0049803. Epub 2012 Nov 28.


Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum.

Schuster CF, Park JH, Prax M, Herbig A, Nieselt K, Rosenstein R, Inouye M, Bertram R.

J Bacteriol. 2013 Jan;195(1):115-25. doi: 10.1128/JB.00400-12. Epub 2012 Oct 26.


REVEAL--visual eQTL analytics.

Jäger G, Battke F, Nieselt K.

Bioinformatics. 2012 Sep 15;28(18):i542-i548. doi: 10.1093/bioinformatics/bts382.


GenomeRing: alignment visualization based on SuperGenome coordinates.

Herbig A, Jäger G, Battke F, Nieselt K.

Bioinformatics. 2012 Jun 15;28(12):i7-15. doi: 10.1093/bioinformatics/bts217.


Transcriptomic studies of phosphate control of primary and secondary metabolism in Streptomyces coelicolor.

Martín JF, Santos-Beneit F, Rodríguez-García A, Sola-Landa A, Smith MC, Ellingsen TE, Nieselt K, Burroughs NJ, Wellington EM.

Appl Microbiol Biotechnol. 2012 Jul;95(1):61-75. doi: 10.1007/s00253-012-4129-6. Epub 2012 May 24. Review.


An eQTL biological data visualization challenge and approaches from the visualization community.

Bartlett CW, Cheong SY, Hou L, Paquette J, Lum PY, Jäger G, Battke F, Vehlow C, Heinrich J, Nieselt K, Sakai R, Aerts J, Ray WC.

BMC Bioinformatics. 2012;13 Suppl 8:S8. doi: 10.1186/1471-2105-13-S8-S8. Epub 2012 May 18.


iHAT: interactive hierarchical aggregation table for genetic association data.

Heinrich J, Vehlow C, Battke F, Jäger G, Weiskopf D, Nieselt K.

BMC Bioinformatics. 2012;13 Suppl 8:S2. doi: 10.1186/1471-2105-13-S8-S2. Epub 2012 May 18.


Phylogeny of the staphylococcal major autolysin and its use in genus and species typing.

Albrecht T, Raue S, Rosenstein R, Nieselt K, Götz F.

J Bacteriol. 2012 May;194(10):2630-6. doi: 10.1128/JB.06609-11. Epub 2012 Mar 16.


Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture.

Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R; STREAM Consortium, Wohlleben W, Rodríguez-García A, Martín JF, Burroughs NJ, Wellington EM, Smith MC.

Mol Cell Proteomics. 2012 Feb;11(2):M111.013797. doi: 10.1074/mcp.M111.013797. Epub 2011 Dec 6.

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