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Items: 25

1.

FastqPuri: high-performance preprocessing of RNA-seq data.

Pérez-Rubio P, Lottaz C, Engelmann JC.

BMC Bioinformatics. 2019 May 3;20(1):226. doi: 10.1186/s12859-019-2799-0.

2.

High-Dimensional Profiling for Computational Diagnosis.

Lottaz C, Gronwald W, Spang R, Engelmann JC.

Methods Mol Biol. 2017;1526:205-229.

PMID:
27896744
3.

EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data.

Winkler TW, Kutalik Z, Gorski M, Lottaz C, Kronenberg F, Heid IM.

Bioinformatics. 2015 Jan 15;31(2):259-61. doi: 10.1093/bioinformatics/btu621. Epub 2014 Sep 25.

4.

Lactate-modulated induction of THBS-1 activates transforming growth factor (TGF)-beta2 and migration of glioma cells in vitro.

Seliger C, Leukel P, Moeckel S, Jachnik B, Lottaz C, Kreutz M, Brawanski A, Proescholdt M, Bogdahn U, Bosserhoff AK, Vollmann-Zwerenz A, Hau P.

PLoS One. 2013 Nov 1;8(11):e78935. doi: 10.1371/journal.pone.0078935. eCollection 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/78d10187-08e3-4a1c-9294-3da679630d00.

5.

LMX1B is essential for the maintenance of differentiated podocytes in adult kidneys.

Burghardt T, Kastner J, Suleiman H, Rivera-Milla E, Stepanova N, Lottaz C, Kubitza M, Böger CA, Schmidt S, Gorski M, de Vries U, Schmidt H, Hertting I, Kopp J, Rascle A, Moser M, Heid IM, Warth R, Spang R, Wegener J, Mierke CT, Englert C, Witzgall R.

J Am Soc Nephrol. 2013 Nov;24(11):1830-48. doi: 10.1681/ASN.2012080788. Epub 2013 Aug 29.

6.

Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing.

Dolnik A, Engelmann JC, Scharfenberger-Schmeer M, Mauch J, Kelkenberg-Schade S, Haldemann B, Fries T, Krönke J, Kühn MW, Paschka P, Kayser S, Wolf S, Gaidzik VI, Schlenk RF, Rücker FG, Döhner H, Lottaz C, Döhner K, Bullinger L.

Blood. 2012 Nov 1;120(18):e83-92. doi: 10.1182/blood-2011-12-401471. Epub 2012 Sep 13.

PMID:
22976956
7.

T cells become licensed in the lung to enter the central nervous system.

Odoardi F, Sie C, Streyl K, Ulaganathan VK, Schläger C, Lodygin D, Heckelsmiller K, Nietfeld W, Ellwart J, Klinkert WE, Lottaz C, Nosov M, Brinkmann V, Spang R, Lehrach H, Vingron M, Wekerle H, Flügel-Koch C, Flügel A.

Nature. 2012 Aug 30;488(7413):675-9. doi: 10.1038/nature11337.

PMID:
22914092
8.

Prognostic value of genetic alterations in children with first bone marrow relapse of childhood B-cell precursor acute lymphoblastic leukemia.

Krentz S, Hof J, Mendioroz A, Vaggopoulou R, Dörge P, Lottaz C, Engelmann JC, Groeneveld TW, Körner G, Seeger K, Hagemeier C, Henze G, Eckert C, von Stackelberg A, Kirschner-Schwabe R.

Leukemia. 2013 Feb;27(2):295-304. doi: 10.1038/leu.2012.155. Epub 2012 Jun 13.

PMID:
22699455
9.

CALM/AF10-positive leukemias show upregulation of genes involved in chromatin assembly and DNA repair processes and of genes adjacent to the breakpoint at 10p12.

Mulaw MA, Krause A, Deshpande AJ, Krause LF, Rouhi A, La Starza R, Borkhardt A, Buske C, Mecucci C, Ludwig WD, Lottaz C, Bohlander SK.

Leukemia. 2012 May;26(5):1012-9. doi: 10.1038/leu.2011.307. Epub 2011 Nov 8. Erratum in: Leukemia. 2012 Dec;26(12):2570. Krause, A J [corrected to Krause, A].

PMID:
22064352
10.

Transcriptional profiles of CD133+ and CD133- glioblastoma-derived cancer stem cell lines suggest different cells of origin.

Lottaz C, Beier D, Meyer K, Kumar P, Hermann A, Schwarz J, Junker M, Oefner PJ, Bogdahn U, Wischhusen J, Spang R, Storch A, Beier CP.

Cancer Res. 2010 Mar 1;70(5):2030-40. doi: 10.1158/0008-5472.CAN-09-1707. Epub 2010 Feb 9.

11.

ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly.

Thieme M, Lottaz C, Niederstätter H, Parson W, Spang R, Oefner PJ.

BMC Bioinformatics. 2009 Dec 22;10:440. doi: 10.1186/1471-2105-10-440.

12.

Comparison of gene expression profiles between human and mouse monocyte subsets.

Ingersoll MA, Spanbroek R, Lottaz C, Gautier EL, Frankenberger M, Hoffmann R, Lang R, Haniffa M, Collin M, Tacke F, Habenicht AJ, Ziegler-Heitbrock L, Randolph GJ.

Blood. 2010 Jan 21;115(3):e10-9. doi: 10.1182/blood-2009-07-235028. Epub 2009 Nov 12. Erratum in: Blood. 2010 Aug 5;116(5):857.

13.

Integrative normalization and comparative analysis for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

Almstetter MF, Appel IJ, Gruber MA, Lottaz C, Timischl B, Spang R, Dettmer K, Oefner PJ.

Anal Chem. 2009 Jul 15;81(14):5731-9. doi: 10.1021/ac900528b.

PMID:
19522528
14.

Computational diagnostics with gene expression profiles.

Lottaz C, Kostka D, Markowetz F, Spang R.

Methods Mol Biol. 2008;453:281-96. doi: 10.1007/978-1-60327-429-6_15.

PMID:
18712310
15.

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Nucleic Acids Res. 2008 Sep;36(16):e105. doi: 10.1093/nar/gkn425. Epub 2008 Jul 26.

16.

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Genome Res. 2007 Nov;17(11):1697-706. Epub 2007 Oct 1.

17.

Neutrality, compensation, and negative selection during evolution of B-cell development transcriptomes.

Hoffmann R, Lottaz C, Kühne T, Rolink A, Melchers F.

Mol Biol Evol. 2007 Dec;24(12):2610-8. Epub 2007 Sep 21.

PMID:
17890238
18.

Annotation-based distance measures for patient subgroup discovery in clinical microarray studies.

Lottaz C, Toedling J, Spang R.

Bioinformatics. 2007 Sep 1;23(17):2256-64. Epub 2007 Jun 22.

PMID:
17586546
19.

Gene-expression profiling identifies distinct subclasses of core binding factor acute myeloid leukemia.

Bullinger L, Rücker FG, Kurz S, Du J, Scholl C, Sander S, Corbacioglu A, Lottaz C, Krauter J, Fröhling S, Ganser A, Schlenk RF, Döhner K, Pollack JR, Döhner H.

Blood. 2007 Aug 15;110(4):1291-300. Epub 2007 May 7.

PMID:
17485551
20.

Expression of late cell cycle genes and an increased proliferative capacity characterize very early relapse of childhood acute lymphoblastic leukemia.

Kirschner-Schwabe R, Lottaz C, Tödling J, Rhein P, Karawajew L, Eckert C, von Stackelberg A, Ungethüm U, Kostka D, Kulozik AE, Ludwig WD, Henze G, Spang R, Hagemeier C, Seeger K.

Clin Cancer Res. 2006 Aug 1;12(15):4553-61.

21.

OrderedList--a bioconductor package for detecting similarity in ordered gene lists.

Lottaz C, Yang X, Scheid S, Spang R.

Bioinformatics. 2006 Sep 15;22(18):2315-6. Epub 2006 Jul 14.

PMID:
16844712
22.
23.

Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.

Lottaz C, Spang R.

Bioinformatics. 2005 May 1;21(9):1971-8. Epub 2005 Jan 27.

PMID:
15677704
24.

Activation of the HIF pathway in childhood ALL, prognostic implications of VEGF.

Wellmann S, Guschmann M, Griethe W, Eckert C, von Stackelberg A, Lottaz C, Moderegger E, Einsiedel HG, Eckardt KU, Henze G, Seeger K.

Leukemia. 2004 May;18(5):926-33. Erratum in: Leukemia. 2004 Jun;18(6):1164. Stackelberg Av [corrected to von Stackelberg A].

PMID:
15014526
25.

Modeling sequencing errors by combining Hidden Markov models.

Lottaz C, Iseli C, Jongeneel CV, Bucher P.

Bioinformatics. 2003 Oct;19 Suppl 2:ii103-12.

PMID:
14534179

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