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Items: 1 to 20 of 21

1.

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies.

Sousa IG, Simi KCR, do Almo MM, Bezerra MAG, Doose G, Raiol T, Stadler PF, Hoffmann S, Maranhão AQ, Brigido MM.

BMC Genomics. 2019 Jul 19;20(1):593. doi: 10.1186/s12864-019-5967-8.

2.

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.

López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W; ICGC MMML-Seq Consortium, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R.

Nat Commun. 2019 Mar 29;10(1):1459. doi: 10.1038/s41467-019-08578-3.

3.

Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.

Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M.

Gigascience. 2019 Feb 1;8(2). pii: giy160. doi: 10.1093/gigascience/giy160.

4.

RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas.

Kunz M, Löffler-Wirth H, Dannemann M, Willscher E, Doose G, Kelso J, Kottek T, Nickel B, Hopp L, Landsberg J, Hoffmann S, Tüting T, Zigrino P, Mauch C, Utikal J, Ziemer M, Schulze HJ, Hölzel M, Roesch A, Kneitz S, Meierjohann S, Bosserhoff A, Binder H, Schartl M.

Oncogene. 2018 Nov;37(47):6136-6151. doi: 10.1038/s41388-018-0385-y. Epub 2018 Jul 11.

PMID:
29995873
5.

Author Correction: The landscape of genomic alterations across childhood cancers.

Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H, Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM, Korbel JO, Schlesner M, Eils R, Jones DTW, Lichter P, Chavez L, Zapatka M, Pfister SM; ICGC PedBrain-Seq Project; ICGC MMML-Seq Project.

Nature. 2018 Jul;559(7714):E10. doi: 10.1038/s41586-018-0167-2.

PMID:
29875405
6.

Rare Splice Variants in Long Non-Coding RNAs.

Sen R, Doose G, Stadler PF.

Noncoding RNA. 2017 Jul 5;3(3). pii: E23. doi: 10.3390/ncrna3030023.

7.

The landscape of genomic alterations across childhood cancers.

Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H; ICGC PedBrain-Seq Project; ICGC MMML-Seq Project, Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM, Korbel JO, Schlesner M, Eils R, Jones DTW, Lichter P, Chavez L, Zapatka M, Pfister SM.

Nature. 2018 Mar 15;555(7696):321-327. doi: 10.1038/nature25480. Epub 2018 Feb 28. Erratum in: Nature. 2018 Jul;559(7714):E10.

PMID:
29489754
8.

DIEGO: detection of differential alternative splicing using Aitchison's geometry.

Doose G, Bernhart SH, Wagener R, Hoffmann S.

Bioinformatics. 2018 Mar 15;34(6):1066-1068. doi: 10.1093/bioinformatics/btx690.

9.

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2017 Jan 11;7:39421. doi: 10.1038/srep39421. No abstract available.

10.

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer.

Bernhart SH, Kretzmer H, Holdt LM, Jühling F, Ammerpohl O, Bergmann AK, Northoff BH, Doose G, Siebert R, Stadler PF, Hoffmann S.

Sci Rep. 2016 Nov 23;6:37393. doi: 10.1038/srep37393.

11.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2016 Oct 7;6:34589. doi: 10.1038/srep34589. Erratum in: Sci Rep. 2017 Jan 11;7:39421.

12.

MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation.

Shostak A, Ruppert B, Ha N, Bruns P, Toprak UH; ICGC MMML-Seq Project, Eils R, Schlesner M, Diernfellner A, Brunner M.

Nat Commun. 2016 Jun 24;7:11807. doi: 10.1038/ncomms11807.

13.

Reply to Hart et al.: MINCR and MYC: More than expression correlation.

Doose G, Hoffmann S, Iaccarino I.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E498. doi: 10.1073/pnas.1520413113. Epub 2016 Jan 25. No abstract available.

14.

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.

Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HHD, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RAF, Martens JHA, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B.

Nat Genet. 2015 Nov;47(11):1316-1325. doi: 10.1038/ng.3413. Epub 2015 Oct 5.

15.

MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells.

Doose G, Haake A, Bernhart SH, López C, Duggimpudi S, Wojciech F, Bergmann AK, Borkhardt A, Burkhardt B, Claviez A, Dimitrova L, Haas S, Hoell JI, Hummel M, Karsch D, Klapper W, Kleo K, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Lenze D, Loeffler M, Mantovani-Löffler L, Möller P, Ott G, Richter J, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schneider M, Scholz I, Stilgenbauer S, Stunnenberg HG, Szczepanowski M, Trümper L, Weniger MA; ICGC MMML-Seq Consortium, Hoffmann S, Siebert R, Iaccarino I.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5261-70. doi: 10.1073/pnas.1505753112. Epub 2015 Sep 8.

16.

The PCBP1 gene encoding poly(rC) binding protein I is recurrently mutated in Burkitt lymphoma.

Wagener R, Aukema SM, Schlesner M, Haake A, Burkhardt B, Claviez A, Drexler HG, Hummel M, Kreuz M, Loeffler M, Rosolowski M, López C, Möller P, Richter J, Rohde M, Betts MJ, Russell RB, Bernhart SH, Hoffmann S, Rosenstiel P, Schilhabel M, Szczepanowski M, Trümper L, Klapper W, Siebert R; ICGC MMML-Seq-Project; "Molecular Mechanisms in Malignant Lymphomas" Network Project of the Deutsche Krebshilfe.

Genes Chromosomes Cancer. 2015 Sep;54(9):555-64. doi: 10.1002/gcc.22268. Epub 2015 Jul 14.

PMID:
26173642
17.

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.

Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF.

Genome Biol. 2014 Feb 10;15(2):R34. doi: 10.1186/gb-2014-15-2-r34.

18.

Atypical RNAs in the coelacanth transcriptome.

Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):342-51. doi: 10.1002/jez.b.22542. Epub 2013 Oct 30.

PMID:
24174405
19.

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.

Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF.

RNA Biol. 2013 Jul;10(7):1204-10. doi: 10.4161/rna.24972. Epub 2013 May 13.

20.

Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.

Doose G, Metzler D.

Bioinformatics. 2012 Sep 1;28(17):2242-8. doi: 10.1093/bioinformatics/bts369. Epub 2012 Jul 13.

PMID:
22796961

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