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Paired proteomics, transcriptomics and miRNomics in non-small cell lung cancers: known and novel signaling cascades.

Backes C, Ludwig N, Leidinger P, Huwer H, Tenzer S, Fehlmann T, Franke A, Meese E, Lenhof HP, Keller A.

Oncotarget. 2016 Aug 31. doi: 10.18632/oncotarget.11723. [Epub ahead of print]


Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes.

Ludwig N, Werner TV, Backes C, Trampert P, Gessler M, Keller A, Lenhof HP, Graf N, Meese E.

Int J Mol Sci. 2016 Mar 30;17(4):475. doi: 10.3390/ijms17040475.


Integrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase.

Tenzer S, Leidinger P, Backes C, Huwer H, Hildebrandt A, Lenhof HP, Wesse T, Franke A, Meese E, Keller A.

Oncotarget. 2016 Mar 22;7(12):14857-70. doi: 10.18632/oncotarget.7562.


CausalTrail: Testing hypothesis using causal Bayesian networks.

Stöckel D, Schmidt F, Trampert P, Lenhof HP.

F1000Res. 2015 Dec 30;4. pii: ISCB Comm J-1520. doi: 10.12688/f1000research.7647.1. eCollection 2015.


EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon-Mann-Whitney Test.

Marx A, Backes C, Meese E, Lenhof HP, Keller A.

Genomics Proteomics Bioinformatics. 2016 Feb;14(1):55-61. doi: 10.1016/j.gpb.2015.11.004. Epub 2016 Jan 29.


Multi-omics enrichment analysis using the GeneTrail2 web service.

Stöckel D, Kehl T, Trampert P, Schneider L, Backes C, Ludwig N, Gerasch A, Kaufmann M, Gessler M, Graf N, Meese E, Keller A, Lenhof HP.

Bioinformatics. 2016 May 15;32(10):1502-8. doi: 10.1093/bioinformatics/btv770. Epub 2016 Jan 18.


DrugTargetInspector: An assistance tool for patient treatment stratification.

Schneider L, Stöckel D, Kehl T, Gerasch A, Ludwig N, Leidinger P, Huwer H, Tenzer S, Kohlbacher O, Hildebrandt A, Kaufmann M, Gessler M, Keller A, Meese E, Graf N, Lenhof HP.

Int J Cancer. 2016 Apr 1;138(7):1765-76. doi: 10.1002/ijc.29897.


BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms.

Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof HP, Meese E, Keller A.

Genome Med. 2015 Jul 1;7(1):65. doi: 10.1186/s13073-015-0190-y. eCollection 2015.


Combination of Autoantibody Signature with PSA Level Enables a Highly Accurate Blood-Based Differentiation of Prostate Cancer Patients from Patients with Benign Prostatic Hyperplasia.

Leidinger P, Keller A, Milchram L, Harz C, Hart M, Werth A, Lenhof HP, Weinhäusel A, Keck B, Wullich B, Ludwig N, Meese E.

PLoS One. 2015 Jun 3;10(6):e0128235. doi: 10.1371/journal.pone.0128235. eCollection 2015.


Circulating serum miRNAs as potential biomarkers for nephroblastoma.

Ludwig N, Nourkami-Tutdibi N, Backes C, Lenhof HP, Graf N, Keller A, Meese E.

Pediatr Blood Cancer. 2015 Aug;62(8):1360-7. doi: 10.1002/pbc.25481. Epub 2015 Mar 18.


Phylogenomics with paralogs.

Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2058-63. doi: 10.1073/pnas.1412770112. Epub 2015 Feb 2.


ballaxy: web services for structural bioinformatics.

Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.

Bioinformatics. 2015 Jan 1;31(1):121-2. doi: 10.1093/bioinformatics/btu574. Epub 2014 Sep 2.


Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis.

Backes C, Rühle F, Stoll M, Haas J, Frese K, Franke A, Lieb W, Wichmann HE, Weis T, Kloos W, Lenhof HP, Meese E, Katus H, Meder B, Keller A.

BMC Genomics. 2014 Jul 22;15:622. doi: 10.1186/1471-2164-15-622.


BiNA: a visual analytics tool for biological network data.

Gerasch A, Faber D, Küntzer J, Niermann P, Kohlbacher O, Lenhof HP, Kaufmann M.

PLoS One. 2014 Feb 13;9(2):e87397. doi: 10.1371/journal.pone.0087397. eCollection 2014.


Efficient computation of root mean square deviations under rigid transformations.

Hildebrandt AK, Dietzen M, Lengauer T, Lenhof HP, Althaus E, Hildebrandt A.

J Comput Chem. 2014 Apr 15;35(10):765-71. doi: 10.1002/jcc.23513. Epub 2013 Dec 19.


NetworkTrail--a web service for identifying and visualizing deregulated subnetworks.

Stöckel D, Müller O, Kehl T, Gerasch A, Backes C, Rurainski A, Keller A, Kaufmann M, Lenhof HP.

Bioinformatics. 2013 Jul 1;29(13):1702-3. doi: 10.1093/bioinformatics/btt204. Epub 2013 Apr 26.


Myeloid cell RelA/p65 promotes lung cancer proliferation through Wnt/β-catenin signaling in murine and human tumor cells.

Li D, Beisswenger C, Herr C, Hellberg J, Han G, Zakharkina T, Voss M, Wiewrodt R, Bohle RM, Menger MD, Schmid RM, Stöckel D, Lenhof HP, Bals R.

Oncogene. 2014 Mar 6;33(10):1239-48. doi: 10.1038/onc.2013.75. Epub 2013 Apr 8.


NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.

Dehof AK, Loew S, Lenhof HP, Hildebrandt A.

BMC Bioinformatics. 2013 Mar 16;14:98. doi: 10.1186/1471-2105-14-98.


Treatment-independent miRNA signature in blood of Wilms tumor patients.

Schmitt J, Backes C, Nourkami-Tutdibi N, Leidinger P, Deutscher S, Beier M, Gessler M, Graf N, Lenhof HP, Keller A, Meese E.

BMC Genomics. 2012 Aug 7;13:379. doi: 10.1186/1471-2164-13-379.


Is there a general autoantibody signature for cancer?

Ludwig N, Keller A, Leidinger P, Harz C, Backes C, Lenhof HP, Meese E.

Eur J Cancer. 2012 Oct;48(15):2451-61. doi: 10.1016/j.ejca.2012.01.017. Epub 2012 Feb 22.

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