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miR-34a as hub of T cell regulation networks.

Hart M, Walch-Rückheim B, Krammes L, Kehl T, Rheinheimer S, Tänzer T, Glombitza B, Sester M, Lenhof HP, Keller A, Meese E.

J Immunother Cancer. 2019 Jul 16;7(1):187. doi: 10.1186/s40425-019-0670-5.


ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification.

Schneider L, Kehl T, Thedinga K, Grammes NL, Backes C, Mohr C, Schubert B, Lenhof K, Gerstner N, Daniel Hartkopf A, Wallwiener M, Kohlbacher O, Keller A, Meese E, Graf N, Lenhof HP.

Bioinformatics. 2019 Apr 30. pii: btz302. doi: 10.1093/bioinformatics/btz302. [Epub ahead of print]


The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals.

Fehlmann T, Backes C, Pirritano M, Laufer T, Galata V, Kern F, Kahraman M, Gasparoni G, Ludwig N, Lenhof HP, Gregersen HA, Francke R, Meese E, Simon M, Keller A.

Nucleic Acids Res. 2019 May 21;47(9):4431-4441. doi: 10.1093/nar/gkz227.


An estimate of the total number of true human miRNAs.

Alles J, Fehlmann T, Fischer U, Backes C, Galata V, Minet M, Hart M, Abu-Halima M, Grässer FA, Lenhof HP, Keller A, Meese E.

Nucleic Acids Res. 2019 Apr 23;47(7):3353-3364. doi: 10.1093/nar/gkz097.


miR-34a: a new player in the regulation of T cell function by modulation of NF-κB signaling.

Hart M, Walch-Rückheim B, Friedmann KS, Rheinheimer S, Tänzer T, Glombitza B, Sester M, Lenhof HP, Hoth M, Schwarz EC, Keller A, Meese E.

Cell Death Dis. 2019 Jan 18;10(2):46. doi: 10.1038/s41419-018-1295-1.


Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity.

Fehlmann T, Laufer T, Backes C, Kahramann M, Alles J, Fischer U, Minet M, Ludwig N, Kern F, Kehl T, Galata V, Düsterloh A, Schrörs H, Kohlhaas J, Bals R, Huwer H, Geffers L, Krüger R, Balling R, Lenhof HP, Meese E, Keller A.

RNA Biol. 2019 Jan;16(1):93-103. doi: 10.1080/15476286.2018.1559689. Epub 2018 Dec 26.


Modulation of intracellular calcium signaling by microRNA-34a-5p.

Diener C, Hart M, Alansary D, Poth V, Walch-Rückheim B, Menegatti J, Grässer F, Fehlmann T, Rheinheimer S, Niemeyer BA, Lenhof HP, Keller A, Meese E.

Cell Death Dis. 2018 Sep 27;9(10):1008. doi: 10.1038/s41419-018-1050-7.


The role of TCF3 as potential master regulator in blastemal Wilms tumors.

Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP.

Int J Cancer. 2019 Mar 15;144(6):1432-1443. doi: 10.1002/ijc.31834. Epub 2018 Nov 13.


Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development.

Keller A, Fehlmann T, Ludwig N, Kahraman M, Laufer T, Backes C, Vogelmeier C, Diener C, Biertz F, Herr C, Jörres RA, Lenhof HP, Meese E, Bals R; COSYCONET Study Group.

Genomics Proteomics Bioinformatics. 2018 Jun;16(3):162-171. doi: 10.1016/j.gpb.2018.06.001. Epub 2018 Jul 5.


REGGAE: a novel approach for the identification of key transcriptional regulators.

Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Schick M, Keller U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP.

Bioinformatics. 2018 Oct 15;34(20):3503-3510. doi: 10.1093/bioinformatics/bty372.


About miRNAs, miRNA seeds, target genes and target pathways.

Kehl T, Backes C, Kern F, Fehlmann T, Ludwig N, Meese E, Lenhof HP, Keller A.

Oncotarget. 2017 Nov 9;8(63):107167-107175. doi: 10.18632/oncotarget.22363. eCollection 2017 Dec 5.


A high-resolution map of the human small non-coding transcriptome.

Fehlmann T, Backes C, Alles J, Fischer U, Hart M, Kern F, Langseth H, Rounge T, Umu SU, Kahraman M, Laufer T, Haas J, Staehler C, Ludwig N, Hübenthal M, Meder B, Franke A, Lenhof HP, Meese E, Keller A.

Bioinformatics. 2018 May 15;34(10):1621-1628. doi: 10.1093/bioinformatics/btx814.


miRCarta: a central repository for collecting miRNA candidates.

Backes C, Fehlmann T, Kern F, Kehl T, Lenhof HP, Meese E, Keller A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D160-D167. doi: 10.1093/nar/gkx851.


RegulatorTrail: a web service for the identification of key transcriptional regulators.

Kehl T, Schneider L, Schmidt F, Stöckel D, Gerstner N, Backes C, Meese E, Keller A, Schulz MH, Lenhof HP.

Nucleic Acids Res. 2017 Jul 3;45(W1):W146-W153. doi: 10.1093/nar/gkx350.


miRPathDB: a new dictionary on microRNAs and target pathways.

Backes C, Kehl T, Stöckel D, Fehlmann T, Schneider L, Meese E, Lenhof HP, Keller A.

Nucleic Acids Res. 2017 Jan 4;45(D1):D90-D96. doi: 10.1093/nar/gkw926. Epub 2016 Oct 13.


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 Nov 1;7(44):71514-71525. doi: 10.18632/oncotarget.11723.


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.


miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases.

Laczny C, Leidinger P, Haas J, Ludwig N, Backes C, Gerasch A, Kaufmann M, Vogel B, Katus HA, Meder B, Stähler C, Meese E, Lenhof HP, Keller A.

BMC Bioinformatics. 2012 Feb 22;13:36. doi: 10.1186/1471-2105-13-36.


An integer linear programming approach for finding deregulated subgraphs in regulatory networks.

Backes C, Rurainski A, Klau GW, Müller O, Stöckel D, Gerasch A, Küntzer J, Maisel D, Ludwig N, Hein M, Keller A, Burtscher H, Kaufmann M, Meese E, Lenhof HP.

Nucleic Acids Res. 2012 Mar;40(6):e43. doi: 10.1093/nar/gkr1227. Epub 2011 Dec 30.


Autoantibody signature differentiates Wilms tumor patients from neuroblastoma patients.

Schmitt J, Keller A, Nourkami-Tutdibi N, Heisel S, Habel N, Leidinger P, Ludwig N, Gessler M, Graf N, Berthold F, Lenhof HP, Meese E.

PLoS One. 2011;6(12):e28951. doi: 10.1371/journal.pone.0028951. Epub 2011 Dec 16.


Multicenter study identified molecular blood-born protein signatures for Wilms Tumor.

Schmitt J, Heisel S, Keller A, Leidinger P, Ludwig N, Habel N, Furtwängler R, Nourkami-Tutdibi N, Wegert J, Grundy P, Gessler M, Graf N, Lenhof HP, Meese E.

Int J Cancer. 2012 Aug 1;131(3):673-82. doi: 10.1002/ijc.26419. Epub 2011 Oct 23.


Toward the blood-borne miRNome of human diseases.

Keller A, Leidinger P, Bauer A, Elsharawy A, Haas J, Backes C, Wendschlag A, Giese N, Tjaden C, Ott K, Werner J, Hackert T, Ruprecht K, Huwer H, Huebers J, Jacobs G, Rosenstiel P, Dommisch H, Schaefer A, Müller-Quernheim J, Wullich B, Keck B, Graf N, Reichrath J, Vogel B, Nebel A, Jager SU, Staehler P, Amarantos I, Boisguerin V, Staehler C, Beier M, Scheffler M, Büchler MW, Wischhusen J, Haeusler SF, Dietl J, Hofmann S, Lenhof HP, Schreiber S, Katus HA, Rottbauer W, Meder B, Hoheisel JD, Franke A, Meese E.

Nat Methods. 2011 Sep 4;8(10):841-3. doi: 10.1038/nmeth.1682.


Immunogenicity of autoantigens.

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

BMC Genomics. 2011 Jul 4;12:340. doi: 10.1186/1471-2164-12-340.


Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana.

Schuler M, Keller A, Backes C, Philippar K, Lenhof HP, Bauer P.

BMC Plant Biol. 2011 May 18;11:87. doi: 10.1186/1471-2229-11-87.


The Roche Cancer Genome Database 2.0.

Küntzer J, Maisel D, Lenhof HP, Klostermann S, Burtscher H.

BMC Med Genomics. 2011 May 17;4:43. doi: 10.1186/1755-8794-4-43.


Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis.

Keller A, Leidinger P, Gislefoss R, Haugen A, Langseth H, Staehler P, Lenhof HP, Meese E.

RNA Biol. 2011 May-Jun;8(3):506-16. Epub 2011 May 1.


Specific peripheral miRNA profiles for distinguishing lung cancer from COPD.

Leidinger P, Keller A, Borries A, Huwer H, Rohling M, Huebers J, Lenhof HP, Meese E.

Lung Cancer. 2011 Oct;74(1):41-7. doi: 10.1016/j.lungcan.2011.02.003. Epub 2011 Mar 8.


Automated bond order assignment as an optimization problem.

Dehof AK, Rurainski A, Bui QB, Böcker S, Lenhof HP, Hildebrandt A.

Bioinformatics. 2011 Mar 1;27(5):619-25. doi: 10.1093/bioinformatics/btq718. Epub 2011 Jan 17.


BALL--biochemical algorithms library 1.3.

Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O.

BMC Bioinformatics. 2010 Oct 25;11:531. doi: 10.1186/1471-2105-11-531.


Protein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples.

Melchior K, Tholey A, Heisel S, Keller A, Lenhof HP, Meese E, Huber CG.

J Chromatogr A. 2010 Oct 1;1217(40):6159-68. doi: 10.1016/j.chroma.2010.07.044. Epub 2010 Jul 21.


High-throughput miRNA profiling of human melanoma blood samples.

Leidinger P, Keller A, Borries A, Reichrath J, Rass K, Jager SU, Lenhof HP, Meese E.

BMC Cancer. 2010 Jun 7;10:262. doi: 10.1186/1471-2407-10-262.


Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%.

Ludwig N, Keller A, Heisel S, Leidinger P, Rheinheimer S, Andres C, Stephan B, Steudel WI, Donauer E, Graf N, Burgeth B, Weickert J, Lenhof HP, Meese E.

Int J Cancer. 2011 Mar 15;128(6):1493-501. doi: 10.1002/ijc.25467.

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