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The deterministic role of 5-mers in microRNA-gene targeting.

Hart M, Kern F, Backes C, Rheinheimer S, Fehlmann T, Keller A, Meese E.

RNA Biol. 2018 May 11:1-7. doi: 10.1080/15476286.2018.1462652. [Epub ahead of print]


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 May 7. doi: 10.1093/bioinformatics/bty372. [Epub ahead of print]


Small ncRNA-Seq Results of Human Tissues: Variations Depending on Sample Integrity.

Ludwig N, Fehlmann T, Galata V, Franke A, Backes C, Meese E, Keller A.

Clin Chem. 2018 Apr 24. pii: clinchem.2017.285767. doi: 10.1373/clinchem.2017.285767. [Epub ahead of print]


Deregulated microRNA and mRNA expression profiles in the peripheral blood of patients with Marfan syndrome.

Abu-Halima M, Kahraman M, Henn D, Rädle-Hurst T, Keller A, Abdul-Khaliq H, Meese E.

J Transl Med. 2018 Mar 12;16(1):60. doi: 10.1186/s12967-018-1429-3.


Gene amplification in mesenchymal stem cells and during differentiation towards adipocytes or osteoblasts.

Altmayer NC, Galata V, Warschburger N, Keller A, Meese E, Fischer U.

Oncotarget. 2017 Dec 1;9(2):1803-1812. doi: 10.18632/oncotarget.22804. eCollection 2018 Jan 5.


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.


A comprehensive profile of circulating RNAs in human serum.

Umu SU, Langseth H, Bucher-Johannessen C, Fromm B, Keller A, Meese E, Lauritzen M, Leithaug M, Lyle R, Rounge TB.

RNA Biol. 2018 Feb 1;15(2):242-250. doi: 10.1080/15476286.2017.1403003. Epub 2017 Dec 8.


Micro-ribonucleic acids and extracellular vesicles repertoire in the spent culture media is altered in women undergoing In Vitro Fertilization.

Abu-Halima M, Häusler S, Backes C, Fehlmann T, Staib C, Nestel S, Nazarenko I, Meese E, Keller A.

Sci Rep. 2017 Oct 19;7(1):13525. doi: 10.1038/s41598-017-13683-8.


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.


IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions.

Palmieri V, Backes C, Ludwig N, Fehlmann T, Kern F, Meese E, Keller A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D770-D775. doi: 10.1093/nar/gkx701.


Altered miRNA-profile dependent on ART outcome in early pregnancy targets Wnt-pathway.

Freis A, Keller A, Ludwig N, Meese E, Jauckus J, Rehnitz J, Capp E, Strowitzki T, Germeyer A.

Reproduction. 2017 Dec;154(6):799-805. doi: 10.1530/REP-17-0396. Epub 2017 Sep 29.


MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins.

Alles J, Ludwig N, Rheinheimer S, Leidinger P, Grässer FA, Keller A, Meese E.

Oncotarget. 2017 May 7;8(34):56417-56427. doi: 10.18632/oncotarget.17662. eCollection 2017 Aug 22.


Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs.

Fehlmann T, Backes C, Kahraman M, Haas J, Ludwig N, Posch AE, Würstle ML, Hübenthal M, Franke A, Meder B, Meese E, Keller A.

Nucleic Acids Res. 2017 Sep 6;45(15):8731-8744. doi: 10.1093/nar/gkx595.


Sources to variability in circulating human miRNA signatures.

Keller A, Rounge T, Backes C, Ludwig N, Gislefoss R, Leidinger P, Langseth H, Meese E.

RNA Biol. 2017 Dec 2;14(12):1791-1798. doi: 10.1080/15476286.2017.1367888. Epub 2017 Sep 13.


Bias in recent miRBase annotations potentially associated with RNA quality issues.

Ludwig N, Becker M, Schumann T, Speer T, Fehlmann T, Keller A, Meese E.

Sci Rep. 2017 Jul 12;7(1):5162. doi: 10.1038/s41598-017-05070-0.


Analysis of circulating microRNAs in patients with repaired Tetralogy of Fallot with and without heart failure.

Abu-Halima M, Meese E, Keller A, Abdul-Khaliq H, Rädle-Hurst T.

J Transl Med. 2017 Jul 10;15(1):156. doi: 10.1186/s12967-017-1255-z.


Technical Stability and Biological Variability in MicroRNAs from Dried Blood Spots: A Lung Cancer Therapy-Monitoring Showcase.

Kahraman M, Laufer T, Backes C, Schrörs H, Fehlmann T, Ludwig N, Kohlhaas J, Meese E, Wehler T, Bals R, Keller A.

Clin Chem. 2017 Sep;63(9):1476-1488. doi: 10.1373/clinchem.2017.271619. Epub 2017 Jul 5.


Characterization of micro-RNA Profile in the Blood of Patients with Marfan's Syndrome.

Abu-Halima M, Ludwig N, Rädle-Hurst T, Keller A, Motsch L, Marsollek I, El Rahman MA, Abdul-Khaliq H, Meese E.

Thorac Cardiovasc Surg. 2018 Jan;66(1):116-124. doi: 10.1055/s-0037-1604083. Epub 2017 Jul 5.


TRPC1- and TRPC3-dependent Ca2+ signaling in mouse cortical astrocytes affects injury-evoked astrogliosis in vivo.

Belkacemi T, Niermann A, Hofmann L, Wissenbach U, Birnbaumer L, Leidinger P, Backes C, Meese E, Keller A, Bai X, Scheller A, Kirchhoff F, Philipp SE, Weissgerber P, Flockerzi V, Beck A.

Glia. 2017 Sep;65(9):1535-1549. doi: 10.1002/glia.23180. Epub 2017 Jun 21.


Differential expression of microRNAs following cardiopulmonary bypass in children with congenital heart diseases.

Abu-Halima M, Poryo M, Ludwig N, Mark J, Marsollek I, Giebels C, Petersen J, Schäfers HJ, Grundmann U, Pickardt T, Keller A, Meese E, Abdul-Khaliq H.

J Transl Med. 2017 May 30;15(1):117. doi: 10.1186/s12967-017-1213-9.


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.


Specific amplifications and copy number decreases during human neural stem cells differentiation towards astrocytes, neurons and oligodendrocytes.

Fischer U, Kim E, Keller A, Meese E.

Oncotarget. 2017 Apr 18;8(16):25872-25884. doi: 10.18632/oncotarget.15980.


MiR-34a-3p alters proliferation and apoptosis of meningioma cells in vitro and is directly targeting SMAD4, FRAT1 and BCL2.

Werner TV, Hart M, Nickels R, Kim YJ, Menger MD, Bohle RM, Keller A, Ludwig N, Meese E.

Aging (Albany NY). 2017 Mar 23;9(3):932-954. doi: 10.18632/aging.101201.


Exploring ncRNAs in Alzheimer's disease by miRMaster.

Fehlmann T, Meese E, Keller A.

Oncotarget. 2017 Jan 17;8(3):3771-3772. doi: 10.18632/oncotarget.14054. No abstract available.


miRNAs in Ancient Tissue Specimens of the Tyrolean Iceman.

Keller A, Kreis S, Leidinger P, Maixner F, Ludwig N, Backes C, Galata V, Guerriero G, Fehlmann T, Franke A, Meder B, Zink A, Meese E.

Mol Biol Evol. 2017 Apr 1;34(4):793-801. doi: 10.1093/molbev/msw291.


cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs.

Fehlmann T, Reinheimer S, Geng C, Su X, Drmanac S, Alexeev A, Zhang C, Backes C, Ludwig N, Hart M, An D, Zhu Z, Xu C, Chen A, Ni M, Liu J, Li Y, Poulter M, Li Y, Stähler C, Drmanac R, Xu X, Meese E, Keller A.

Clin Epigenetics. 2016 Nov 21;8:123. eCollection 2016.


The miRNome of Alzheimer's disease: consistent downregulation of the miR-132/212 cluster.

Pichler S, Gu W, Hartl D, Gasparoni G, Leidinger P, Keller A, Meese E, Mayhaus M, Hampel H, Riemenschneider M.

Neurobiol Aging. 2017 Feb;50:167.e1-167.e10. doi: 10.1016/j.neurobiolaging.2016.09.019. Epub 2016 Oct 3.


Distribution of microRNA biomarker candidates in solid tissues and body fluids.

Fehlmann T, Ludwig N, Backes C, Meese E, Keller A.

RNA Biol. 2016 Nov;13(11):1084-1088. Epub 2016 Sep 29.


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.


Erratum to: miRNAs and sports: tracking training status and potentially confounding diagnoses.

Hecksteden A, Leidinger P, Backes C, Rheinheimer S, Pfeiffer M, Ferrauti A, Kellmann M, Sedaghat-Hamedani F, Meder B, Meese E, Meyer T, Keller A.

J Transl Med. 2016 Oct 13;14(1):293. No abstract available.


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.


miRNAs and sports: tracking training status and potentially confounding diagnoses.

Hecksteden A, Leidinger P, Backes C, Rheinheimer S, Pfeiffer M, Ferrauti A, Kellmann M, Sedaghat-Hamedani F, Meder B, Meese E, Meyer T, Keller A.

J Transl Med. 2016 Jul 26;14(1):219. doi: 10.1186/s12967-016-0974-x. Erratum in: J Transl Med. 2016 Oct 13;14 (1):293.


Altered micro-ribonucleic acid expression profiles of extracellular microvesicles in the seminal plasma of patients with oligoasthenozoospermia.

Abu-Halima M, Ludwig N, Hart M, Leidinger P, Backes C, Keller A, Hammadeh M, Meese E.

Fertil Steril. 2016 Oct;106(5):1061-1069.e3. doi: 10.1016/j.fertnstert.2016.06.030. Epub 2016 Jul 14.


Specific miRNA Disease Biomarkers in Blood, Serum and Plasma: Challenges and Prospects.

Backes C, Meese E, Keller A.

Mol Diagn Ther. 2016 Dec;20(6):509-518. Review.


BALL-SNPgp-from genetic variants toward computational diagnostics.

Mueller SC, Backes C, Gress A, Baumgarten N, Kalinina OV, Moll A, Kohlbacher O, Meese E, Keller A.

Bioinformatics. 2016 Jun 15;32(12):1888-90. doi: 10.1093/bioinformatics/btw084. Epub 2016 Feb 15.


Identification of miR-34a-target interactions by a combined network based and experimental approach.

Hart M, Rheinheimer S, Leidinger P, Backes C, Menegatti J, Fehlmann T, Grässer F, Keller A, Meese E.

Oncotarget. 2016 Jun 7;7(23):34288-99. doi: 10.18632/oncotarget.9103.


miEAA: microRNA enrichment analysis and annotation.

Backes C, Khaleeq QT, Meese E, Keller A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W110-6. doi: 10.1093/nar/gkw345. Epub 2016 Apr 29.


Syntaxin 8 is required for efficient lytic granule trafficking in cytotoxic T lymphocytes.

Bhat SS, Friedmann KS, Knörck A, Hoxha C, Leidinger P, Backes C, Meese E, Keller A, Rettig J, Hoth M, Qu B, Schwarz EC.

Biochim Biophys Acta. 2016 Jul;1863(7 Pt A):1653-64. doi: 10.1016/j.bbamcr.2016.04.014. Epub 2016 Apr 17.


MiRTargetLink--miRNAs, Genes and Interaction Networks.

Hamberg M, Backes C, Fehlmann T, Hart M, Meder B, Meese E, Keller A.

Int J Mol Sci. 2016 Apr 14;17(4):564. doi: 10.3390/ijms17040564.


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.


Human alveolar epithelial cells expressing tight junctions to model the air-blood barrier.

Kuehn A, Kletting S, de Souza Carvalho-Wodarz C, Repnik U, Griffiths G, Fischer U, Meese E, Huwer H, Wirth D, May T, Schneider-Daum N, Lehr CM.

ALTEX. 2016;33(3):251-60. doi: 10.14573/altex.1511131. Epub 2016 Mar 17.


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.


Distribution of miRNA expression across human tissues.

Ludwig N, Leidinger P, Becker K, Backes C, Fehlmann T, Pallasch C, Rheinheimer S, Meder B, Stähler C, Meese E, Keller A.

Nucleic Acids Res. 2016 May 5;44(8):3865-77. doi: 10.1093/nar/gkw116. Epub 2016 Feb 25.


Deep characterization of blood cell miRNomes by NGS.

Schwarz EC, Backes C, Knörck A, Ludwig N, Leidinger P, Hoxha C, Schwär G, Grossmann T, Müller SC, Hart M, Haas J, Galata V, Müller I, Fehlmann T, Eichler H, Franke A, Meder B, Meese E, Hoth M, Keller A.

Cell Mol Life Sci. 2016 Aug;73(16):3169-81. doi: 10.1007/s00018-016-2154-9. Epub 2016 Feb 13.


Differential blood-based diagnosis between benign prostatic hyperplasia and prostate cancer: miRNA as source for biomarkers independent of PSA level, Gleason score, or TNM status.

Leidinger P, Hart M, Backes C, Rheinheimer S, Keck B, Wullich B, Keller A, Meese E.

Tumour Biol. 2016 Aug;37(8):10177-85. doi: 10.1007/s13277-016-4883-7. Epub 2016 Jan 29.


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.


Validating Alzheimer's disease micro RNAs using next-generation sequencing.

Keller A, Backes C, Haas J, Leidinger P, Maetzler W, Deuschle C, Berg D, Ruschil C, Galata V, Ruprecht K, Stähler C, Würstle M, Sickert D, Gogol M, Meder B, Meese E.

Alzheimers Dement. 2016 May;12(5):565-76. doi: 10.1016/j.jalz.2015.12.012. Epub 2016 Jan 22.


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.


Gene amplification during myogenic differentiation.

Fischer U, Ludwig N, Raslan A, Meier C, Meese E.

Oncotarget. 2016 Feb 9;7(6):6864-77. doi: 10.18632/oncotarget.6845.

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