Publikationen von Engelmann, Julia C.

Linck-Paulus, Lisa , Lämmerhirt, Lisa, Völler, Daniel, Meyer, Katharina, Engelmann, Julia C. , Spang, Rainer, Eichner, Norbert, Meister, Gunter, Kuphal, Silke und Bosserhoff, Anja Katrin (2021) Learning from Embryogenesis—A Comparative Expression Analysis in Melanoblast Differentiation and Tumorigenesis Reveals miRNAs Driving Melanoma Development. Journal of Clinical Medicine 10 (11), S. 2259.

Arlt, A., von Bonin, F., Rehberg, Thorsten, Perez-Rubio, Paula, Engelmann, Julia C. , Limm, Katharina , Reinke, S., Dullin, C., Sun, Xueni, Specht, R., Maulhardt, M., Linke, F. , Bunt, G., Klapper, W., Vockerodt, M., Wilting, J., Pukrop, T., Dettmer, Katja, Gronwald, Wolfram, Oefner, Peter J., Spang, Rainer und Kube, D. (2019) High CD206 levels in Hodgkin lymphoma-educated macrophages are linked to matrix-remodeling and lymphoma dissemination. Mol Oncol. Volltext nicht vorhanden.

Perez-Rubio, Paula, Lottaz, Claudio und Engelmann, Julia C. (2019) FastqPuri: high-performance preprocessing of RNA-seq data. BMC Bioinformatics 20 (1), S. 226. Volltext nicht vorhanden.

Kleo, K., Dimitrova, L., Oker, E., Tomaszewski, N., Berg, E., Taruttis, Franziska, Engelmann, Julia C. , Schwarzfischer, Philipp, Reinders, Jörg , Spang, Rainer, Gronwald, Wolfram , Oefner, Peter J. und Hummel, Michael (2019) Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma. BMC Cancer 19 (1), S. 322.

Perez-Rubio, Paula, Lottaz, Claudio und Engelmann, Julia C. (2018) FastqPuri: high-performance preprocessing of RNA-seq data. bioRxiv. (Eingereicht)

Feist, M., Schwarzfischer, Philipp, Heinrich, Paul, Sun, Xueni, Kemper, J., von Bonin, F., Perez-Rubio, Paula, Taruttis, Franziska, Rehberg, Thorsten, Dettmer, Katja, Gronwald, Wolfram, Reinders, Jörg, Engelmann, Julia C. , Dudek, J., Klapper, W., Trumper, L., Spang, Rainer, Oefner, Peter J. und Kube, D. (2018) Cooperative STAT/NF-κB signaling regulates lymphoma metabolic reprogramming and aberrant GOT2 expression. Nat Commun 9 (1), S. 1514.

Chen, J., Strieder, Nicholas, Krohn, Nadia G., Cyprys, P., Sprunck, Stefanie, Engelmann, Julia C. und Dresselhaus, Thomas (2017) Zygotic Genome Activation Occurs Shortly After Fertilization in Maize. Plant Cell.

Rohde, M., Bonn, B. R., Zimmermann, M., Lange, J., Moricke, A., Klapper, W., Oschlies, I., Szczepanowski, M., Nagel, I., Schrappe, M., Loeffler, M., Siebert, R., Reiter, A., Burkhardt, B., Altenbuchinger, Michael, Dettmer-Wilde, Katja, Engelmann, Julia C. , Gronwald, Wolfram , Oefner, Peter J. , Schwarzfischer, Philipp, Taruttis, Franziska und Spang, Rainer (2017) Relevance of ID3-TCF3-CCND3 pathway mutations in pediatric aggressive B-cell lymphoma treated according to the non-Hodgkin Lymphoma Berlin-Frankfurt-Münster protocols. Haematologica 102 (6), S. 1091-1098. Volltext nicht vorhanden.

Feist, M., Kemper, J., Taruttis, Franziska, Rehberg, Thorsten, Engelmann, Julia C. , Gronwald, Wolfram, Hummel, Michael, Spang, Rainer und Kube, Dieter (2017) Synergy of interleukin 10 and toll-like receptor 9 signalling in B cell proliferation: Implications for lymphoma pathogenesis. International Journal of Cancer: Int. J. Cancer. Volltext nicht vorhanden.

Schwarzfischer, Philipp, Reinders, Jörg, Dettmer, Katja , Kleo, K., Dimitrova, L., Hummel, M., Feist, M., Kube, D., Szczepanowski, M., Klapper, W., Taruttis, Franziska, Engelmann, Julia C. , Spang, Rainer, Gronwald, Wolfram und Oefner, Peter J. (2017) Comprehensive metaboproteomics of Burkitt's and diffuse large B-cell lymphoma cell lines and primary tumor tissues reveals distinct differences in pyruvate content and metabolism. Journal of Proteome Research 16, S. 1105-1120. Volltext nicht vorhanden.

Taruttis, Franziska, Feist, M., Schwarzfischer, Philipp, Gronwald, Wolfram, Kube, D., Spang, Rainer und Engelmann, Julia C. (2017) External calibration with Drosophila whole-cell spike-ins delivers absolute mRNA fold changes from human RNA-Seq and qPCR data. BioTechniques 62 (2), S. 53-61. Volltext nicht vorhanden.

Lottaz, Claudio, Gronwald, Wolfram , Spang, Rainer und Engelmann, Julia C. (2017) High-Dimensional Profiling for Computational Diagnosis. In: Bioinformatics : Volume II: Structure, Function, and Applications. Methods in Molecular Biology, 1526. Springer, New York, S. 205-229. ISBN 978-1-4939-6611-0. Volltext nicht vorhanden.

Quévillon Huberdeau, Miguel, Zeitler, Daniela M., Hauptmann, Judith, Bruckmann, Astrid, Fressigné, Lucile, Danner, Johannes, Piquet, Sandra, Strieder, Nicholas, Engelmann, Julia C. , Jannot, Guillaume, Deutzmann, Rainer, Simard, Martin J. und Meister, Gunter (2017) Phosphorylation of Argonaute proteins affects mRNA binding and is essential for microRNA‐guided gene silencing in vivo. The EMBO Journal 36 (14), S. 2088-2106. Volltext nicht vorhanden.

Dueck, A., Evers, M., Henz, S. R., Unger, K., Eichner, N., Merkl, Rainer , Berezikov, E. , Engelmann, Julia C., Weigel, D. , Wenzl, S. und Meister, Gunter (2016) Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. BMC Genomics 17 (1), S. 853.

Coll-Bonfill, N., Peinado, V. I. , Pisano, M. V., Parrizas, M. , Blanco, I., Evers, Maurits, Engelmann, Julia C. , Garcia-Lucio, J., Tura-Ceide, O., Meister, Gunter, Barbera, J. A. und Musri, M. M. (2016) Slug Is Increased in Vascular Remodeling and Induces a Smooth Muscle Cell Proliferative Phenotype. PLoS ONE 11 (7), e0159460.

Loedige, Inga, Jakob, Leonhard, Treiber, Thomas, Ray, Debashish, Stotz, Mathias, Treiber, Nora, Hennig, Janosch, Cook, Kate B., Morris, Quaid, Hughes, Timothy R., Engelmann, Julia C., Krahn, Michael P. und Meister, Gunter (2015) The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Rep (Cell Reports) 13 (6), S. 1206-1220.

Evers, Maurits, Huttner, Michael, Dueck, Anne, Meister, Gunter und Engelmann, Julia C. (2015) miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. BMC Bioinformatics 16 (370), S. 1-10.

Hochrein, Jochen, Zacharias, Helena, Taruttis, Franziska, Samol, Claudia, Engelmann, Julia C., Spang, Rainer, Oefner, Peter J. und Gronwald, Wolfram (2015) Data Normalization of (1)H NMR Metabolite Fingerprinting Data Sets in the Presence of Unbalanced Metabolite Regulation. J. Proteome Res. 14 (8), S. 3217-3228. Volltext nicht vorhanden.

Taruttis, Franziska, Spang, Rainer und Engelmann, Julia C. (2015) A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA). Bioinformatics 31, S. 22.

Engelmann, Julia C., Amann, Thomas, Ott-Rötzer, Brigitta, Nützel, Margit, Reinders, Yvonne, Reinders, Jörg, Thasler, Wolfgang E., Kristl, Theresa, Teufel, Andreas, Huber, Christian G., Oefner, Peter J., Spang, Rainer und Hellerbrand, Claus (2015) Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. PLoS Computational Biology 11 (5), S. 1-22.

Hannus, Michael, Beitzinger, Michaela, Engelmann, Julia C., Weickert, Marie-Theresa, Spang, Rainer, Hannus, Stefan und Meister, Gunter (2014) siPools: highly complex but accurately defined siRNA pools eliminate off-target effects. Nucleic Acids Research 42, S. 8049-8061.

Dorn, Christoph, Engelmann, Julia C., Saugspier, Michael Sebastian, Koch, Andreas, Hartmann, Arndt, Spang, Rainer, Bosserhoff, Anja Katrin und Hellerbrand, Claus (2014) Increased expression of c-Jun in nonalcoholic fatty liver disease. Laboratory Investigation 94, S. 394-408. Volltext nicht vorhanden.

Dorn, Christoph , Engelmann, Julia C., Saugspier, Michael, Koch, Andreas, Hartmann, Arndt, Müller, Martina, Spang, Rainer, Bosserhoff, Anja und Hellerbrand, Claus (2014) Increased expression of c-Jun in nonalcoholic fatty liver disease. Laboratory Investigation 94 (4), S. 394-408. Volltext nicht vorhanden.

Aryee, Martin J., Liu, Wennuan, Engelmann, Julia C., Nuhn, Philipp, Gurel, Meltem, Haffner, Michael C., Esopi, David, Irizarry, Rafael A., Getzenberg, Robert H., Nelson, William G., Luo, Jun, Xu, Jianfeng, Isaacs, William B., Bova, G. Steven und Yegnasubramanian, Srinivasan (2013) DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Science translational medicine 5 (169), 169ra10.

Dolnik, Anna, Engelmann, Julia C., Scharfenberger-Schmeer, Maren, Mauch, Julian, Kelkenberg-Schade, Sabine, Haldemann, Berit, Fries, Tamara, Krönke, Jan, Kühn, Michael W. M., Paschka, Peter, Kayser, Sabine, Wolf, Stephan, Gaidzik, Verena I., Schlenk, Richard F., Rücker, Frank G., Döhner, Hartmut, Lottaz, Claudio, Döhner, Konstanze und Bullinger, Lars (2012) Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing. Blood 120 (18), e83-e92. Volltext nicht vorhanden.

Vogelmann, Katja, Drechsel, Gabriele, Bergler, Johannes, Subert, Christa, Philippar, Katrin, Soll, Jürgen, Engelmann, Julia C., Engelsdorf, Timo, Voll, Lars M. und Hoth, Stefan (2012) Early senescence and cell death in Arabidopsis saul1 mutants involves the PAD4-dependent salicylic acid pathway. Plant physiology 159 (4), S. 1477-1487. Volltext nicht vorhanden.

Engelmann, Julia C. und Spang, Rainer (2012) A least angle regression model for the prediction of canonical and non-canonical miRNA-mRNA interactions. PloS ONE 7 (7), e40634.

Förster, Frank, Beisser, Daniela, Grohme, Markus A., Liang, Chunguang, Mali, Brahim, Siegl, Alexander Matthias, Engelmann, Julia C., Shkumatov, Alexander V., Schokraie, Elham, Müller, Tobias, Schnölzer, Martina, Schill, Ralph O., Frohme, Marcus und Dandekar, Thomas (2012) Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. Bioinformatics and biology insights 6, S. 69-96.

Förster, Frank, Liang, Chunguang, Shkumatov, Alexander V., Beisser, Daniela, Engelmann, Julia C., Schnölzer, Martina, Frohme, Marcus, Müller, Tobias, Schill, Ralph O. und Dandekar, Thomas (2009) Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. BMC genomics 10, S. 469.

Lee, Chil-Woo, Efetova, Marina, Engelmann, Julia C., Kramell, Robert, Wasternack, Claus, Ludwig-Müller, Jutta, Hedrich, Rainer und Deeken, Rosalia (2009) Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana. The Plant cell 21 (9), S. 2948-2962. Volltext nicht vorhanden.

Engelmann, Julia C., Rahmann, Sven, Wolf, Matthias, Schultz, Jörg, Fritzilas, Epameinondas, Kneitz, Susanne, Dandekar, Thomas und Müller, Tobias (2009) Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular ecology resources 9 (1), S. 83-93. Volltext nicht vorhanden.

Engelmann, Julia C., Deeken, R., Muller, T., Nimtz, G., Roelfsema, M. R. und Hedrich, R. (2008) Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach. Advances and Applications in Bioinformatics and Chemistry (Adv Appl Bioinform Chem) 1, S. 71-83.

Engelmann, Julia C., Schwarz, Roland, Blenk, Steffen, Friedrich, Torben, Seibel, Philipp N., Dandekar, Thomas und Müller, Tobias (2008) Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation. Bioinformatics and biology insights 2, S. 265-280.

Blenk, Steffen, Engelmann, Julia C., Pinkert, Stefan, Weniger, Markus, Schultz, Jörg, Rosenwald, Andreas, Müller-Hermelink, Hans K., Müller, Tobias und Dandekar, Thomas (2008) Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis. BMC cancer 8, S. 106.

Blenk, S., Engelmann, Julia C., Weniger, M., Schultz, J., Dittrich, M., Rosenwald, A., Müller-Hermelink, H. K., Müller, T. und Dandekar, T. (2007) Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): analysis of molecular predictors, signatures, cell cycle state and patient survival. Cancer Informatics 3, S. 399-420.

Weniger, M., Engelmann, Julia C. und Schultz, J. (2007) Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. BMC Bioinformatics 8, S. 179.