Entries of Engelmann, Julia C. on the publication server

Linck-Paulus, Lisa , Lämmerhirt, Lisa, Völler, Daniel, Meyer, Katharina, Engelmann, Julia C. , Spang, Rainer, Eichner, Norbert, Meister, Gunter, Kuphal, Silke and 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), p. 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 and Kube, D. (2019) High CD206 levels in Hodgkin lymphoma-educated macrophages are linked to matrix-remodeling and lymphoma dissemination. Mol Oncol. Fulltext not available.

Perez-Rubio, Paula, Lottaz, Claudio and Engelmann, Julia C. (2019) FastqPuri: high-performance preprocessing of RNA-seq data. BMC Bioinformatics 20 (1), p. 226. Fulltext not available.

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. and Hummel, Michael (2019) Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma. BMC Cancer 19 (1), p. 322.

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

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. and Kube, D. (2018) Cooperative STAT/NF-κB signaling regulates lymphoma metabolic reprogramming and aberrant GOT2 expression. Nat Commun 9 (1), p. 1514.

Chen, J., Strieder, Nicholas, Krohn, Nadia G., Cyprys, P., Sprunck, Stefanie, Engelmann, Julia C. and 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 and 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), pp. 1091-1098. Fulltext not available.

Feist, M., Kemper, J., Taruttis, Franziska, Rehberg, Thorsten, Engelmann, Julia C. , Gronwald, Wolfram, Hummel, Michael, Spang, Rainer and 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. Fulltext not available.

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 and 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, pp. 1105-1120. Fulltext not available.

Taruttis, Franziska, Feist, M., Schwarzfischer, Philipp, Gronwald, Wolfram, Kube, D., Spang, Rainer and 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), pp. 53-61. Fulltext not available.

Lottaz, Claudio, Gronwald, Wolfram , Spang, Rainer and 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, pp. 205-229. ISBN 978-1-4939-6611-0. Fulltext not available.

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. and 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), pp. 2088-2106. Fulltext not available.

Dueck, A., Evers, M., Henz, S. R., Unger, K., Eichner, N., Merkl, Rainer , Berezikov, E. , Engelmann, Julia C., Weigel, D. , Wenzl, S. and 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), p. 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. and 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. and 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), pp. 1206-1220.

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

Hochrein, Jochen, Zacharias, Helena, Taruttis, Franziska, Samol, Claudia, Engelmann, Julia C. , Spang, Rainer, Oefner, Peter J. and 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), pp. 3217-3228. Fulltext not available.

Taruttis, Franziska, Spang, Rainer and Engelmann, Julia C. (2015) A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA). Bioinformatics 31, p. 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 and 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), pp. 1-22.

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

Dorn, Christoph, Engelmann, Julia C. , Saugspier, Michael Sebastian, Koch, Andreas, Hartmann, Arndt, Spang, Rainer, Bosserhoff, Anja Katrin, Hellerbrand, Claus and make_name_string expected hash reference (2014) Increased expression of c-Jun in nonalcoholic fatty liver disease. Laboratory Investigation 94, pp. 394-408. Fulltext not available.

Dorn, Christoph, Engelmann, Julia C. , Saugspier, Michael, Koch, Andreas, Hartmann, Arndt, Müller, Martina, Spang, Rainer, Bosserhoff, Anja and Hellerbrand, Claus (2014) Increased expression of c-Jun in nonalcoholic fatty liver disease. Laboratory Investigation 94 (4), pp. 394-408. Fulltext not available.

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 and 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 and 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. Fulltext not available.

Vogelmann, Katja, Drechsel, Gabriele, Bergler, Johannes, Subert, Christa, Philippar, Katrin , Soll, Jürgen, Engelmann, Julia C. , Engelsdorf, Timo , Voll, Lars M. and Hoth, Stefan (2012) Early senescence and cell death in Arabidopsis saul1 mutants involves the PAD4-dependent salicylic acid pathway. Plant physiology 159 (4), pp. 1477-1487. Fulltext not available.

Engelmann, Julia C. and 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 and Dandekar, Thomas (2012) Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. Bioinformatics and biology insights 6, pp. 69-96.

Förster, Frank, Liang, Chunguang, Shkumatov, Alexander V., Beisser, Daniela, Engelmann, Julia C., Schnölzer, Martina, Frohme, Marcus, Müller, Tobias, Schill, Ralph O. and 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, p. 469.

Lee, Chil-Woo, Efetova, Marina, Engelmann, Julia C., Kramell, Robert, Wasternack, Claus, Ludwig-Müller, Jutta, Hedrich, Rainer and Deeken, Rosalia (2009) Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana. The Plant cell 21 (9), pp. 2948-2962. Fulltext not available.

Engelmann, Julia C., Rahmann, Sven, Wolf, Matthias, Schultz, Jörg, Fritzilas, Epameinondas, Kneitz, Susanne, Dandekar, Thomas and Müller, Tobias (2009) Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular ecology resources 9 (1), pp. 83-93. Fulltext not available.

Engelmann, Julia C., Deeken, R., Muller, T., Nimtz, G., Roelfsema, M. R. and 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, pp. 71-83.

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

Blenk, Steffen, Engelmann, Julia C., Pinkert, Stefan, Weniger, Markus, Schultz, Jörg, Rosenwald, Andreas, Müller-Hermelink, Hans K., Müller, Tobias and 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, p. 106.

Blenk, S., Engelmann, Julia C., Weniger, M., Schultz, J., Dittrich, M., Rosenwald, A., Müller-Hermelink, H. K., Müller, T. and 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, pp. 399-420.

Weniger, M., Engelmann, Julia C. and 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, p. 179.