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Bibliography of the Universität Regensburg

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Number of items at this level: 208.

2024

Pfahler, Simon, Georg, Peter, Schill, Rudolf , Klever, Maren, Grasedyck, Lars, Spang, Rainer and Wettig, Tilo (2024) Taming numerical imprecision by adapting the KL divergence to negative probabilities. arXiv.

Rupp, Kevin, Lösch, Andreas, Hu, Y. Linda , Nie, Chenxi, Schill, Rudolf , Klever, Maren, Pfahler, Simon, Grasedyck, Lars, Wettig, Tilo, Beerenwinkel, Niko and Spang, Rainer (2024) Modeling metastatic progression from cross-sectional cancer genomics data. Bioinformatics 40 (suppl1), i140-i150.

Glehr, Gunther , Riquelme, Paloma , Kronenberg, Katharina, Lohmayer, Robert, López-Madrona, Víctor J., Kapinsky, Michael, Schlitt, Hans J. , Geissler, Edward K. , Spang, Rainer, Haferkamp, Sebastian and Hutchinson, James A. (2024) Restricting datasets to classifiable samples augments discovery of immune disease biomarkers. Nature Communications 15 (1).

Huttner, Michael (2024) Infrastructure for digital medicine and AI enhanced pathology. PhD, Universität Regensburg.

Rupp, Kevin, Schill, Rudolf , Süskind, Jonas, Georg, Peter, Klever, Maren, Lösch, Andreas, Grasedyck, Lars, Wettig, Tilo and Spang, Rainer (2024) Differentiated uniformization: a new method for inferring Markov chains on combinatorial state spaces including stochastic epidemic models. Computational Statistics.

Schill, Rudolf , Klever, Maren, Rupp, Kevin, Hu, Y. Linda , Lösch, Andreas, Georg, Peter, Pfahler, Simon, Vocht, Stefan, Hansch, Stefan, Wettig, Tilo , Grasedyck, Lars and Spang, Rainer (2024) Reconstructing Disease Histories in Huge Discrete State Spaces. KI - Künstliche Intelligenz.

2023

Schill, Rudolf, Klever, Maren, Lösch, Andreas, Hu, Y. Linda , Vocht, Stefan, Rupp, Kevin, Grasedyck, Lars, Spang, Rainer and Beerenwinkel, Niko (2023) Overcoming Observation Bias for Cancer Progression Modeling. bioRxiv. (Submitted)

Leich, E., Brodtkorb, Marianne, Schmidt, T., Altenbuchinger, Michael, Lingjærde, Ole Christian, Lockmer, S., Holte, H., Nedeva, T., Grieb, T., Sander, B., Sundström, C., Spang, Rainer, Kimby, E. and Rosenwald, A. (2023) Gene expression and copy number profiling of follicular lymphoma biopsies from patients treated with first-line rituximab without chemotherapy. Leukemia & lymphoma, pp. 1-11. Fulltext not available.

Buck, Lena, Schmidt, Tobias, Feist, Maren, Schwarzfischer, Philipp, Kube, Dieter, Oefner, Peter J. , Zacharias, Helena U., Altenbuchinger, Michael , Dettmer, Katja , Gronwald, Wolfram and Spang, Rainer (2023) Anomaly detection in mixed high dimensional molecular data. Bioinformatics 39 (8), btad501.

Rösler, Wiebke, Altenbuchinger, Michael, Baeßler, Bettina, Beissbarth, Tim, Beutel, Gernot, Bock, Robert, von Bubnoff, Nikolas, Eckardt, Jan-Niklas, Foersch, Sebastian, Loeffler, Chiara M L, Middeke, Jan Moritz, Mueller, Martha-Lena, Oellerich, Thomas, Risse, Benjamin, Scherag, André, Schliemann, Christoph, Scholz, Markus, Spang, Rainer , Thielscher, Christian, Tsoukakis, Ioannis and Kather, Jakob Nikolas (2023) An overview and a roadmap for artificial intelligence in hematology and oncology. Journal of cancer research and clinical oncology.

Hu, Linda, Lösch, Andreas and Spang, Rainer (2023) Maschinelles lernen enthüllt den verborgenen Prozess der Tumorentstehung. Blick in die Wissenschaft : Forschungsmagazin der Universität Regensburg 31 (44/45), pp. 52-53. Fulltext not available.

2022

Schill, Rudolf (2022) Mutual Hazard Networks: Markov chain models of cancer progression. PhD, Universität Regensburg.

Georg, Peter, Grasedyck, Lars, Klever, Maren, Schill, Rudolf , Spang, Rainer and Wettig, Tilo (2022) Low-rank tensor methods for Markov chains with applications to tumor progression models. Journal of Mathematical Biology 86 (7).

Hassel, Jessica C., Schank, Timo E., Smetak, Heiko, Mühlbauer, Jasmin, Salzmann, Martin, Machiraju, Devayani, Menzer, Christian, Lang, Kristin, König, Laila, Haefner, Matthias F., Hülsmeyer, Ingrid, Kohler, Christian , Spang, Rainer , Enk, Alexander, Debus, Jürgen and Beckhove, Philipp (2022) Evaluation of radio-immunotherapy sequence on immunological responses and clinical outcomes in patients with melanoma brain metastases (ELEKTRA). Oncoimmunology 11 (1), p. 2066609.

Schrod, Stefan, Schäfer, Andreas, Solbrig, Stefan, Lohmayer, Robert, Gronwald, Wolfram , Oefner, Peter J. , Beißbarth, Tim, Spang, Rainer , Zacharias, Helena U. and Altenbuchinger, Michael (2022) BITES: Balanced Individual Treatment Effect for Survival data. arXiv. (Submitted)

2021

Schilling, Hannah-Lou, Glehr, Gunther , Kapinsky, Michael, Ahrens, Norbert , Riquelme, Paloma , Cordero, Laura, Bitterer, Florian, Schlitt, Hans J. , Geissler, Edward K. , Haferkamp, Sebastian, Hutchinson, James A. and Kronenberg, Katharina (2021) Development of a Flow Cytometry Assay to Predict Immune Checkpoint Blockade-Related Complications. Frontiers in Immunology 2021 (12), pp. 1-12. Fulltext restricted.

Richter, Julia , John, Katharina, Staiger, Annette M., Rosenwald, Andreas, Kurz, Katrin, Michgehl, Ulf, Ott, German, Franzenburg, Sören, Kohler, Christian , Finger, Jasmin, Oschlies, Ilske, Paul, Ulrike, Siebert, Reiner, Spang, Rainer , Burkhardt, Birgit and Klapper, Wolfram (2021) Epstein-Barr virus status of sporadic Burkitt lymphoma is associated with patient age and mutational features. British journal of haematology 196 (3), pp. 681-689.

Croci, G. A., Au-Yeung, R. K. H., Reinke, S., Staiger, A. M., Koch, K., Oschlies, I., Richter, J., Poeschel, V., Held, G., Loeffler, M., Trümper, L., Rosenwald, A., Ott, G., Spang, Rainer, Altmann, B., Ziepert, M. and Klapper, W. (2021) SPARC-positive macrophages are the superior prognostic factor in the microenvironment of diffuse large B-cell lymphoma and independent of MYC rearrangement and double-/triple-hit status. Annals of Oncology. Fulltext not available.

Jachimowicz, Ron D., Klapper, Wolfram, Glehr, Gunther , Müller, Horst, Haverkamp, Heinz, Thorns, Christoph, Hansmann, Martin Leo, Möller, Peter, Stein, Harald, Rehberg, Thorsten, von Tresckow, Bastian, Reinhardt, H. C., Borchmann, Peter, Chan, Fong Chun, Spang, Rainer, Scott, David W., Engert, Andreas, Steidl, Christian, Altenbuchinger, Michael and Rosenwald, Andreas (2021) Gene expression-based outcome prediction in advanced stage classical Hodgkin lymphoma treated with BEACOPP. Leukemia.

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.

Zacharias, Helena U. , Altenbuchinger, Michael, Schultheiss, Ulla T., Raffler, Johannes , Kotsis, Fruzsina, Ghasemi, Sahar, Ali, Ibrahim, Kollerits, Barbara, Metzger, Marie, Steinbrenner, Inga, Sekula, Peggy , Massy, Ziad A., Combe, Christian, Kalra, Philip A., Kronenberg, Florian, Stengel, Bénédicte , Eckardt, Kai-Uwe, Köttgen, Anna, Schmid, Matthias , Gronwald, Wolfram and Oefner, Peter J. (2021) A Predictive Model for Progression of CKD to Kidney Failure Based on Routine Laboratory Tests. American Journal of Kidney Diseases. Fulltext not available.

Nordmo, Carmen, Glehr, Gunther, Altenbuchinger, Michael, Spang, Rainer, Ziepert, Marita, Horn, Heike, Staiger, Annette M., Ott, German, Schmitz, Norbert, Held, Gerhard, Einsele, Hermann, Topp, Max, Rosenwald, Andreas and Rauert-Wunderlich, Hilka (2021) Identification of a miRNA based model to detect prognostic subgroups in patients with aggressive B-cell lymphoma. Leukemia & Lymphoma 62 (5), pp. 1107-1115. Fulltext not available.

Taruttis-Glagoleff, Franziska (2021) Modeling MYC-dependent regulation of gene expression and cell metabolism in B-cell lymphomas. PhD, Universität Regensburg.

Hutchinson, James A. , Kronenberg, Katharina, Riquelme, Paloma, Wenzel, Jürgen J. , Glehr, Gunther , Schilling, Hannah-Lou , Zeman, Florian, Evert, Katja, Schmiedel, Martin, Mickler, Marion, Drexler, Konstantin, Bitterer, Florian, Cordero, Laura, Beyer, Lukas Philipp, Bach, Christian, Koestler, Josef, Burkhardt, Ralph , Schlitt, Hans J., Hellwig, Dirk, Werner, Jens M., Spang, Rainer, Schmidt, Barbara, Geissler, Edward K. and Haferkamp, Sebastian (2021) Virus-specific memory T cell responses unmasked by immune checkpoint blockade cause hepatitis. Nature Communications 12, p. 1439.

2020

Görtler, Franziska (2020) Loss-Function Learning for Digital Tissue Deconvolution. PhD, Universität Regensburg.

Reinders, Jörg, Altenbuchinger, Michael, Limm, Katharina , Schwarzfischer, Philipp, Scheidt, Tamara, Strasser, Lisa, Richter, Julia, Szczepanowski, Monika, Huber, Christian G. , Klapper, Wolfram, Spang, Rainer and Oefner, Peter J. (2020) Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue. Scientific Reports 10 (7876), pp. 1-11.

Stämmler, Frank Michael Nikolaus (2020) Standardisation and optimisation techniques in gut microbiome community analysis. PhD, Universität Regensburg.

Schoen, Marian, Simeth, Jakob , Heinrich, Paul, Goertler, F., Solbrig, Stefan, Wettig, Tilo, Oefner, Peter J., Altenbuchinger, Michael and Spang, Rainer (2020) DTD: An R Package for Digital Tissue Deconvolution. J. Comput. Biol.. Fulltext not available.

Goertler, Franziska, Schoen, Marian, Simeth, Jakob , Solbrig, Stefan, Wettig, Tilo, Oefner, Peter J., Spang, Rainer and Altenbuchinger, Michael (2020) Loss-Function Learning for Digital Tissue Deconvolution. J. Comput. Biol.. Fulltext not available.

Minderjahn, Julia, Schmidt, Andreas, Fuchs, Andreas , Schill, Rudolf, Raithel, Johanna, Babina, Magda , Schmidl, C. , Gebhard, Claudia, Schmidhofer, Sandra, Mendes, Karina , Ratermann, Anna, Glatz, Dagmar, Nützel, Margit, Edinger, Matthias, Hoffmann, Petra, Spang, Rainer , Längst, Gernot, Imhof, A. and Rehli, Michael (2020) Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. Nat Commun 11, p. 402.

Schill, Rudolf, Solbrig, Stefan, Wettig, Tilo and Spang, Rainer (2020) Modelling cancer progression using Mutual Hazard Networks. Bioinformatics 36 (1), pp. 241-249. Fulltext not available.

Klim, S. M., Amerstorfer, F., Glehr, G. , Hauer, G., Smolle, M. A., Leitner, L. , Leithner, A. and Glehr, M. (2020) Combined serum biomarker analysis shows no benefit in the diagnosis of periprosthetic joint infection. International Orthopaedics 44 (12), pp. 2515-2520. Fulltext not available.

2019

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.

Altenbuchinger, Michael, Zacharias, Helena, Solbrig, S., Schaefer, Andreas, Buyukozkan, M., Schultheiss, U. T. , Kotsis, F., Köttgen, Anna, Spang, Rainer, Oefner, Peter J., Krumsiek, J. and Gronwald, Wolfram (2019) A multi-source data integration approach reveals novel associations between metabolites and renal outcomes in the German Chronic Kidney Disease study. Scientific Reports 9 (1), p. 13954.

Staiger, A. M., Altenbuchinger, Michael, Ziepert, M., Kohler, Christian, Horn, H., Huttner, Michael , Huttl, K. S., Glehr, Gunther , Klapper, W., Szczepanowski, M., Richter, J., Stein, H., Feller, A. C., Moller, P., Hansmann, M. L., Poeschel, V., Held, G., Loeffler, M., Schmitz, N., Trumper, L., Pukrop, T., Rosenwald, A., Ott, G., Spang, Rainer , Emed Demonstrator Project, and German High Grade Non-Hodgkin’s Lymphoma Study Group (DSHNHL), (2019) A novel lymphoma-associated macrophage interaction signature (LAMIS) provides robust risk prognostication in diffuse large B-cell lymphoma clinical trial cohorts of the DSHNHL. Leukemia 34, pp. 543-552. Fulltext not available.

Wagner, M., Hansel, R., Reinke, S., Richter, J., Altenbuchinger, Michael, Braumann, U. D., Spang, Rainer, Loffler, M. and Klapper, W. (2019) Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach. Biol Proced Online 21, p. 13.

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.

Itzel, T., Spang, Rainer, Maass, T., Munker, S., Roessler, S. , Ebert, M. P., Schlitt, Hans J., Herr, Wolfgang, Evert, Matthias and Teufel, A. (2019) Random gene sets in predicting survival of patients with hepatocellular carcinoma. J. Mol. Med.. 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.

Zacharias, Helena, Altenbuchinger, Michael, Schultheiss, U. T., Samol, Claudia, Kotsis, F., Poguntke, I., Sekula, P. , Krumsiek, J., Köttgen, Anna, Spang, Rainer, Oefner, Peter J. and Gronwald, Wolfram (2019) A Novel Metabolic Signature To Predict the Requirement of Dialysis or Renal Transplantation in Patients with Chronic Kidney Disease. Journal of Proteome Research. Fulltext not available.

Schnitter, A., Kohler, Christian , Reddemann, K., Reinke, S., Thorns, C., Fend, F., Federmann, B., Moeller, P., Szczepanowski, Monika, Spang, Rainer and Klapper, Wolfram (2019) Therapeutic targets and microenvironment in sequential biopsies of classical Hodgkin lymphoma at diagnosis and relapse. Journal of Hematopathology 12 (1), pp. 11-17.

Ziegler, Christian, Graf, Johannes, Faderl, Stefan, Schedlbauer, Jessica, Strieder, Nicholas, Förstl, Bianca, Spang, Rainer, Bruckmann, Astrid, Merkl, Rainer , Hombach, Sonja and Kretz, Markus (2019) The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis. EMBO Rep., e46612. Fulltext not available.

2018

Wagener, R., Seufert, J., Raimondi, F., Bens, S., Kleinheinz, K., Nagel, I., Altmueller, J., Thiele, H., Huebschmann, D., Kohler, Christian, Nürnberg, P., Au-Yeung, R., Burkhardt, B., Horn, H., Leoncini, L., Jaffe, E. S., Ott, G., Rymkiewicz, G. , Schlesner, M. , Russell, R. B. , Klapper, W. and Siebert, R. (2018) The mutational landscape of Burkitt-like lymphoma with 11q aberration is distinct from that of Burkitt lymphoma. Blood. Fulltext not available.

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

Heinrich, Paul, Kohler, Christian , Ellmann, Lisa, Kuerner, Paul, Spang, Rainer, Oefner, Peter J. and Dettmer, Katja (2018) Correcting for natural isotope abundance and tracer impurity in MS-, MS/MS- and high-resolution-multiple-tracer-data from stable isotope labeling experiments with IsoCorrectoR. Scientific Reports 8 (17910), pp. 1-10.

Zacharias, Helena , Altenbuchinger, Michael and Gronwald, Wolfram (2018) Statistical Analysis of NMR Metabolic Fingerprints: Established Methods and Recent Advances. Metabolites 8 (3).

Fröhlich, Holger, Balling, R. , Beerenwinkel, N., Kohlbacher, O., Kumar, S., Lengauer, T., Maathuis, M. H., Moreau, Y., Murphy, S. A., Przytycka, T. M. , Rebhan, M., Rost, H. , Schuppert, A. , Schwab, M., Spang, Rainer, Stekhoven, D., Sun, J., Weber, A., Ziemek, D. and Zupan, B. (2018) From hype to reality: data science enabling personalized medicine. BMC Med 16 (1), p. 150.

Cho, H., Berger, B., Peng, J., Galitzine, C., Vitek, O., Beltran, P. M. J., Cristea, I. M., Görtler, Franziska, Solbrig, Stefan, Wettig, Tilo, Oefner, Peter J. , Spang, Rainer, Altenbuchinger, Michael, Basso, R. S., Hochbaum, D., Vandin, F., Silverbush, D., Cristea, S., Yanovich, G., Geiger, T., Beerenwinkel, N., Sharan, R., Zhou, Z., Luhmann, N., Alikhan, N. F. and Achtman, M. (2018) Principles of Systems Biology, No. 31. Cell Syst 7 (2), pp. 133-135. Fulltext not available.

Reinke, Sarah , Richter, Julia, Fend, Falko, Feller, Alfred, Hansmann, Martin-Leo, Hüttl, Katrin, Oschlies, Ilske, Ott, German, Möller, Peter, Rosenwald, Andreas, Stein, Harald, Altenbuchinger, Michael, Spang, Rainer and Klapper, Wolfram (2018) Round-robin test for the cell-of-origin classification of diffuse large B-cell lymphoma—a feasibility study using full slide staining. Virchows Archiv. Fulltext not available.

Görtler, Franziska, Solbrig, Stefan, Wettig, Tilo, Oefner, Peter J. , Spang, Rainer and Altenbuchinger, Michael (2018) Loss-function learning for digital tissue deconvolution. In: Raphael, Benjamin J., (ed.) Research in Computational Molecular Biology : 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings. Lecture Notes in Computer Science, 10812. Springer International Publishing, Cham, pp. 75-89. ISBN 978-3-319-89929-9 ; 978-3-319-89928-2. Fulltext not available.

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.

Horn, H., Kohler, Christian, Witzig, R., Kreuz, M. , Leich, E., Klapper, W., Hummel, M., Loeffler, M., Trumper, L., Spang, Rainer, Rosenwald, A. and Ott, G. (2018) Gene expression profiling reveals a close relationship between follicular lymphoma grade 3A and 3B, but distinct profiles of follicular lymphoma grade 1 and 2. Haematologica. Fulltext not available.

Moll, Anton G. (2018) Semi-supervised Classification of Breast Cancer Expression Profiles Using Neural Networks. PhD, Universität Regensburg.

Schill, Rudolf, Solbrig, Stefan, Wettig, Tilo and Spang, Rainer (2018) Modelling cancer progression using Mutual Hazard Networks. biorxiv.org. (Submitted)

Riquelme, Paloma , Haarer, Jan, Kammler, Anja, Walter, Lisa , Tomiuk, Stefan, Ahrens, Norbert , Wege, Anja K. , Goecze, Ivan, Zecher, Daniel, Banas, Bernhard , Spang, Rainer , Fändrich, Fred, Lutz, Manfred B., Sawitzki, Birgit, Schlitt, Hans J. , Ochando, Jordi , Geissler, Edward K. and Hutchinson, James A. (2018) TIGIT+ iTregs elicited by human regulatory macrophages control T cell immunity. Nature Communications 9 (2858), pp. 1-18.

2017

Paul, U., Richter, J., Stuhlmann-Laiesz, C., Kreuz, M. , Nagel, I., Horn, H., Staiger, A. M., Aukema, S. M., Hummel, M., Ott, G., Spang, Rainer, Rosenwald, A., Feller, A. C., Cogliatti, S., Stein, H., Hansmann, M. L., Moller, P., Szczepanowski, M., Burkhardt, B., Pfreundschuh, M., Schmitz, N., Loeffler, M., Trumper, L., Siebert, R. and Klapper, W. (2017) Advanced patient age at diagnosis of diffuse large B-cell lymphoma is associated with molecular characteristics including ABC-subtype and high expression of MYC. Leuk. Lymphoma, pp. 1-9. Fulltext not available.

Zacharias, Helena, Rehberg, Thorsten, Mehrl, S., Richtmann, D., Wettig, Tilo, Oefner, Peter J., Spang, Rainer, Gronwald, Wolfram and Altenbuchinger, Michael (2017) Scale-Invariant Biomarker Discovery in Urine and Plasma Metabolite Fingerprints. J. Proteome Res.. Fulltext not available.

Cascione, L., Rinaldi, A., Chiappella, A., Kwee, I., Ciccone, G., Altenbuchinger, Michael, Kohler, Christian , Vitolo, U., Inghirami, G. and Bertoni, F. (2017) Diffuse large B cell lymphoma cell of origin by digital expression profiling in the REAL07 Phase 1-2 study. Br J Haematol. Fulltext not available.

Altenbuchinger, Michael, Schwarzfischer, Philipp, Rehberg, Thorsten, Reinders, Jörg , Kohler, Christian , Gronwald, Wolfram , Richter, J., Szczepanowski, M., Masqué-Soler, N., Klapper, W., Oefner, Peter J. and Spang, Rainer (2017) Molecular signatures that can be transferred across different omics platforms. Bioinformatics 33 (14), i333-i340. Fulltext not available.

Oschlies, I., Kohler, Christian, Szczepanowski, Monika, Koch, K., Gontarewicz, A., Metze, D., Hillen, U., Richter, J., Spang, Rainer and Klapper, W. (2017) Spindle-cell variant of primary cutaneous follicle center B-cell lymphomas are germinal center B-cell lymphomas by gene expression profiling using formalin-fixed paraffin embedded specimen. J Invest Dermatol. Fulltext not available.

Szczepanowski, M., Lange, J., Kohler, Christian, Masque-Soler, N., Zimmermann, M., Aukema, S. M., Altenbuchinger, Michael, Rehberg, Thorsten, Mahn, F., Siebert, R., Spang, Rainer, Burkhardt, B. and Klapper, W. (2017) Cell-of-origin classification by gene expression and MYC-rearrangements in diffuse large B-cell lymphoma of children and adolescents. Br. J. Haematol.. Fulltext not available.

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.

Maliniemi, P. , Laukkanen, K., Vakeva, L., Dettmer, Katja , Lipsanen, T., Jeskanen, L., Bessede, A., Oefner, Peter J., Kadin, M. E. and Ranki, A. (2017) Biological and clinical significance of tryptophan-catabolizing enzymes in cutaneous T-cell lymphomas. Oncoimmunology 6 (3), e1273310. 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.

2016

Hosseini, H., Obradovic, M. M., Hoffmann, M., Harper, K. L., Sosa, M. S., Werner-Klein, M., Nanduri, L. K. , Werno, C., Ehrl, C., Maneck, M., Patwary, N., Haunschild, G., Guzvic, M., Reimelt, C., Grauvogl, Michael, Eichner, N., Weber, F., Hartkopf, A. D., Taran, F. A., Brucker, S. Y., Fehm, T., Rack, B., Buchholz, S., Spang, Rainer, Meister, Gunter, Aguirre-Ghiso, J. A. and Klein, Christoph A. (2016) Early dissemination seeds metastasis in breast cancer. Nature 540, pp. 552-558. 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.

Altenbuchinger, Michael, Rehberg, Thorsten, Zacharias, Helena, Stämmler, Frank, Dettmer, Katja , Weber, Daniela, Hiergeist, Andreas, Gessner, Andre, Holler, Ernst, Oefner, Peter J. and Spang, Rainer (2016) Reference point insensitive molecular data analysis. Bioinformatics.

Pirkl, Martin Franz-Xaver (2016) Indirect inference of synergistic and alternative signalling of intracellular pathways. PhD, Universität Regensburg.

Stämmler, Frank, Glasner, J., Hiergeist, Andreas, Holler, Ernst, Weber, Daniela, Oefner, Peter J. , Gessner, Andre and Spang, Rainer (2016) Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome 4 (1), p. 28.

Moffa, Giusi, Erdmann, Gerrit, Voloshanenko, Oksana, Hundsrucker, Christian, Sadeh, Mohammad Javad, Boutros, Michael and Spang, Rainer (2016) Refining Pathways: A Model Comparison Approach. PLoS One 11 (6), e0155999.

Teufel, Andreas, Itzel, Timo, Erhart, W., Brosch, M. , Wang, X. Y., Kim, Y. O., von Schoenfels, Witigo, Herrmann, A., Bruckner, S., Stickel, F., Dufour, J. F. , Chavakis, T., Hellerbrand, Claus, Spang, Rainer, Maass, Thorsten, Becker, T., Schreiber, S., Schafmayer, C., Schuppan, D. and Hampe, J. (2016) Comparison of Gene Expression Patterns Between Mouse Models of Nonalcoholic Fatty Liver Disease and Liver Tissues from Patients. Gastroenterology. Fulltext not available.

Schrader, A., Meyer, Katharina, Walther, N., Stolz, A., Feist, M., Hand, E., Bonin, F. von, Evers, Maurits, Kohler, Christian, Shirneshan, K., Vockerodt, M., Klapper, W., Szczepanowski, M., Murray, P. G., Bastians, H., Trümper, Lorenz, Spang, Rainer and Kube, Dieter (2016) Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data. OncoTarget.

Weber, Daniela, Oefner, Peter J., Dettmer, Katja , Hiergeist, Andreas, Koestler, Josef, Gessner, Andre, Weber, Markus, Stämmler, Frank, Hahn, Joachim, Wolff, Daniel, Herr, Wolfgang and Holler, Ernst (2016) Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation. Bone Marrow Transplant.. Fulltext not available.

Moeckel, Sylvia, Vollmann-Zwerenz, Arabel, Proescholdt, Martin A., Brawanski, Alexander, Riemenschneider, Markus J., Bogdahn, Ulrich, Bosserhoff, A. K. , Spang, Rainer and Hau, Peter (2016) Validation Study: Response-Predictive Gene Expression Profiling of Glioma Progenitor Cells In Vitro. PLoS ONE 11 (3), e0151312.

Voelxen, N. F., Walenta, S., Proescholdt, Martin A., Dettmer, Katja , Pusch, S. and Mueller-Klieser, W. (2016) Quantitative Imaging of D-2-Hydroxyglutarate in Selected Histological Tissue Areas by a Novel Bioluminescence Technique. Frontiers in Oncology 6, p. 46.

Mönchgesang, Susann, Strehmel, Nadine, Schmidt, Stephan, Westphal, Lore, Taruttis, Franziska, Müller, Erik, Herklotz, Siska, Neumann, Steffen and Scheel, Dierk (2016) Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data. Scientific Reports 6 (1). Fulltext not available.

2015

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.

Pirkl, Martin, Hand, E., Kube, D. and Spang, Rainer (2015) Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models. Bioinformatics.

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.

Masqué-Soler, Neus, Szczepanowski, Monika, Kohler, Christian W., Aukema, Sietse M., Nagel, Inga, Richter, Julia, Siebert, Reiner, Spang, Rainer, Burkhardt, Birgit and Klapper, Wolfram (2015) Clinical and pathological features of Burkitt lymphoma showing expression of BCL2 - an analysis including gene expression in formalin-fixed paraffin-embedded tissue. British Journal of Haematology = Br J Haematol 171, pp. 501-508.

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.

Weber, Daniela, Oefner, Peter J., Hiergeist, Andreas, Koestler, Josef, Gessner, Andre, Weber, Markus, Hahn, Joachim, Wolff, Daniel, Stämmler, Frank, Spang, Rainer, Herr, Wolfgang, Dettmer, Katja and Holler, Ernst (2015) Low urinary indoxyl sulfate levels early after transplantation reflect a disrupted microbiome and are associated with poor outcome. Blood 126 (14), pp. 1723-1728.

2014

Hau, Peter, Moeckel, Sylvia, Meyer, Katharina, Leukel, Petra, Heudorfer, Fabian, Seliger, Corinna, Stangl, Christina, Bogdahn, Ulrich, Proescholdt, Martin A., Brawanski, Alexander, Vollmann-Zwerenz, Arabel, Riemenschneider, Markus J., Bosserhoff, Anja-Katrin and Spang, Rainer (2014) Response-Predictive Gene Expression Profiling of Glioma Progenitor Cells In Vitro. PLoS ONE 9 (9), e108632.

Winkler, Thomas W., Kutalik, Zoltan, Gorski, Mathias, Lottaz, Claudio, Kronenberg, Florian and Heid, Iris M. (2014) EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data. Bioinformatics, btu621. Fulltext not available.

Vossenkämper, Anna, Hundsrucker, Christian, Page, Kevin, van Maurik, Andre, Sanders, Theodore J., Stagg, Andrew J., Das, Lisa and MacDonald, Thomas T. (2014) A CD3-Specific Antibody Reduces Cytokine Production and Alters Phosphoprotein Profiles in Intestinal Tissues From Patients With Inflammatory Bowel Disease. The American Journal of Gastroenterology 147 (1), pp. 172-183. Fulltext not available.

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.

Holler, Ernst, Butzhammer, Peter, Schmid, Karin, Hundsrucker, Christian, Koestler, Josef, Peter, Katrin, Zhu, Wentao, Sporrer, Daniela, Hehlgans, Thomas, Kreutz, Marina, Holler, Barbara, Wolff, Daniel, Edinger, Matthias, Andreesen, Reinhard, Levine, John E., Ferrara, James L., Gessner, Andre, Spang, Rainer and Oefner, Peter J. (2014) Metagenomic analysis of the stool microbiome in patients receiving allogeneic SCT: Loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal GvHD. Biology of Blood and Marrow Transplantation 20 (5), pp. 640-645. Fulltext not available.

del Jel, Miriam M., Engelmann, Julia, Kunz, Manfred, Schiffner, Susanne, Kuphal, Silke and Bosserhoff, Anja (2014) Transcriptome sequencing of melanocytic nevi and melanomas from Grm1 transgenic mice to determine melanoma driver mutations. Pigment Cell & Melanoma Research 27, pp. 678-680. Fulltext not available.

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

Dümcke, Sebastian, Bräuer, Johannes, Anchang, Benedict Nchang, Spang, Rainer, Beerenwinkel, Niko and Tresch, Achim (2014) Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. Bioinformatics 30 (3), pp. 414-419.

Salaverria, Itziar, Martin-Guerrero, Idoia, Wagener, Rabea, Kreuz, Markus, Kohler, Christian, Richter, Julia, Pienkowska-Grela, Barbara, Adam, Patrick, Burkhardt, Birgit, Claviez, Alexander, Damm-Welk, Christine, Drexler, H. G., Hummel, Michael, Jaffe, Elaine S., Kueppers, Ralf, Lefebvre, Christine, Lisfeld, Jasmin, Loeffler, Markus, Mcleod, Roderick A., Nagel, Inga, Oschlies, Ilske, Rosolowski, Maciej, Russell, Robert B., Rymkiewicz, Grzegorz, Schindler, Detlev, Schlesner, Matthias, Scholtysik, Rene, Schwaenen, Carsten, Spang, Rainer, Szczepanowski, Monika, Truemper, Lorenz, Vater, Inga, Wessendorf, Swen, Klapper, Wolfram and Siebert, Rainer (2014) A recurrent 11q aberration pattern characterizes a subset of MYC-negative high-grade B-cell lymphomas resembling Burkitt lymphoma. Blood 123, pp. 1187-1198. Fulltext not available.

Kuipers, Jack, Moffa, Giusi and Heckerman, David (2014) Addendum on the scoring of Gaussian directed acyclic graphical models. Annals of Statistics 42 (4), pp. 1689-1691. (In Press) Fulltext not available.

Moffa, Giusi and Kuipers, Jack (2014) Sequential Monte Carlo EM for multivariate probit models. Comp. Stats. & Data An. 72, pp. 252-272. Fulltext not available.

2013

Schmid, Rainer, Meyer, Katharina, Spang, Rainer, Schittek, Birgit and Bosserhoff, Anja-Katrin (2013) YBX1 is a modulator of MIA/CD-RAP-dependent chondrogenesis. PLoS ONE 8 (12).

Sadeh, Mohammad Javad, Moffa, Giusi and Spang, Rainer (2013) Considering unknown unknowns: reconstruction of nonconfoundable causal relations in biological networks. Journal of computational biology 20 (11), pp. 920-932. Fulltext not available.

Voloshanenko, Oksana, Erdmann, Gerrit, Dubash, Taronish D., Augustin, Iris, Metzig, Marie, Moffa, Giusi, Hundsrucker, Christian, Kerr, Grainne, Sandmann, Thomas, Anchang, Benedikt, Demir, Kubilay, Boehm, Christina, Leible, Svenja, Ball, Claudia R., Glimm, Hanno, Spang, Rainer and Boutros, Michael (2013) Wnt secretion is required to maintain high levels of Wnt activity in colon cancer cells. Nature communications 4, p. 2610.

Masqué-Soler, Neus, Szczepanowski, Monika, Kohler, Christian, Spang, Rainer and Klapper, Wolfram (2013) Molecular classification of mature aggressive B-cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens. Blood 122 (11), pp. 1985-1986.

Schmid, Rainer, Meyer, Katharina, Spang, Rainer, Schittek, Birgit and Bosserhoff, Anja-Katrin (2013) Melanoma inhibitory activity promotes melanoma development through activation of YBX1. Pigment cell & melanoma research 26 (5), pp. 685-696. Fulltext not available.

Sadeh, Mohammad Javad (2013) Considering unknown unknown: reconstruction of non-confoundable causal relations in biological networks. PhD, Universität Regensburg.

Meyer, Katharina (2013) Dissolving heterogeneity in cancer. PhD, Universität Regensburg.

Walther, Neele, Ulrich, Antje, Vockerodt, Martina, von Bonin, Frederike, Klapper, Wolfram, Meyer, Katharina, Eberth, Sonja, Pukrop, Tobias, Spang, Rainer, Trümper, Lorenz and Kube, Dieter (2013) Aberrant lymphocyte enhancer-binding factor 1 expression is characteristic for sporadic Burkitt's lymphoma. The American journal of pathology 182 (4), pp. 1092-1098. Fulltext not available.

Kelly, Gemma L, Stylianou, Julianna, Rasaiyaah, Jane, Wei, Wenbin, Thomas, Wendy, Croom-Carter, Deborah, Kohler, Christian, Spang, Rainer, Woodman, Ciaran, Kellam, Paul, Rickinson, Alan N. and Bell, Andrew I. (2013) Different patterns of Epstein-Barr virus latency in endemic Burkitt lymphoma (BL) lead to distinct variants within the BL-associated gene expression signature. Journal of virology 87 (5), pp. 2882-2894.

Krentz, S., Hof, J., Mendioroz, A., Vaggopoulou, R., Dörge, P., Lottaz, Claudio, Engelmann, Julia, Groeneveld, T. W. L., Körner, G., Seeger, K., Hagemeier, C., Henze, G., Eckert, C., von Stackelberg, A. and Kirschner-Schwabe, R. (2013) Prognostic value of genetic alterations in children with first bone marrow relapse of childhood B-cell precursor acute lymphoblastic leukemia. Leukemia 27 (2), pp. 295-304. 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.

Aukema, Sietse M., Kreuz, Markus, Kohler, Christian, Rosolowski, Maciej, Hasenclever, Dirk, Hummel, Michael, Küppers, Ralf, Lenze, Dido, Ott, German, Pott, Christiane, Richter, Julia, Rosenwald, Andreas, Szczepanowski, Monika, Schwaenen, Carsten, Stein, Harald, Trautmann, Heiko, Wessendorf, Swen, Trümper, Lorenz, Loeffler, Markus, Spang, Rainer, Kluin, Philip M., Klapper, Wolfram and Siebert, Reiner (2013) Biological characterization of adult MYC-translocation-positive mature B-cell lymphomas other than molecular Burkitt lymphoma. Haematologica 99 (4), pp. 726-735.

Schif, Birgit, Lennerz, Jochen K., Kohler, Christian, Bentink, Stefan, Kreuz, Markus, Melzner, Ingo, Ritz, Olga, Trümper, Lorenz, Loeffler, Markus, Spang, Rainer and Möller, Peter (2013) SOCS1 mutation subtypes predict divergent outcomes in diffuse large B-Cell lymphoma (DLBCL) patients. Oncotarget 4 (1), pp. 35-47.

Seliger, Corinna, Leukel, Petra, Moeckel, Sylvia, Jachnik, Birgit, Lottaz, Claudio, Kreutz, Marina, Brawanski, Alexander, Proescholdt, Martin, Bogdahn, Ulrich, Bosserhoff, Anja-Katrin, Vollmann-Zwerenz, Arabel and Hau, Peter (2013) Lactate-Modulated Induction of THBS-1 Activates Transforming Growth Factor (TGF)-beta2 and Migration of Glioma Cells In Vitro. PloS one 8 (11), e78935.

Kuipers, Jack and Moffa, Giusi (2013) Uniform random generation of large acyclic digraphs. Stats. & Comp.. Fulltext not available.

2012

Hochrein, Jochen, Klein, Matthias S., Zacharias, Helena, Li, Juan, Wijffels, Gene, Schirra, Horst Joachim, Spang, Rainer, Oefner, Peter J. and Gronwald, Wolfram (2012) Performance evaluation of algorithms for the classification of metabolic 1H NMR fingerprints. Journal of proteome research 11 (12), pp. 6242-6251. Fulltext not available.

Richter, Julia, Schlesner, Matthias, Hoffmann, Steve, Kreuz, Markus, Leich, Ellen, Burkhardt, Birgit, Rosolowski, Maciej, Ammerpohl, Ole, Wagener, Rabea, Bernhart, Stephan H., Lenze, Dido, Szczepanowski, Monika, Paulsen, Maren, Lipinski, Simone, Russell, Robert B., Adam-Klages, Sabine, Apic, Gordana, Claviez, Alexander, Hasenclever, Dirk, Hovestadt, Volker, Hornig, Nadine, Korbel, Jan O., Kube, Dieter, Langenberger, David, Lawerenz, Chris, Lisfeld, Jasmin, Meyer, Katharina, Picelli, Simone, Pischimarov, Jordan, Radlwimmer, Bernhard, Rausch, Tobias, Rohde, Marius, Schilhabel, Markus, Scholtysik, René, Spang, Rainer, Trautmann, Heiko, Zenz, Thorsten, Borkhardt, Arndt, Drexler, Hans G., Möller, Peter, MacLeod, Roderick A. F., Pott, Christiane, Schreiber, Stefan, Trümper, Lorenz, Loeffler, Markus, Stadler, Peter F., Lichter, Peter, Eils, Roland, Küppers, Ralf, Hummel, Michael, Klapper, Wolfram, Rosenstiel, Philip, Rosenwald, Andreas, Brors, Benedikt and Siebert, Reiner (2012) Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nature genetics 44 (12), pp. 1316-1320. Fulltext not available.

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.

Beier, Christoph P., Kumar, Praveen, Meyer, Katharina, Leukel, Petra, Bruttel, Valentin, Aschenbrenner, Ines, Riemenschneider, Markus J., Fragoulis, Athanassios, Rümmele, Petra, Lamszus, Katrin, Schulz, Jörg B., Weis, Joachim, Bogdahn, Ulrich, Wischhusen, Jörg, Hau, Peter, Spang, Rainer and Beier, Dagmar (2012) The cancer stem cell subtype determines immune infiltration of glioblastoma. Stem Cells and Development 21 (15), pp. 2753-2761. Fulltext not available.

Schrader, Alexandra, Bentink, Stefan, Spang, Rainer, Lenze, Dido, Hummel, Michael, Kuo, Michael, Arrand, John R., Murray, Paul G., Trümper, Lorenz, Kube, Dieter and Vockerodt, Martina (2012) High Myc activity is an independent negative prognostic factor for diffuse large B cell lymphomas. International journal of cancer 131 (4), E348-E361. Fulltext not available.

Odoardi, Francesca, Sie, Christopher, Streyl, Kristina, Ulaganathan, Vijay K., Schläger, Christian, Lodygin, Dmitri, Heckelsmiller, Klaus, Nietfeld, Wilfried, Ellwart, Joachim, Klinkert, Wolfgang E. F., Lottaz, Claudio, Nosov, Mikhail, Brinkmann, Volker, Spang, Rainer, Lehrach, Hans, Vingron, Martin, Wekerle, Hartmut, Flügel-Koch, Cassandra and Flügel, Alexander (2012) T cells become licensed in the lung to enter the central nervous system. Nature 488 (7413), pp. 675-679. Fulltext not available.

Hertwig, Falk, Meyer, Katharina, Braun, Sebastian, Ek, Sara, Spang, Rainer, Pfenninger, Cosima V., Artner, Isabella, Prost, Gaëlle, Chen, Xinbin, Biegel, Jaclyn A., Judkins, Alexander R., Englund, Elisabet and Nuber, Ulrike A. (2012) Definition of genetic events directing the development of distinct types of brain tumors from postnatal neural stem/progenitor cells. Cancer research 72 (13), pp. 3381-3392. Fulltext not available.

Kohl, Stefanie M., Klein, Matthias S., Hochrein, Jochen, Oefner, Peter J., Spang, Rainer and Gronwald, Wolfram (2012) State-of-the art data normalization methods improve NMR-based metabolomic analysis. Metabolomics 8 (Suppl), pp. 146-160. Fulltext not available.

Mulaw, M. A., Krause, A., Krause, A. J., Deshpande, A. J., Krause, L. F., Rouhi, A., La Starza, R., Borkhardt, A., Buske, C., Mecucci, C., Ludwig, W.-D., Lottaz, Claudio and Bohlander, S. K. (2012) CALM/AF10-positive leukemias show upregulation of genes involved in chromatin assembly and DNA repair processes and of genes adjacent to the breakpoint at 10p12. Leukemia 26 (5), pp. 1012-1019. Fulltext not available.

Klapper, Wolfram, Kreuz, Markus, Kohler, Christian, Burkhardt, Birgit, Szczepanowski, Monika, Salaverria, Itziar, Hummel, Michael, Loeffler, Markus, Pellissery, Shoji, Woessmann, Wilhelm, Schwänen, Carsten, Trümper, Lorenz, Wessendorf, Swen, Spang, Rainer, Hasenclever, Dirk and Siebert, Reiner (2012) Patient age at diagnosis is associated with the molecular characteristics of diffuse large B-cell lymphoma. Blood 119 (8), pp. 1882-1887. 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.

2011

Almstetter, Martin F., Appel, Inka, Dettmer, Katja, Gruber, Michael and Oefner, Peter J. (2011) Comparison of two algorithmic data processing strategies for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. Journal of chromatography A 1218 (39), pp. 7031-7038. Fulltext not available.

Appel, Inka, Gronwald, Wolfram and Spang, Rainer (2011) Estimating classification probabilities in high-dimensional diagnostic studies. Bioinformatics 27 (18), pp. 2563-2570. Fulltext not available.

Maneck, Matthias, Schrader, Alexandra, Kube, Dieter and Spang, Rainer (2011) Genomic data integration using guided clustering. Bioinformatics 27 (16), pp. 2231-2238. Fulltext not available.

Salaverria, Itziar, Philipp, Claudia, Oschlies, Ilske, Kohler, Christian, Kreuz, Markus, Szczepanowski, Monika, Burkhardt, Birgit, Trautmann, Heiko, Gesk, Stefan, Andrusiewicz, Miroslaw, Berger, Hilmar, Fey, Miriam, Harder, Lana, Hasenclever, Dirk, Hummel, Michael, Loeffler, Markus, Mahn, Friederike, Martin-Guerrero, Idoia, Pellissery, Shoji, Pott, Christiane, Pfreundschuh, Michael, Reiter, Alfred, Richter, Julia, Rosolowski, Maciej, Schwaenen, Carsten, Stein, Harald, Trümper, Lorenz, Wessendorf, Swen, Spang, Rainer, Küppers, Ralf, Klapper, Wolfram and Siebert, Reiner (2011) Translocations activating IRF4 identify a subtype of germinal center-derived B-cell lymphoma affecting predominantly children and young adults. Blood 118 (1), pp. 139-147. Fulltext not available.

VerMilyea, Matthew, Maneck, Matthias, Yoshida, Naoko, Blochberger, Isabell, Suzuki, Emi, Suzuki, Toru, Spang, Rainer, Klein, Christoph A. and Perry, Anthony C. F. (2011) Transcriptome asymmetry within mouse zygotes but not between early embryonic sister blastomeres. The EMBO journal 30 (9), pp. 1841-1851. Fulltext not available.

Seitz, Volkhard, Butzhammer, Peter, Hirsch, Burkhard, Hecht, Jochen, Gütgemann, Ines, Ehlers, Anke, Lenze, Dido, Oker, Elisabeth, Sommerfeld, Anke, von der Wall, Edda, König, Christoph, Zinser, Christian, Spang, Rainer and Hummel, Michael (2011) Deep sequencing of MYC DNA-binding sites in Burkitt lymphoma. PLoS One 6 (11), e26837.

Lang, Elmar, Schachtner, R., Lutter, D., Herold, Daniela, Kodewitz, A., Blöchl, F..J., Theis, Fabian J., Keck, Ingo R., Gorriz, J. M., Gomez-Vilda, P. and Tome, A. M. (2011) I, 2. Exploratory Matrix Factorization Techniques for Large Scale Biomedical Data Sets. In: Gorriz, Juan Manuel and Lang, Elmar W. and Ramírez, Javier, (eds.) Recent advances in biomedical signal processing. Bentham Science Publishers, Hilversum, pp. 26-47. ISBN 978-1-60805-218-9. Fulltext not available.

2010

Scholtysik, René, Kreuz, Markus, Klapper, Wolfram, Burkhardt, Birgit, Feller, Alfred, Hummel, Michael, Loeffler, Markus, Rosolowski, Maciej, Schwaenen, Carsten, Spang, Rainer, Stein, Harald, Thorns, Christoph, Trümper, Lorenz, Vater, Inga, Wessendorf, Swen, Zenz, Thorsten, Siebert, Reiner and Küppers, Ralf (2010) Detection of genomic aberrations in molecularly defined Burkitt's lymphoma by array-based, high resolution, single nucleotide polymorphism analysis. Haematologica 95 (12), pp. 2047-2055.

Dettmer, Katja, Almstetter, Martin F., Appel, Inka, Nürnberger, Nadine, Schlamberger, Gregor, Gronwald, Wolfram, Meyer, Heinrich H. D. and Oefner, Peter J. (2010) Comparison of serum versus plasma collection in gas chromatography--mass spectrometry-based metabolomics. Electrophoresis 31 (14), pp. 2365-2373. Fulltext not available.

Neusser, Matthias A., Lindenmeyer, Maja T., Moll, Anton G., Segerer, Stephan, Edenhofer, Ilka, Sen, Kontheari, Stiehl, Daniel P., Kretzler, Matthias, Gröne, Hermann-Josef, Schlöndorff, Detlef and Cohen, Clemens D. (2010) Human nephrosclerosis triggers a hypoxia-related glomerulopathy. The American journal of pathology 176 (2), pp. 594-607. Fulltext not available.

Ingersoll, Molly A., Spanbroek, Rainer, Lottaz, Claudio, Gautier, Emmanuel L., Frankenberger, Marion, Hoffmann, Reinhard, Lang, Roland, Haniffa, Muzlifah, Collin, Matthew, Tacke, Frank, Habenicht, Andreas J. R., Ziegler-Heitbrock, Loems and Randolph, Gwendalyn J. (2010) Comparison of gene expression profiles between human and mouse monocyte subsets. Blood 115 (3), e10-e19. Fulltext not available.

Hundsrucker, Christian, Skroblin, Philipp, Christian, Frank, Zenn, Hans-Michael, Popara, Viola, Joshi, Mangesh, Eichhorst, Jenny, Wiesner, Burkhard, Herberg, Friedrich W., Reif, Bernd, Rosenthal, Walter and Klussmann, Enno (2010) Glycogen synthase kinase 3beta interaction protein functions as an A-kinase anchoring protein. The Journal of biological chemistry 285 (8), pp. 5507-5521. Fulltext not available.

Lottaz, Claudio, Beier, Dagmar, Meyer, Katharina, Kumar, Praveen, Hermann, Andreas, Schwarz, Johannes, Junker, Markus, Oefner, Peter J., Bogdahn, Ulrich, Wischhusen, J., Spang, Rainer, Storch, Alexander and Beier, Christoph P. (2010) Transcriptional profiles of CD133+ and CD133- glioblastoma-derived cancer stem cell lines suggest different cells of origin. Cancer research 70 (5), pp. 2030-2040. Fulltext not available.

2009

Thieme, Marian, Lottaz, Claudio, Niederstätter, Harald, Parson, Walther, Spang, Rainer and Oefner, Peter J. (2009) ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly. BMC bioinformatics 10, p. 440.

Geue, Lutz, Klare, Sabrina, Schnick, Christina, Mintel, Birgit, Meyer, Katharina and Conraths, Franz J. (2009) Analysis of the clonal relationship of serotype O26:H11 enterohemorrhagic Escherichia coli isolates from cattle. Applied and environmental microbiology 75 (21), pp. 6947-6953. Fulltext not available.

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.

Lyck, Ruth, Ruderisch, Nadine, Moll, Anton G., Steiner, Oliver, Cohen, Clemens D., Engelhardt, Britta, Makrides, Victoria and Verrey, Francois (2009) Culture-induced changes in blood-brain barrier transcriptome: implications for amino-acid transporters in vivo. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 29 (9), pp. 1491-1502. Fulltext not available.

Allam, Ramanjaneyulu, Lichtnekert, Julia, Moll, Anton G., Taubitz, Anela, Vielhauer, Volker and Anders, Hans-Joachim (2009) Viral RNA and DNA trigger common antiviral responses in mesangial cells. Journal of the American Society of Nephrology : JASN 20 (9), pp. 1986-1996. Fulltext not available.

Eberhart, K., Renner, Kathrin, Ritter, I., Kastenberger, M., Singer, K., Hellerbrand, Claus, Kreutz, Marina, Kofler, R. and Oefner, Peter J. (2009) Low doses of 2-deoxy-glucose sensitize acute lymphoblastic leukemia cells to glucocorticoid-induced apoptosis. Leukemia 23 (11), pp. 2167-2170. Fulltext not available.

Almstetter, Martin F., Appel, Inka, Gruber, Michael, Lottaz, Claudio, Timischl, Birgit, Spang, Rainer, Dettmer, Katja and Oefner, Peter J. (2009) Integrative normalization and comparative analysis for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. Analytical chemistry 81 (14), pp. 5731-5739. Fulltext not available.

Vlad, Marcel O., Corlan, Alexandru D., Morán, Federico, Spang, Rainer, Oefner, Peter J. and Ross, John (2009) Kinetic laws, phase-phase expansions, renormalization group, and INR calibration. Proceedings of the National Academy of Sciences of the United States of America 106 (16), pp. 6465-6470. Fulltext not available.

Anchang, Benedict Nchang, Sadeh, Mohammad Javad, Jacob, Juby, Tresch, Achim, Vlad, Marcel O., Oefner, Peter J. and Spang, Rainer (2009) Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models. Proceedings of the National Academy of Sciences of the United States of America 106 (16), pp. 6447-6452. Fulltext not available.

Martín-Subero, José I., Kreuz, Markus, Bibikova, Marina, Bentink, Stefan, Ammerpohl, Ole, Wickham-Garcia, Eliza, Rosolowski, Maciej, Richter, Julia, Lopez-Serra, Lidia, Ballestar, Esteban, Berger, Hilmar, Agirre, Xabier, Bernd, Heinz-Wolfram, Calvanese, Vincenzo, Cogliatti, Sergio B., Drexler, Hans G., Fan, Jian-Bing, Fraga, Mario F., Hansmann, Martin L., Hummel, Michael, Klapper, Wolfram, Korn, Bernhard, Küppers, Ralf, Macleod, Roderick A. F., Möller, Peter, Ott, German, Pott, Christiane, Prosper, Felipe, Rosenwald, Andreas, Schwaenen, Carsten, Schübeler, Dirk, Seifert, Marc, Stürzenhofecker, Benjamin, Weber, Michael, Wessendorf, Swen, Loeffler, Markus, Trümper, Lorenz, Stein, Harald, Spang, Rainer, Esteller, Manel, Barker, David, Hasenclever, Dirk and Siebert, Reiner (2009) New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling. Blood 113 (11), pp. 2488-2497. Fulltext not available.

Schwaenen, Carsten, Viardot, Andreas, Berger, Hilmar, Barth, Thomas F. E., Bentink, Stefan, Döhner, Hartmut, Enz, Martina, Feller, Alfred C., Hansmann, Martin-Leo, Hummel, Michael, Kestler, Hans A., Klapper, Wolfram, Kreuz, Markus, Lenze, Dido, Loeffler, Markus, Möller, Peter, Müller-Hermelink, Hans-Konrad, Ott, German, Rosolowski, Maciej, Rosenwald, Andreas, Ruf, Sandra, Siebert, Reiner, Spang, Rainer, Stein, Harald, Truemper, Lorenz, Lichter, Peter, Bentz, Martin and Wessendorf, Swen (2009) Microarray-based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status. Genes, Chromosomes and Cancer 48 (1), pp. 39-54. 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.

Moll, Anton G., Lindenmeyer, Maja T., Kretzler, Matthias, Nelson, Peter J., Zimmer, Ralf and Cohen, Clemens D. (2009) Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PloS ONE 4 (3), e4702.

2008

Fröhlich, H., Beissbarth, T., Tresch, A., Kostka, D., Jacob, Juby, Spang, Rainer and Markowetz, F. (2008) Analyzing gene perturbation screens with nested effects models in R and bioconductor. Bioinformatics 24 (21), pp. 2549-2550. 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.

Bentink, Stefan, Wessendorf, S., Schwaenen, C., Rosolowski, M., Klapper, W., Rosenwald, A., Ott, G., Banham, A. H., Berger, H., Feller, A. C., Hansmann, M. L., Hasenclever, D., Hummel, M., Lenze, D., Möller, P., Stuerzenhofecker, B., Loeffler, M., Truemper, L., Stein, H., Siebert, R. and Spang, Rainer (2008) Pathway activation patterns in diffuse large B-cell lymphomas. Leukemia 22 (9), pp. 1746-1754. Fulltext not available.

Klapper, W., Szczepanowski, M., Burkhardt, B., Berger, H., Rosolowski, M., Bentink, Stefan, Schwaenen, C., Wessendorf, S., Spang, Rainer, Moller, P., Hansmann, M. L., Bernd, H. W., Ott, G., Hummel, M., Stein, H., Loeffler, M., Trumper, L., Zimmermann, M., Reiter, A. and Siebert, R. (2008) Molecular profiling of pediatric mature B-cell lymphoma treated in population-based prospective clinical trials. Blood 112 (4), pp. 1374-1381. Fulltext not available.

Cohen, C. D., Lindenmeyer, M. T., Eichinger, F., Hahn, A., Seifert, M., Moll, Anton G., Schmid, H., Kiss, E., Grone, E., Grone, H. J., Kretzler, M., Werner, T. and Nelson, P. J. (2008) Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis. PLoS ONE 3 (8), e2937.

Dohm, Juliane C., Lottaz, Claudio, Borodina, Tatiana and Himmelbauer, Heinz (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research 36 (16), e105.

Dierlamm, J., Murga Penas, E. M., Bentink, Stefan, Wessendorf, S., Berger, H., Hummel, M., Klapper, W., Lenze, D., Rosenwald, A., Haralambieva, E., Ott, G., Cogliatti, S. B., Möller, Peter, Schwaenen, C., Stein, H., Löffler, M., Spang, Rainer, Trumper, L. and Siebert, Reiner (2008) Gain of chromosome region 18q21 including the MALT1 gene is associated with the activated B-cell-like gene expression subtype and increased BCL2 gene dosage and protein expression in diffuse large B-cell lymphoma. Haematologica 93 (5), pp. 688-696.

Jacob, Juby, Jentsch, M., Kostka, Dennis, Bentink, Stefan and Spang, Rainer (2008) Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs. Bioinformatics 24 (7), pp. 995-1001. Fulltext not available.

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.

Lottaz, Claudio, Kostka, Dennis and Spang, Rainer (2008) 26. Classification of Patients. In: Lengauer, Thomas, (ed.) Bioinformatics-From Genomes to Therapies. Wiley-VCH, Weinheim, pp. 957-991. ISBN 9783527619368 (online). Fulltext not available.

Montesinos-Rongen, M., Brunn, A., Bentink, Stefan, Basso, K., Lim, W. K., Klapper, Wolfram, Schaller, C., Reifenberger, G., Rubenstein, J., Wiestler, O. D., Spang, Rainer, Dalla-Favera, R., Siebert, Reiner and Deckert, M. (2008) Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell. Leukemia 22 (2), pp. 400-405. Fulltext not available.

Kostka, Dennis and Spang, Rainer (2008) Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures. PLoS Computational Biology 4 (2), e22.

Lottaz, Claudio, Kostka, Dennis, Markowetz, Florian and Spang, Rainer (2008) 15. Computational diagnostics with gene expression profiles. In: Bioinformatics. Methods in Molecular Biology, 453 (15). Humana Press, Totowa, NJ, pp. 281-296. ISBN 978-1-60327-428-9. Fulltext not available.

2007

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.

Roesch, Alexander, Becker, Bernd, Bentink, Stefan, Spang, Rainer, Vogl, Annegret, Hagen, Ilja, Landthaler, Michael and Vogt, Thomas (2007) Ataxia telangiectasia-mutated gene is a possible biomarker for discrimination of infiltrative deep penetrating nevi and metastatic vertical growth phase melanoma. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Prevention 16 (11), pp. 2486-2490. Fulltext not available.

Hoffmann, Reinhard, Lottaz, Claudio, Kühne, Thomas, Rolink, Antonius and Melchers, Fritz (2007) Neutrality, compensation, and negative selection during evolution of B-cell development transcriptomes. Molecular Biology and Evolution (Mol Biol Evol) 24 (12), pp. 2610-2618. Fulltext not available.

Lottaz, Claudio, Toedling, Joern and Spang, Rainer (2007) Annotation-based distance measures for patient subgroup discovery in clinical microarray studies. Bioinformatics 23 (17), pp. 2256-2264. Fulltext not available.

Markowetz, Florian and Spang, Rainer (2007) Inferring cellular networks - a review. BMC bioinformatics 8 Suppl 6, S5.

Dohm, Juliane C., Lottaz, Claudio, Borodina, Tatiana and Himmelbauer, Heinz (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 17 (11), pp. 1697-1706. Fulltext not available.

Bullinger, Lars, Rücker, Frank G., Kurz, Stephan, Du, Juan, Scholl, Claudia, Sander, Sandrine, Corbacioglu, Andrea, Lottaz, Claudio, Krauter, Jürgen, Fröhling, Stefan, Ganser, Arnold, Schlenk, Richard F., Döhner, Konstanze, Pollack, Jonathan R. and Döhner, Hartmut (2007) Gene-expression profiling identifies distinct subclasses of core binding factor acute myeloid leukemia. Blood 110 (4), pp. 1291-1300. Fulltext not available.

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.

Rhein, P., Scheid, S., Ratei, R., Hagemeier, C., Seeger, K., Kirschner-Schwabe, R., Moericke, A., Schrappe, M., Spang, Rainer, Ludwig, W.-D. and Karawajew, L. (2007) Gene expression shift towards normal B cells, decreased proliferative capacity and distinct surface receptors characterize leukemic blasts persisting during induction therapy in childhood acute lymphoblastic leukemia. Leukemia 21 (5), pp. 897-905. Fulltext not available.

Jaeger, Jochen, Koczan, Dirk, Thiesen, Hans-Juergen, Ibrahim, Saleh M., Gross, Gerd, Spang, Rainer and Kunz, Manfred (2007) Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues. Clinical cancer research 13 (3), pp. 806-815. Fulltext not available.

2006

Jaeger, J. and Spang, Rainer (2006) Selecting normalization genes for small diagnostic microarrays. BMC Bioinformatics 7, p. 388.

Kirschner-Schwabe, R., Lottaz, Claudio, Todling, J., Rhein, P., Karawajew, L., Eckert, C., von Stackelberg, A., Ungethum, U., Kostka, Dennis, Kulozik, A. E., Ludwig, W. D., Henze, G., Spang, Rainer, Hagemeier, C. and Seeger, K. (2006) Expression of late cell cycle genes and an increased proliferative capacity characterize very early relapse of childhood acute lymphoblastic leukemia. Clinical Cancer Research 12 (15), pp. 4553-4561. Fulltext not available.

Lottaz, Claudio, Yang, Xinan, Scheid, Stefanie and Spang, Rainer (2006) OrderedList - a bioconductor package for detecting similarity in ordered gene lists. Bioinformatics 22 (18), pp. 2315-2316. Fulltext not available.

Hummel, M., Bentink, S., Berger, H., Klapper, W., Wessendorf, S., Barth, T. F., Bernd, H. W., Cogliatti, S. B., Dierlamm, J., Feller, A. C. and Spang, Rainer (2006) A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling. New England Journal of Medicine 354 (23), pp. 2419-2430. Fulltext not available.

Toedling, J., Rhein, P., Ratei, R., Karawajew, L. and Spang, Rainer (2006) Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring. BMC Bioinformatics 7, p. 282.

2005

Markowetz, F., Bloch, J. and Spang, Rainer (2005) Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. Bioinformatics 21 (21), pp. 4026-4032. Fulltext not available.

Yang, X., Bentink, Stefan and Spang, Rainer (2005) Detecting common gene expression patterns in multiple cancer outcome entities. Biomedical Microdevices 7 (3), pp. 247-251. Fulltext not available.

Lottaz, Claudio and Spang, Rainer (2005) stam – a Bioconductor compliant R package for structured analysis of microarray data. BMC Bioinformatics 6, p. 211.

Scheid, S. and Spang, Rainer (2005) twilight; a Bioconductor package for estimating the local false discovery rate. Bioinformatics 21 (12), pp. 2921-2922. Fulltext not available.

Jaeger, J., Weichenhan, D., Ivandic, B. and Spang, Rainer (2005) Early diagnostic marker panel determination for microarray based clinical studies. Statistical Applications in Genetics and Molecular Biology 4 (1), article 9. Fulltext not available.

Lottaz, Claudio and Spang, Rainer (2005) Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. Bioinformatics 21 (9), pp. 1971-1978.

Lottaz, Claudio, Kostka, Dennis, Markowetz, Florian and Spang, Rainer (2005) Traces of molecular disease mechanisms on microarrays. Methods in Molecular Biology 453, pp. 281-296. Fulltext not available.

2004

Kostka, Dennis and Spang, Rainer (2004) Finding disease specific alterations in the co-expression of genes. Bioinformatics 20 Suppl 1, i194-i199. Fulltext not available.

Scheid, Stefanie and Spang, Rainer (2004) A stochastic downhill search algorithm for estimating the local false discovery rate. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB 1 (3), pp. 98-108. Fulltext not available.

2003

Blaxall, B. C., Spang, Rainer, Rockman, H. A. and Koch, W. J. (2003) Differential myocardial gene expression in the development and rescue of murine heart failure. Physiological Genomics 15 (2), pp. 105-114. Fulltext not available.

Lottaz, Claudio, Iseli, Christian, Jongeneel, C. Victor and Bucher, Philipp (2003) Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 19 (Suppl2), ii103-ii112.

Grzeskowiak, R., Witt, Henning, Drungowski, M., Thermann, R., Hennig, S., Perrot, A., Osterziel, K., Klingbiel, D., Scheid, Stefanie and Spang, Rainer (2003) Expression profiling of human idiopathic dilated cardiomyopathy. Cardiovascular Research 59, pp. 400-411. Fulltext not available.

2002

Muller, Tobias, Spang, Rainer and Vingron, M. (2002) Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Molecular Biology and Evolution 19 (1), pp. 8-13. Fulltext not available.

Spang, Rainer, Rehmsmeier, M. and Stoye, J. (2002) A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology 9 (5), pp. 747-760. Fulltext not available.

Spang, Rainer, Zuzan, H., West, M., Nevins, J., Blanchette, C. and Marks, J. R. (2002) Prediction and uncertainty in the analysis of gene expression profiles. In Silico Biology 2 (3), pp. 369-381. Fulltext not available.

2001

West, M., Blanchette, C., Dressman, H., Huang, E., Ishida, S., Spang, Rainer, Zuzan, H., Olson, J. A., Marks, J. R. and Nevins, J. R. (2001) Predicting the clinical status of human breast cancer by using gene expression profiles. Proc. Natl. Acad. Sci. U.S.A. 98 (20), pp. 11462-11467. Fulltext not available.

Ishida, S., Huang, E., Zuzan, H., Spang, Rainer, Leone, G., West, M. and Nevins, J. R. (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol. Cell. Biol. 21 (14), pp. 4684-4699. Fulltext not available.

Spang, Rainer and Vingron, M. (2001) Limits of homology detection by pairwise sequence comparison. Bioinformatics 17 (4), pp. 338-342. Fulltext not available.

2000

Lottaz, Claudio, Stouffs, Rudi and Smith, Ian (2000) Increasing Understanding During Collaboration Through Advanced Representations. ITcon : Journal of information technology in construction 5, pp. 1-24.

Spang, Rainer, Rehmsmeier, M. and Stoye, J. (2000) Sequence database search using jumping alignments. Proc Int Conf Intell Syst Mol Biol 8, pp. 367-375. Fulltext not available.

1999

Lottaz, Claudio, Clément, Denis, Faltings, Boi and Smith, I. F. C. (1999) Constraint-Based Support for Collaboration in Design and Construction. Journal of Computing in Civil Engineering 13 (1), pp. 23-35. Fulltext not available.

Lottaz, Claudio (1999) Rewriting numeric constraint satisfaction problems for consistency algorithms (short paper). In: Jaffar, Joxan, (ed.) Principles and Practice of Constraint Programming – CP’99. Lecture Notes in Computer Science, 1713. Springer, Berlin, pp. 486-487. ISBN 978-3-540-48085-3 (online). 978-3-540-66626-4 (print). Fulltext not available.

1998

Lottaz, Claudio, Sam-Haroud, D., Faltings, B. and Smith, I. (1998) Constraint techniques for collaborative design. In: Proceedings Tenth IEEE International Conference on Tools with Artificial Intelligence (Cat. No.98CH36294). IEEE Computer Soc., Los Alamitos, Calif., pp. 34-41. ISBN 0-7803-5214-9. Fulltext not available.

Lottaz, Claudio, Stalker, Ruth and Smith, Ian (1998) Constraint solving and preference activation for interactive design. AI EDAM - Artificial Intelligence for Engineering Design, Analysis and Manufacturing 12, pp. 12-13. Fulltext not available.

Spang, Rainer and Vingron, M. (1998) Statistics of large-scale sequence searching. Bioinformatics 14 (3), pp. 279-284. Fulltext not available.

1996

Lottaz, Claudio (1996) Constraint Solving, Preference Activation and Solution Adaptation in IDIOM. Swiss Federal Institute of Technology (EPFL), Lausanne, Schweiz. Fulltext not available.

Smith, Ian, Stalker, Ruth and Lottaz, Claudio (1996) Creating Design Objects from Cases for Interactive Spatial Composition. In: Gero, J. S. and Sudweeks, F., (eds.) Artificial Intelligence in Design ’96 (Boston MA, USA). Springer, Dordrecht, pp. 97-116. ISBN 978-94-009-0279-4 (online), 978-94-010-6610-5 (Print). Fulltext not available.

1995

Smith, Ian, Lottaz, Claudio and Faltings, Boi (1995) Spatial composition using cases: IDIOM. In: Veloso, M. and Aamodt, A., (eds.) Case-Based Reasoning Research and Development. ICCBR 1995. Lecture Notes in Computer Science (Lecture Notes in Artificial Intelligence), 1010. Springer, Berlin, pp. 88-97. ISBN 978-3-540-48446-2 (online), 978-3-540-60598-0 (print). Fulltext not available.

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