Book chapter: 

Kramer F and Beißbarth T (2016) Working with Ontologies. Methods Mol. Biol. Epub Dec 12 2016;1525:123-35. 

Umbach U, Beissbarth T, Sax U (2016) Molekularbiologische Daten aus Hochdurchsatz-Analysen. In: Drepper J, Semler SC (Hrsg.) IT-Infrastrukturen in der patientenorientierten Forschung. Aktueller Stand und Handlungsbedarf 2016. Aka Verlag, Berlin, 115-42 

Sax U, Bauer CR, Ganslandt T, Kirsten T (2016) Forschungsdatenmanagement. In: Drepper J, Semler SC (Hrsg.) IT-Infrastrukturen in der patientenorientierten Forschung. Aktueller Stand und Handlungsbedarf 2016. Aka Verlag, Berlin, 195-210 

Journals: 
 

Apweiler R,Beißbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O (2018). Whither systems medicine? Exp Mol Med, 50(3):e45

Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F (2017). ndexr - an R package to interface with the Network Data Exchange. Bioinformatics, 34(4):716-17.

Benis N, Schokker D, Kramer F, Smits MA, Suarez-Diez M. (2016) Building pathway graphs from BioPAX data in R. F1000Research 2016, 5:2414, doi:10.12688/f1000research.9582.2

Bauer CR, Ganslandt T, Baum B, Christoph J, Engel I, Löbe M, Mate S, Stäubert S, Drepper J, Prokosch HU, Winter A, Sax U (2016). Integrated Data Repository Toolkit (IDRT). A Suite of Programs to Facilitate Health Analytics on Heterogeneous Medical Data. Methods Inf Med, 55(2):125-35.

Bauer CR, Knecht C, Fretter C, Baum B, Jendrossek S, Rühlemann M, Heinsen FA, Umbach N, Grimbacher B, Franke A, Lieb W, Krawczak M, Hütt MT, Sax U (2017). Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases. Brief Bioinform, 18(3):479-487

Bauer CR, Umbach N, Baum B, Buckow K, Franke T, Grütz R, Gusky L, Nussbeck SY, Quade M, Rey S, Rottmann T, Rienhoff O, Sax U (2016). Architecture of a Biomedical Informatics Research Data Management Pipeline. Stud Health Technol Inform, 228:262-6.

 Baum B, Bauer CR, Franke T, Kusch H, Parciak M, Rottmann T, Umbach N, Sax U (2017). Opinion paper: Data provenance challenges in biomedical research. it - Information Technology, 59(4).

Bayerlová M, Menck K, Klemm F, Wolff A, Pukrop T, Binder C, Beißbarth T, Bleckmann A(2017). Ror2 Signaling and Its Relevance in Breast Cancer Progression. Front Oncol, 7:135

Bocuk D, Wolff A, Krause P, Salinas G, Bleckmann A, Hackl C,Beißbarth T, König S (2017). The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model. BMC Cancer, 17(1):342

Emons G, Spitzner M, Reineke S, Möller J, Auslander N, Kramer F, Hu Y, Beißbarth T, Wolff HA, Rave-Fränk M, Heßmann E, Gaedcke J, Ghadimi BM, Johnsen SA, Ried T, Grade M (2017). Chemoradiotherapy Resistance in Colorectal Cancer Cells is Mediated by Wnt/β-catenin Signaling. Mol Cancer Res, 15(11):1481-1490.

Fromme JE, Schmitz K, Wachter A, Grzelinski M, Zielinski D, Koppel C, Conradi LC, Homayounfar K, Hugo T, Hugo S, Lukat L, Rüschoff J, Ströbel P, Ghadimi M, Beißbarth T, Reuter-Jessen K, Bleckmann A, Schildhaus HU (2018). FGFR3 mRNA overexpression defines a subset of oligometastatic colorectal cancers with worse prognosis. Onkotarget, accepte

Jo P, Azizian A, Salendo J, Kramer F, Bernhardt M, Wolff HA, Gruber J, Grade M, Beißbarth T, Ghadimi BM, Gaedcke J (2017). Changes of Microrna Levels in Plasma of Patients with Rectal Cancer during Chemoradiotherapy. Int J Mol Sci, 18(6).

Perera-Bel J, Hutter B, Heining C, Bleckmann A, Fröhlich M, Fröhling S, Glimm H, Brors B, Beißbarth T (2018). From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Med, 10(1):18.

Wingender E, Schöps T, Haubrock M, Krull M, Dönitz J (2018). TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 46, D343-D347.

Wlochowitz D, Haubrock M, Arackal J, Bleckmann A, Wolff A, Beißbarth T, Wingender E, Gültas M (2016). Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front Genet, 7:42

Boyarskikh U, Pintus S, Mandrik N, Stelmashenko D, Kiselev I, Evshin I, Sharipov R, Stegmaier P, Kolpakov F, Filipenko M, Kel A. (2018) Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. BMC Med. Genomics 11(Suppl 1), 12. doi: 10.1186/s12920-018-0330-5.

Stegmaier P, Kel A, Wingender E (2017) geneXplainR: An R interface for the geneXplain platform. J. Open Source Softw. 2, 412

Kel AE (2017). Search for Master Regulators in Walking Cancer Pathways. Methods Mol. Biol. 1613, 161-191.

Wachter A,Beißbarth T (2016). Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data. Front Genet, 6:351.

Wingender E, Schoeps T, Haubrock M, Krull M and Dönitz J (2018). TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res, 46:D343-D347.

Wlochowitz D, Haubrock M, Arackal J, Bleckmann A, Wolff A, Beißbarth T, Wingender E, Gültas M (2016). Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front Genet, 7:42.

Wolff A, Bayerlová M, Gaedcke J, Kube D, Beißbarth T (2018). A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells. PLoS One, 13(5):e0197162.

Wolff A, Perera-Bel J, Schildhaus HU, Homayounfar K, Schatlo B, Bleckmann A, Beißbarth T (2018). Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations. Stud Health Technol Inform, in press.

Abstracts in Conference Proceedings: 

Knopp C, Bauer CR, Baum B, Löhnhardt B, Nietert M, Beißbarth T, Sax U. A validatable data management solution formulti-center research consortia: research datamanagement with openBIS. HEC 2016 – Health-Exploring Complexity: an Interdisciplinary Systems; 2016; Munich; Düsseldorf: German Medical Science GMS Publishing House. 

Poster und Flash talk: 

“MyPathSem - generating patient-specific pathways for individualized treatment decisions” Florian Auer, Christian Bauer, Halima Al-Achram, Jürgen Dönitz, Annalen Bleckmann, Jochen Gaedcke, Edgar Wingender, Ulrich Sax, Frank Kramer and Tim Beißbarth E:Med annual all hands meeting 2016, CAU Kiel, October 4-6, 2016 
 

Poster: 

„Bringing Pathway Knowledge to Systems Medicine Approaches“ Florian Auer, Christian Bauer, Halima Al-Achram, Jürgen Dönitz, Annalen Bleckmann, Jochen Gaedcke, Edgar Wingender, Ulrich Sax, Frank Kramer and Tim Beißbarth Combine, Newcastle upon Tyne UK

Alachram H, Doenitz J, Wingender E (2017) An Ontology-Based Representation of Biomedical and Clinical Data. Workshop on Systems Biology and Computational Biology (Maastricht).

Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F (2017). ndexr - an R package to interface with the Network Data Exchange. GCB 2017 / ISMB 2017 / e:Med Meeting 2017

Auer F, KramerF, Beißbarth T (2016). Bringing Pathway Knowledge to Systems Medicine Approaches. Combine 2016 / GCB 2016 / GCB 2017 / ISMB 2017.

Auer F, Kramer F, Beißbarth T (2018). Composing a dockerized Ecosystem for the Exchange and Visualization of Biological Networks. ISMB (Chicago)

Kel-Margoulis O, Stegmaier P, Kel A,Wingender E (2018). Motif analysis of regulatory SNPs reveals Krüppel-like tran-scription factors as putative tumor suppressors in colorectal carcinoma. BGRS (Novosibirsk)

Umbach N, Beißbarth T, Duttge G, Flatau L, Kuhn-Aldea J, Perera-Bel J, Roschauer J, Schulze TG, Schweda M, Trostmann J, Urban A, Zimmermann A, Sax U (2017). Challenges and Recommendations for Managing Genomic High-Throughput Data in the Clinic. GMDS Conference (Oldenburg).

Knopp C, Bauer CR, Baum B, Löhnhardt B, Nietert M, Beißbarth T, Sax U (2016).. A validatable data management solution formulti-center research consortia: research datamanagement with openBIS. HEC (Munich).

Knopp C, Bauer CR, Sax U (2017). Research data management with openBIS: A validatable data management solution for a multi-center e:Med consortia. e:Med Meeting (Göttingen).