PUBLICATIONS:

Dmitrijeva M, Ossowski S, Serrano L, Schaefer MH. Tissue-specic DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates. Nucleic Acids Research. gky498.

Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer MH. Negative selection in tumour genome evolution acts on essential cellular functions and the immunopeptidome. Genome biology, 19(1), 67.

Cramer D, Serrano L, Schaefer MH. A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference. eLife (2016): 10.7554.

Alanis G, Andrade-Navarro M, Schaefer MH. HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Research (2016)): gkw985.

Schaefer MH, and Luis Serrano. Cell type-specific properties and environment shape tissue specificity of cancer genes. Scientific reports 6 (2016).

Schaefer MH, Serrano L, Andrade-Navarro MA. Correcting for the study bias associated with protein–protein interaction measurements reveals differences between protein degree distributions from different cancer types. Frontiers in genetics 6 (2015).

Suratanee A, Schaefer MH, Betts M, Soons Z, Mannsperger H, Harder N, Oswald M, Gipp M, Ramminger E, Marcus G, Maenner R, Rohr K, Wanker E, Russel RB, Andrade-Navarro M, Eils R, Koenig R. Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. PloS Computational Biology. 10.9 (2014):e1003814.

Schaefer MH, Yang J-S, Serrano L, Kiel C. Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways. PloS Computational Biology. 10.6 (2014):e1003659.

Fournier D, Palidwor GA, Shcherbinin S, Szengel A, Schaefer MH, Andrade-Navarro M. Functional and genomic analyses of alpha-solenoid proteins. Functional and genomic analyses of alpha-solenoid proteins. PloS one 8.11 (2013): e79894.

Petrakis S, Schaefer MH, Wanker EE, Andrade-Navarro MA. Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners. Bioessays. (2013): 503-507.

Schaefer MH, Lopes TJ, Mah N, Shoemaker J, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA. Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. PloS Computational Biology. 9.1 (2013): e1002860.

Suter B, Fontaine JF, Yildirimman R, Rasko T, Schaefer MH, Rasche A, Porras P, Vazquez-Alvarez B, Russ J, Rau K, Saar K, Foulle R, Zenkner M, Herwig R, Andrade-Navarro MA, Wanker EE. Development and application of a DNA microarray-based yeast two-hybrid system. Nucleic Acids Research. 41.3 (2013): 1496-1507.

von Eichborn J, Dunkel M, Gohlke B, Preissner S, Hoffmann M, Bauer J, Armstrong J, Schaefer MH, Andrade-Navarro MA, Le Novere N, Croning M, Grant S, van Nierop P, Smit A, Preissner R. SynSysNet: Integration of experimental data on synaptic protein-protein interactions with drug-target relations. Nucleic Acids Research 41.D1 (2013): D834-D840.

Petrakis S, Rasko T, Russ J, Friedrich RP, Stroedicke M, Riechers SP, Muehlenberg K, Moeller A, Reinhardt A, Vinayagam A, Schaefer MH, Boutros M, Tricoire H, Andrade-Navarro MA and Wanker EE. Identification of Human Proteins that Modify Misfolding and Proteotoxicity of Pathogenic Ataxin-1. PLoS Genetics 8.8 (2012): e1002897.

Sorge S, Ha N, Polychronidou M, Friedrich J, Bezdan D, Kaspar P, Schaefer MH, Ossowski S, Henz SR, Mundorf J, Rätzer J, Papagiannouli F, Lohmann I. The cis-regulatory code of Hox function in Drosophila. The EMBO Journal (2012).2

Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA. HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. PloS one 7.2 (2012): e31826.

Schaefer MH, Wanker EE, Andrade-Navarro MA. Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic acids research 40.10 (2012): 4273-4287.

Mah N, Wang Y, Liao MC, Prigione A, Jozefczuk J, Lichtner B, Wolfrum K, Haltmeier M, Floettmann M, Schaefer M, Hahn A, Mrowka R, Klipp E, Andrade-Navarro MA, Adjaye J. Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network. PloS one 6.8 (2011): e24351.

Lopes TJ, Schaefer M, Shoemaker J, Matsuoka Y, Fontaine JF, Neumann G, Andrade-Navarro MA, Kawaoka Y, Kitano H. Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. Bioinformatics 27.17 (2011): 2414-2421.

Fontaine J, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA. MedlineRanker: flexible ranking of biomedical literature. Nucleic acids research 37.suppl 2 (2009): W141-W146.

Dezulian T, Schaefer M, Wiese R, Weigel D, Huson DH. CrossLink: visualization and exploration of sequence relationships between (micro) RNAs. Nucleic acids research 34.suppl 2 (2006): W400-W404.