Maximilian Collatz



  • [DOI] M. Collatz, F. Mock, E. Barth, M. Hölzer, K. Sachse, and M. Marz, “EpiDope: a deep neural network for linear B-cell epitope prediction,” Bioinformatics, 2020.
    author = {Maximilian Collatz and Florian Mock and Emanuel Barth and Martin Hölzer and Konrad Sachse and Manja Marz},
    journal = {Bioinformatics},
    title = {{EpiDope}: A Deep Neural Network for linear {B}-cell epitope prediction},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa773},
    editor = {Lenore Cowen},
    publisher = {Oxford University Press ({OUP})},
  • [DOI] N. F. Mostajo, M. Lataretu, S. Krautwurst, F. Mock, D. Desirò, K. Lamkiewicz, M. Collatz, A. Schoen, F. Weber, M. Marz, and M. Hölzer, “A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes,” NAR Genomics Bioinf, vol. 2, iss. 1, p. lqz006, 2020.
    author = {Mostajo, Nelly F and Lataretu, Marie and Krautwurst, Sebastian and Mock, Florian and Desirò, Daniel and Lamkiewicz, Kevin and Collatz, Maximilian and Schoen, Andreas and Weber, Friedemann and Marz, Manja and H\"{o}lzer, Martin},
    title = {A comprehensive annotation and differential expression analysis of short and long non-coding {R}{N}{A}s in 16 bat genomes},
    journal = {{NAR Genomics Bioinf}},
    year = {2020},
    volume = {2},
    number = {1},
    pages = {lqz006},
    doi = {10.1093/nargab/lqz006},
    eprint = {},
    url = {},


  • [DOI] K. Riege, M. Hölzer, T. E. Klassert, E. Barth, J. Bräuer, M. Collatz, F. Hufsky, N. Mostajo, M. Stock, B. Vogel, H. Slevogt, and M. Marz, “Massive effect on lncRNAs in human monocytes during fungal and bacterial infections and in response to vitamins A and D,” Sci Rep, vol. 7, p. 40598, 2017.
    author = {Riege, Konstantin and H\"{o}lzer, Martin and Klassert, Tilman E and Barth, Emanuel and Br\"{a}uer, Julia and Collatz, Maximilian and Hufsky, Franziska and Mostajo, Nelly and Stock, Magdalena and Vogel, Bertram and Slevogt, Hortense and Marz, Manja},
    title = {Massive Effect on Lnc{RNA}s in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins {A} and {D}},
    journal = {{Sci Rep}},
    year = {2017},
    volume = {7},
    pages = {40598},
    abstract = {Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.},
    doi = {10.1038/srep40598},
    keywords = {Bacterial Infections, genetics, microbiology; Gene Expression Regulation, drug effects; Humans; Monocytes, metabolism; Mycoses, genetics, microbiology; RNA, Antisense, genetics; RNA, Long Noncoding, chemistry, genetics; RNA, Messenger, genetics; RNA, Untranslated, genetics; Vitamin A, metabolism, pharmacology; Vitamin D, metabolism, pharmacology},
    pmid = {28094339},


  • [DOI] M. Hölzer, V. Krähling, F. Amman, E. Barth, S. H. Bernhart, V. A. O. Carmelo, M. Collatz, G. Doose, F. Eggenhofer, J. Ewald, J. Fallmann, L. M. Feldhahn, M. Fricke, J. Gebauer, A. J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N. Mostajo, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A. H. Sahyoun, S. J. Saunders, S. E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M. T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P. F. Stadler, S. Becker, and M. Marz, “Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells,” Sci Rep, vol. 6, p. 34589, 2016.
    author = {H\"{o}lzer, Martin and Kr\"{a}hling, Verena and Amman, Fabian and Barth, Emanuel and Bernhart, Stephan H and Carmelo, Victor A O and Collatz, Maximilian and Doose, Gero and Eggenhofer, Florian and Ewald, Jan and Fallmann, J\"{o}rg and Feldhahn, Lasse M and Fricke, Markus and Gebauer, Juliane and Gruber, Andreas J and Hufsky, Franziska and Indrischek, Henrike and Kanton, Sabina and Linde, J\"{o}rg and Mostajo, Nelly and Ochsenreiter, Roman and Riege, Konstantin and Rivarola-Duarte, Lorena and Sahyoun, Abdullah H and Saunders, Sita J and Seemann, Stefan E and Tanzer, Andrea and Vogel, Bertram and Wehner, Stefanie and Wolfinger, Michael T and Backofen, Rolf and Gorodkin, Jan and Grosse, Ivo and Hofacker, Ivo and Hoffmann, Steve and Kaleta, Christoph and Stadler, Peter F and Becker, Stephan and Marz, Manja},
    title = {Differential transcriptional responses to {E}bola and {M}arburg virus infection in bat and human cells},
    journal = {{Sci Rep}},
    year = {2016},
    volume = {6},
    pages = {34589},
    abstract = {The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.},
    doi = {10.1038/srep34589},
    keywords = {Animals; Cell Line, Tumor; Chiroptera; Ebolavirus, metabolism; Gene Expression Regulation; Hemorrhagic Fever, Ebola, metabolism; Humans; Marburg Virus Disease, metabolism; Marburgvirus, metabolism; Signal Transduction; Transcription, Genetic},
    pmid = {27713552},