For any project enquiries phone +49 (0)761 76 999 422
My publications
Blüher, M., Saunders, S. J., Mittard, V., Torrejon Torres, R., Davis, J. A., & Saunders, R. (2019). Critical Review of European Health-Economic Guidelines for the Health Technology Assessment of Medical Devices. Frontiers in Medicine, Section Regulatory Science. https://doi.org/10.3389/fmed.2019.00278
Davis, J. A., Saunders, S. J., Mann, M., & Backofen, R. (2017). Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data. NAR, 45(15), 8745–8757. https://doi.org/10.1093/nar/gkx605
Reimann, V., Alkhnbashi, O. S., Saunders, S. J., Scholz, I., Hein, S., Backofen, R., & Hess, W. R. (2017). Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs. NAR, 45(2), 915–925. https://doi.org/10.1093/nar/gkw786
Del Vecchio, G., De Vito, F., Saunders, S. J., Risi, A., Mannironi, C., Bozzoni, I., & Presutti, C. (2016). RNA-binding protein HuR and the members of the miR-200 family play an unconventional role in the regulation of c-Jun mRNA. RNA, 22(10), 1510–1521. https://doi.org/10.1261/rna.057588.116
Alkhnbashi, O. S., Shah, S. A., Garrett, R. A., Saunders, S. J., Costa, F., & Backofen, R. (2016). Characterizing leader sequences of CRISPR loci. Bioinformatics, 32(17), i576–i585. https://doi.org/10.1093/bioinformatics/btw454
Holzer, M., Krahling, V., Amman, F., Barth, E., Bernhart, S. H., Carmelo, V. A. O., Collatz, M., Doose, G., Eggenhofer, F., Ewald, J., Fallmann, J., Feldhahn, L. M., Fricke, M., Gebauer, J., Gruber, A. J., Hufsky, F., Indrischek, H., Kanton, S., Linde, J., … Marz, M. (2016). Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep, 6, 34589. https://doi.org/10.1038/srep34589
Maier, L.-K., Stachler, A.-E., Saunders, S. J., Backofen, R., & Marchfelder, A. (2015). An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein. JBC, 290(7), 4192–4201. https://doi.org/10.1074/jbc.M114.617506
Preusse, M., Marr, C., Saunders, S., Maticzka, D., Lickert, H., Backofen, R., & Theis, F. (2015). SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biology, 12(9), 998–1009. https://doi.org/10.1080/15476286.2015.1068496
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns, R. M., Terns, M. P., White, M. F., Yakunin, A. F., Garrett, R. A., van der Oost, J., … Koonin, E. V. (2015). An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol, 13(11), 722–736. https://doi.org/10.1038/nrmicro3569
Saunders, S. J. (2014). Computational analyses of post-transcriptional regulatory mechanisms [PhD Thesis]. Albert-Ludwigs-University Freiburg.
Maticzka, D., Lange, S. J., Costa, F., & Backofen, R. (2014). GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol, 15(1), R17. https://doi.org/10.1186/gb-2014-15-1-r17
Brendel, J., Stoll, B., Lange, S. J., Sharma, K., Lenz, C., Stachler, A.-E., Maier, L.-K., Richter, H., Nickel, L., Schmitz, R. A., Randau, L., Allers, T., Urlaub, H., Backofen, R., & Marchfelder, A. (2014). A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of crRNAs in Haloferax volcanii. JBC, 289(10), 7164–7177. https://doi.org/10.1074/jbc.M113.508184
Alkhnbashi, O. S., Costa, F., Shah, S. A., Garrett, R. A., Saunders, S. J., & Backofen, R. (2014). CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics, 30(17), i489–i496. https://doi.org/10.1093/bioinformatics/btu459
Richter, H., Lange, S. J., Backofen, R., & Randau, L. (2013). Comparative analysis of Cas6b processing and CRISPR RNA stability. RNA Biology, 10(5), 700–707. https://doi.org/10.4161/rna.23715
Scholz, I., Lange, S. J., Hein, S., Hess, W. R., & Backofen, R. (2013). CRISPR-Cas Systems in the Cyanobacterium Synechocystis sp. PCC6803 Exhibit Distinct Processing Pathways Involving at Least Two Cas6 and a Cmr2 Protein. PLoS One, 8(2), e56470. https://doi.org/10.1371/journal.pone.0056470
Maier, L.-K., Lange, S. J., Stoll, B., Haas, K. A., Fischer, S., Fischer, E., Duchardt-Ferner, E., Wohnert, J., Backofen, R., & Marchfelder, A. (2013). Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biology, 10(5), 865–874. https://doi.org/10.4161/rna.24282
Nickel, L., Weidenbach, K., Jager, D., Backofen, R., Lange, S. J., Heidrich, N., & Schmitz, R. A. (2013). Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III. RNA Biol, 10(5), 779–791. https://doi.org/10.4161/rna.23928
Lange, S. J., Alkhnbashi, O. S., Rose, D., Will, S., & Backofen, R. (2013). CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. NAR, 41(17), 8034–8044. https://doi.org/10.1093/nar/gkt606
Stoll, B., Maier, L.-K., Lange, S. J., Brendel, J., Fischer, S., Backofen, R., & Marchfelder, A. (2013). Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system. Biochem Soc Trans, 41(6), 1444–1448. https://doi.org/10.1042/BST20130098
Lange, S. J., Maticzka, D., Möhl, M., Gagnon, J. N., Brown, C. M., & Backofen, R. (2012). Global or local? Predicting secondary structure and accessibility in mRNAs. NAR, 40(12), 5215–5226. https://doi.org/10.1093/nar/gks181
Wittkop, T., Emig, D., Lange, S., Rahmann, S., Albrecht, M., Morris, J. H., Bocker, S., Stoye, J., & Baumbach, J. (2010). Partitioning biological data with transitivity clustering. Nat Methods, 7(6), 419–420. https://doi.org/10.1038/nmeth0610-419
Albaum, S. P., Neuweger, H., Franzel, B., Lange, S., Mertens, D., Trotschel, C., Wolters, D., Kalinowski, J., Nattkemper, T. W., & Goesmann, A. (2009). Qupe–a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics, 25(23), 3128–3134. https://doi.org/10.1093/bioinformatics/btp568
Baumbach, J., Bunkowski, A., Lange, S., Oberwahrenbrock, T., Kleinbölting, N., Rahmann, S., & Baumbach, J. I. (2007). IMS2 – An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. Journal of Integrative Bioinformatics, 4(3), 75. https://doi.org/doi:10.2390/biecoll-jib-2007-75
Team member

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Team publications
Team publications