It is with great sadness that I announce that Marc Rehmsmeier, my partner of 24 years and long- term collaborator, died on 29th April 2022. You can find Marc’s obituary here.
Leonie Ringrose, 09.05.2022
The Rehmsmeier group uses machine learning methods to identify the PRE/TRE code in the fruitfly, mouse and human genomes.
PEP NET
Publications
Bredesen BA., Rehmsmeier M. (2019). DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements. Nucleic Acids Res. (PubMed abstract)
Rehmsmeier, M. (2017). Computational Identification of Polycomb/Trithorax Response Elements. Epigenetics and Systems Biology, pages 7-24, Elsevier. (Contents)
Saito T., Rehmsmeier M. (2017). Precrec: fast and accurate precision-recall and ROC curve calculations in R. Bioinformatics. (PubMed abstract)
List M., Schmidt S., Christiansen H., Rehmsmeier M., Tan Q., Mollenhauer J., Baumbach J. (2016). Comprehensive analysis of high-throughput screens with HiTSeekR. Nucleic Acids Res. (PubMed abstract)
Alcaraz N., List M., Dissing-Hansen M., Rehmsmeier M., Tan Q., Mollenhauer J., Ditzel HJ., Baumbach J. (2016). Robust de novo pathway enrichment with KeyPathwayMiner 5. F1000 Research. (PubMed abstract)
Saito, T., Rehmsmeier, M. (2015). A fast microRNA target prediction tool that provides a single-entry interface to multiple algorithms. F1000 Research (abstract)
Saito T., Rehmsmeier M. (2015). The precision-recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets. PLoS One (PubMed abstract)
Rehmsmeier M. (2013). A computational approach to developing mathematical models of polyploid meiosis. Genetics (PubMed abstract)
Rehmsmeier M. (2012). Response to Wang and Luo. BMC Biol. (PubMed abstract)
Wolff P., Weinhofer I., Seguin J., Roszak P.., Beisel C, Donoghue MT., Spillane C., Nordborg M., Rehmsmeier M., Köhler C. (2011). High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. PLoS Genet. (PubMed abstract)
Pecinka A., Fang W., Rehmsmeier M., Levy AA., Mittelsten Scheid O. (2011). Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biol. (PubMed abstract)
Alves L. Jr., Niemeier S., Hauenschild A., Rehmsmeier M., Merkle T. (2009). Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Research (PubMed abstract)
Siegel G., Obernosterer G., Fiore R., Oehmen M., Bicker S., Christensen M., Khudayberdiev S., Leuschner PF., Busch CJ., Kane C., Hübel K., Dekker F., Hedberg C.., Rengarajan B., Drepper C., Waldmann H., Kauppinen S., Greenberg ME., Draguhn A., Rehmsmeier M., Martinez J., Schratt GM. (2009). A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nat Cell Biol. (PubMed abstract)
Mittelsten Scheid, O., Baubec, T., Dinh, HQ., Fang, W., Foerster, AM., Lettner, N., Pecinka, A., Rehmsmeier, M., Rosa, M., Sedman, L. (2009). Genetics and epigenetics in diploid and tetraploid Arabidopsis. FEBS JOURNAL, 276, 7-7. WILEY-Blackwell Publishing.
Homann R., Fleer D., Giegerich R., Rehmsmeier M. (2009). mkESA: enhanced suffix array construction tool.Bioinformatics. (PubMed abstract)
Hauenschild A., Ringrose L., Altmutter C., Paro R., Rehmsmeier M. (2008). Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species. PLoS Biol. (PubMed abstract)
Fiedler T., Rehmsmeier M. (2006). jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Res. (PubMed abstract)
Krüger J., Rehmsmeier M. (2006). RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res. (PubMed abstract)
Reeder J., Höchsmann M., Rehmsmeier M., Voss B., Giegerich R. (2006). Beyond Mfold: recent advances in RNA bioinformatics. J Biotechnol. (PubMed abstract)
Steffen P., Voss B., Rehmsmeier M., Reeder J., Giegerich R. (2006). RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. (PubMed abstract)
Voss B., Giegerich R., Rehmsmeier M. (2006). Complete probabilistic analysis of RNA shapes. BMC Biol. (PubMed abstract)
Rehmsmeier M. (2006). Prediction of microRNA targets. Methods Mol Biol. (PubMed abstract)
Rehmsmeier M., Steffen P., Hochsmann M., Giegerich R. (2004). Fast and effective prediction of microRNA/target duplexes. RNA (PubMed abstract)
Alam I., Dress A., Rehmsmeier M., Fuellen G. (2004). Comparative homology agreement search: an effective combination of homology-search methods. Proc Natl Acad Sci USA. (PubMed abstract)
Giegerich R., Voss B., Rehmsmeier M. (2004). Abstract shapes of RNA. Nucleic Acids Res. (PubMed abstract)
Ringrose L., Rehmsmeier M., Dura JM., Paro R. (2003). Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev Cell. (PubMed abstract)
Rehmsmeier M. (2002). Phase4: automatic evaluation of database search methods. Brief Bioinform. (PubMed abstract)
Spang R., Rehmsmeier M., Stoye J. (2002). A novel approach to remote homology detection: jumping alignments. J Comput Biol. (PubMed abstract)
Rehmsmeier M., Vingron M. (2001). Phylogenetic information improves homology detection. Proteins (PubMed abstract)
Müller T., Rahmann S., Rehmsmeier M. (2001). Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics (PubMed abstract)
Spang R., Rehmsmeier M., Stoye J. (2000). Sequence database search using jumping alignments. Proc Int Conf Intell Syst Mol Biol. (PubMed abstract)
Krause A., Nicodème P., Bornberg-Bauer E., Rehmsmeier M., Vingron M. (1999) WWW access to the SYSTERS protein sequence cluster set. Bioinformatics. (PubMed abstract)
Giegerich R., Haase D., Rehmsmeier M. (1999). Prediction and visualization of structural switches in RNA. Pac Symp Biocomput. (PubMed abstract)
Rehmsmeier, M., Vingron, M. (1999). Phylogeny meets sequence search. Proceedings of the German Conference on Bioinformatics GCB. 66-72. (Link)
Krause, A., Nicodème, P., Rehmsmeier, M., Vingron, M. (1998). Automatic clustering of large sequence databases. Proceedings of the German Conference on Bioinformatics GCB. (Link)