J Perner, J Lasserre, S Kinkley, M Vingron, HR Chung (2014) Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling. Nucleic Acids Res., 42 (22): 13689-95
D Emmerich et al. (2015) Somatic neurofibromatosis type I (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient. Eur J Hum Genet.,23 (6): 870-3
X Yu et al. (2014) Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Front Plant Sci., 5: 273
C Rintisch et al. (2014) Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res.,24 (6): 942-53
N Misra, E Szczurek, M Vingron (2014) Inferring the paths of somatic evolution in cancer. Bioinformatics, 30 (17): 2456-63
G Meng, M Vingron (2014) Condition-specific target prediction from motifs and expression. Bioinformatics, 30 (12): 1643-50
L Fernandez-Cuesta et al. (2014) CD74-NRG1 fusions in lung adenocarcinoma. Cancer Discovery,4 (4): 415-22
A Dress, M Linial, O Troyanskaya, M Vingron (2013) ISCB/SPRINGER series in computational biology. Bioinformatics, 29 (24): 3246-7
M Thomas-Chollier et al. (2013) A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms. Proc Natl Acad Sci., 110 (44): 17826-31
J Lasserre, HR Chung, M Vingron (2013) Finding associations among histone modifications using sparse partial correlation networks. PLoS Comput Biol., 9 (9): e1003168
A Mammana, M Vingron, HR Chung (2013) Inferring nucleosome positions with their histone mark annotation from ChIP data. Bioinformatics, 29 (20): 2547-2554
A Marsico et al. (2013) PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol.,14 (8): R84
J Göke, YS Chan, J Yan, M Vingron, HH Ng (2013) Genome-wide kinase-chromatin interactions reveal the regulatory network of ERK signaling in human embryonic stem cells. Mol Cell,50 (6): 844-55
E Szczurek, N Misra, M Vingron (2013) Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma. Int J Cancer, 133 (9): 2123-32
R Feldmann et al. (2013) Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. Nucleic Acids Res., 41 (6): 3518-31
MT Weirauch et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol., 31 (2): 126-34
F Odoardi et al. (2012) T cells become licensed in the lung to enter the central nervous system. Nature, 488 (7413): 675-9
S Ni, M Vingron (2012) R2KS: A novel measure for comparing gene expression based on ranked gene lists. J Comput Biol., 19 (6): 766-75
T Zemojtel, M Vingron (2012) P53 binding sites in transposons. Front Genet., 3: 40
A Myšičková, M Vingron (2012) Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. BMC Genomics, 13 Suppl 1: S2
D Adams et al. (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol., 30 (3): 224-6
MH Schulz, DR Zerbino, M Vingron, E Birney (2012) Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 28 (8): 1086-92
R Sun, MI Love, T Zemojtel, AK Emde, HR Chung, M Vingron, S Haas (2012) Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics, 28 (7): 1024-5
J Göke, MH Schulz, J Lasserre, M Vingron (2012) Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics, 28 (5): 656-63
AK Emde et al. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5): 619-27
J Göke et al. (2011) Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Comput Biol., 7 (12): e1002304
S Roepcke, S Stahlberg, H Klein, MH Schulz, L Theobald, S Gohlke, M Vingron, DJ Walther A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ. BMC Genomics, 12 (1): 624
M Thomas-Chollier, A Hufton, M Heinig, S O'Keeffe, NE Masri, HG Roider, T Manke, M Vingron (2011) Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat Protoc., 6 (12): 1860-9
T Zemojtel, SM Kielbasa, PF Arndt, S Behrens, G Bourque, M Vingron (2011) CpG deamination creates transcription factor binding sites with high efficiency. Genome Biol Evol., 3: 1304-11
Y Yuan et al. (2011) Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics, 12: 347
J Lasserre et al. (2011) Predicting the outcome of renal transplantation. J Am Med Inform Assoc., 19 (2): 255-62
Y Yuan et al. (2011) Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics, 12 (1): 347
A Serin, M Vingron (2011) DeBi: Discovering differentially expressed biclusters using a frequent itemset approach. Algorithms Mol Biol., 6 (1): 18
E Szczurek, F Markowetz, I Gat-Viks, P Biecek, J Tiuryn, M Vingron (2011) Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. BMC Bioinformatics, 12 (1): 249
HJ Warnatz et al. (2011) The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in the control of the cell cycle. J Biol Chem., 286 (26): 23521-32
L Hallen et al. (2011) The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. Hum Mol Genet., 20(1):104-14
HR Chung, I Dunkel, F Heise, C Linke, S Krobitsch, AE Ehrenhofer-Murray, SR Sperling, M Vingron (2010) The effect of micrococcal nuclease digestion on nucleosome positioning data. PLoS One.5(12):e15754
S Lin, S Haas, T Zemojtel, P Xiao, M Vingron, R Li Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators Gene, 473 (2):139-49
M Kolanczyk et al. (2010) NOA1 is an essential GTPase required for mitochondrial protein synthesis. Mol Biol Cell, 22(1):1-11
M Heinig et al. (2010) A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature, 467(7314):460-4
S Behrens, M Vingron (2010) Studying the evolution of promoter sequences: a waiting time problem. J Comput Biol., 17(12):1591-606
E Szczurek, P Biecek, J Tiuryn, M Vingron (2010) Introducing knowledge into differential expression analysis. J Comput Biol., 17(8):953-67
SM Kielbasa, H Klein, HG Roider, M Vingron, N Blüthgen (2010) TransFind--predicting transcriptional regulators for gene sets. Nucleic Acids Res., 38 Suppl:W275-80
HJ Warnatz, R Querfurth et al. (2010) Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res., 38(18):6112-23
G Meng, A Mosig, M Vingron (2010) A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes. BMC Bioinformatics, 11:267
H Richard et al. (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res.38(10):e112
R Karlic, HR Chung, J Lasserre, K Vlahovicek, M Vingron (2010) Histone modification levels are predictive for gene expression Proc Natl Acad Sci USA107(7):2926-31
T Manke, M Heinig, M Vingron (2010) Quantifying the effect of sequence variation on regulatory interactions Hum Mutat.31(4):477-83
HG Roider, B Lenhard, A Kanhere, SA Haas, M Vingron (2009) CpG-depleted promoters harbor tissue-specific transcription factor binding signals - implications for motif overrepresentation analyses Nucleic Acids Res.37(19):6305-15
E Szczurek, I Gat-Viks, J Tiuryn, M Vingron (2009) Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments Mol Syst Biol.5:287
X Huang, M Vingron Maximum similarity: a new formulation of phylogenetic reconstruction J Comput Biol.16(7):887-98
HR Chung, M Vingron (2009) Comparison of sequence-dependent tiling array normalization approaches BMC Bioinformatics10:204
C Steinhoff, M Paulsen, S Kielbasa, J Walter, M Vingron (2009) Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse BMC Genomics10:144
UJ Pape, H Klein, M Vingron Statistical detection of cooperative transcription factors with similarity adjustment Bioinformatics25(16):2103-9
Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E. (2009) Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol.10(1):202
Gat-Viks I, Vingron M (2009) Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions PLoS Comput Biol.5(2):e1000282
Kanhere A, Vingron M. (2009) Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes BMC Evol Biol.9:9
Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M. (2009) Methylation and deamination of CpGs generate p53-binding sites on a genomic scale Trends Genet.25(2):63-6
Roider HG, Manke T, O'Keeffe S, Vingron M, Haas SA (2009) PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics.25(4):435-42
Zhang J, Vingron M, Roepcke S (2008) Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast. BMC Res Notes.1:109
Kielbasa SM, Vingron M (2008) Transcriptional autoregulatory loops are highly conserved in vertebrate evolution. PLoS One3(9):e3210
Pape UJ, Rahmann S, Sun F, Vingron M. (2008) Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands J Comput Biol.15(6):547-64
Klein H, Vingron M. (2007) Using transcription factor binding site co-occurrence to predict regulatory regions. Genome Inform.18:109-18
Bauer S, Grossmann S, Vingron M, Robinson PN. (2008) Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics24(14):1650-1
Toenjes M, Schueler M, Hammer S, Pape UJ, Fischer JJ, Berger F, Vingron M, Sperling S (2008) Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes Mol Biosyst.4(6):589-98
Manke T, Roider HG, Vingron M. (2008) Statistical modeling of transcription factor binding affinities predicts regulatory interactions PLoS Comput Biol.4(3):e1000039
Chen W et al. (2008) Mapping translocation breakpoints by next-generation sequencing Genome Res.18(7):1143-9
Lee HJ, Manke T, Bringas R, Vingron M. (2008) Prioritization of gene regulatory interactions from large-scale modules in yeast BMC Bioinformatics.9:32
Pape UJ, Rahmann S, Vingron M. (2008) Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics24(3):350-7
Zemojtel T, Penzkofer T, Schultz J, Dandekar T, Badge R, Vingron M (2007) Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics.8:392
Bais AS, Grossmann S, Vingron M (2007) Incorporating evolution of transcription factor binding sites into annotated alignments J Biosci.32(5):841-50
HG Roider, A Kanhere, T Manke, M Vingron (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics, 23(2):134-141
Grossmann S, Bauer S, Robinson PN, Vingron M. (2007) Improved Detection of Overrepresentation of Gene-Ontology Annotations with Parent-Child Analysis. Bioinformatics23(22):3024-31
Bais AS, Grossmann S, Vingron M. (2007) Simultaneous alignment and annotation of cis-regulatory regions. Bioinformatics, 15;23(2)
H Luz, M Vingron. (2006) Family specific rates of protein evolution. Bioinformatics, 15;22(10):1166-1171
Krause A, Stoye J, Vingron M. (2005) Large scale hierarchical clustering of protein sequences. BMC Bioinformatics, 22
Dieterich C, Rahmann S, Vingron M. (2004) Functional inference from non-random distributions of conserved predicted transcription factor binding sites. Bioinformatics, 20 Suppl 1:i109-15.
Huber, W., Heydebreck, A. von, Sueltmann, H., Poustka, A. and Vingron, M. (2003). Parameter estimation for the calibration and variance stabilization of microarray data. Statistical Applications in Genetics and Molecular Biology2(1), Article 3 (http://www.bepress.com/sagmb/vol2/iss1/art3).
Manke T, Bringas R, Vingron M. (2003). Correlating Protein-DNA and Protein-Protein Interaction Networks. J. Mol. Biol.333, 75-85.
W Huber, A von Heydebreck, H Sültmann, A Poustka, M Vingron (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18 Suppl 1: S96-104
Fellenberg, K., Hauser, N., Brors, B., Neutzner, A., Hoheisel, J., Vingron, M. (2001). Correspondence Analysis Applied to Microarray Data. Proc. Natl. Acad. Sci. USA98, 10781-10786.
Müller, T. and Vingron, M. (2000). Modeling amino acid replacement. J. Comp. Biol.7(6), 761-776.
Vingron, M. (1996). Near-optimal sequence alignment. Current Opinion in Structural Biology6, 346-352.
Vingron, M. and Pevzner, P.A. (1995). Multiple Sequence Comparison and Consistency on Multipartite Graphs. Advances in Applied Mathematics16, 1-22.
Vingron, M., Argos, P. (1991). Motif recognition and alignment for many sequences by comparison of dotmatrices. J. Mol. Biol.218, 33-43.
Waterman, M.S., Vingron, M. (1994). Sequence Comparison Significance and Poisson Approximation. Statistical Science9, 367-381.
Vingron, M. and Waterman, M.S. (1994). Sequence Alignment and Penalty Choice: Review of Concepts, Case Studies and Implications. J. Mol. Biol.235, 1-12.