List of Publications

|in 2010 |in 2009 |in 2008 | in 2007 |in 2006 | in 2005 |in 2004 | in 2003 | in 2002 | in 2001

Names in bold indicate group members.

2010

Cheng X., Guerasimova A., Manke T., Rosenstiel P., Haas S., Warnatz H.J., Querfurth R., Nietfeld W., Vanhecke D., Lehrach H., Yaspo ML., Janitz M. (2010)
Screening of human gene promoter activities using transfected-cell arrays
Gene. 2010 Jan 15;450(1-2):48-54 [full text]
Karlic, R., Chung, HR., Lasserre, J., Vlahovicek, K., Vingron, M. (2010)
Histone modification levels are predictive for gene expression
Proc Natl Acad Sci U S A. February 16, 2010 vol. 107 no. 7 2926-2931 [full text]
Manke, T., Heinig, M., Vingron, M. (2010) Quantifying the effect of sequence variation on regulatory interactions
Hum Mutat. 2010 Feb 2. [Epub ahead of print]
May, P., Kreuchwig, A., Steinke, T., Koch, I. (2010)
PTGL: A database for secondary structure-based protein topologies
Nucleic Acids Research (2010 [full text]
Schaefer A.S., Richter G.M., Nothnagel M., Manke T., Dommisch H., Jacobs G., Arlt A., Rosenstiel P., Noack B., Groessner-Schreiber B., Jepsen S., Loos B.G., Schreiber S. (2010)
A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis
Hum Mol Genet. 2010 Feb 1;19(3):553-62 [full text]

2009

Baek,Y.S., Haas,S., Hackstein,H., Bein,G., Santana,M.H., Lehrach,H., Sauer,S. and Seitz,H. (2009)
Identification of novel transcriptional regulators involved in macrophage differentiation and activation in U937 cells
BMC Immunology, 10:18 [full text]
Bozek K, Relogio A, Kielbasa SM, Heine M, Dame C, et al. (2009)
Regulation of Clock-Controlled Genes in Mammals
PLoS ONE 4(3): e4882 [full text]
Chavez, L., Bais, A., Vingron, M., Lehrach, H., Adjaye, J., Herwig, R. (2009)
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach
BMC Genomics 2009, 10:314 [full text]
Diella F, Chabanis S, Luck K, Chica C, Chenna R , Nerlov C, Gibson TJ (200p)
KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
Bioinformatics, Vol 25,1-5
Chung, H-R., Vingron, M. (2009)
Comparison of sequence-dependent tiling array normalization approaches
BMC Bioinformatics 2009, 10:204 [full text]
Chung, H.R., Vingron, M. (2009)
Sequence-dependent Nucleosome Positioning
J Mol Biol. 2009 Mar 13;386(5):1411-22 [full text]
Gambin A, Szczurek E, Dutkowski J, Bakun M, Dadlez M. (2009)
Classification of peptide mass fingerprint data by novel no-regret boosting method
Comput Biol Med., 39(5):460-73. Epub 2009 Apr 21 [full text]
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 (2009) [full text]
Huang, X., Vingron, M. (2009)
Maximum Similarity: A New Formulation of Phylogenetic Reconstruction
Journal of Computational Biology. July 2009, 16(7): 887-896 [full text]
Hufton, A.L., Mathia, S., Braun, H., Georgi, U., Lehrach, H., Vingron,M. Poustka, A.J., Panopoulou, G. (2009)
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
Genome Res. 2009. 19: 2036-2051 [full text]
Kanhere, A., Vingron, M. (2009)
Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes
BMC Evolutionary Biology 2009, 9:9 [full text]
Kielbassa, J., Bortfeldt, R., Schuster, S., Koch, I. (2009)
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
Computational Biology and Chemistry (2009) 33: 46-61 [full text]
Koch, I. (2009)
Petri nets and GRN Models In Computational Methodologies in Gene Regulatory Networks
IGI Global PA (USA),chapt. 25:604-637 (2010)
Koehler, S., Schulz, M.H., Krawitz, P., Bauer, S., Doelken, S., Ott, C.E., Mundlos, C., Horn, D., Mundlos, S., Robinson, P.N. (2009)
Clinical Diagnostics with Semantic Similarity Searches in Ontologies
The American Journal of Human Genetics, Vol.85, Issue 4, 457-464, October 2009 [full text]
Loehr, U., Chung, HR., Beller, M., Jaeckle, H. (2009)
Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains
Proc Natl Acad Sci U S A. December 22, 2009 vol. 106 no. 51 21695-21700 [full text]
Ott CE, Bauer S, Manke T, Ahrens S, Rödelsperger C, Grünhagen J, Kornak U, Duda G, Mundlos S, Robinson PN (2009)
Promiscuous and Depolarization-Induced Immediate-Early Response Genes are Induced by Mechanical Strain of Osteoblasts Original Study
J Bone Miner Res. 2009 Mar 3 [full text]
Pape, U.J., Klein, H., Vingron, M. (2009)
Statistical detection of cooperative transcription factors with similarity adjustment
Bioinformatics 2009 25(16):2103-2109 [full text]
Roedelsperger, C., Koehler, S., Schulz, M.H., Manke, T., Bauer, S., Robinson, P.N. (2009)
Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts
Genomics 2009 Aug 4 [full text]
Roider, H.G., Lenhard, B., Kanhere, A., Haas, S.A., Vingron, M. (2009)
CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses
Nucleic Acids Research, 2009, 1–11 [full text]
Roider,H.G., Manke,T., O'Keeffe,S., Vingron,M., Haas,S.A. (2009)
PASTAA: identifying transcription factors associated with sets of co-regulated genes
Bioinformatics, 25(4):435-442 [full text]
Roytberg, M.A., Gambin A., Noe, L., Lasota, S., Furletova, E., Szczurek, E., Kucherov, G. (2009)
On Subset Seeds for Protein Alignment
IEEE/ACM Trans., Comput. Biology Bioinform. 6(3): 483-494 [full text]
Schulz, M.H. Koehler, S., Bauer, S., Vingron, M., Robinson, P.N. (2009)
Exact Score Distribution Computation for Similarity Searches in Ontologies
Proceedings WABI 2009, Springer LNCS, Volume 5724, 2009 [full text]
Steinhoff, C., Paulsen, M., Kielbasa, S., WalterJ., Vingron,M. (2009)
Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse
BMC Genomics 2009, 10:144 [full text]
Stritt C, Stern S, Harting K, Manke T, Sinske D, Schwarz H, Vingron M, Nordheim A, Knöll B. (2009)
Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression
Nat Neurosci. 2009 Apr;12(4):418-27. Epub 2009 Mar 8 [full text]
Szczurek, E., Gat-Viks, I., Tiuryn, J., Vingron, M. (2009)
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments
Molecular systems biology. 01/02/2009; 5:287 [full text]
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 Biology 2009, 10:202 [full text]
Ye, K., Schulz, M.H., Long, Q., Apweiler, R., Ning, Z. (2009)
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short read data
Short-read SIG ISMB 2009, Bioinformatics 2009 25(21):2865-2871 [full text]
Zemojtel, T., Kielbasa, S.Z., Arndt, P.F., Chung, H.R., Vingron, M. (2009)
Methylation and deamination of CpGs generate p53-binding sites on a genomic scale
Trends in Genetics, Volume 25, Issue 2, February 2009, Pages 63-66 [full text]

2008

Bauer, S., Grossman, S., Vingron, M., Robinson, P.N. (2008)
Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration
Bioinformatics 2008 24(14):1650-1651 [full text]
Bluethgen, N., Legewie, S., Kielbasa, S.M., Schramme, A., Tchernitsa, O., Keil, J., Solf, A., Vingron, M., Schaefer, R., Herzel, HP., Sers, C. (2008)
A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts
FEBS Journal, Volume 276 Issue 4, Pages 1024 - 1035 [full text]
Chen, W., Kalscheu, V., Tzschach, A., Menzel, C., Ullmann, R., Schulz, M.H., Erdogan, F., Li, N., Kijas, Z., Arkesteijn, G., Pajares, I.L., Goetz-Sothmann, M., Heinrich, U., Rost, I., Dufke, A., Grasshoff, U., Glaeser, B.G., Vingron, M., Ropers, H.H. (2008)
Mapping translocation breakpoints by next-generation sequencing
Genome Research 2008 Jul;18(7):1143-9. Epub 2008 Mar 7 [full text]
Costa, I.G., Roepcke, S., Hafemeister, C., Schliep, A. (2008)
Inferring differentiation pathways from gene expression
Bioinformatics 2008 24(13):i156-i164 [full text]
Coulson, R., Manke, T., Palin, K., Roider, H., Sand, O., van Helden, J., Ukkonen, E., Vingron M., Brazma, A. (2008)
From gene expression profiling to gene regulation
Modern Genome Annotation. The BioSapiens Network. Springer, Chapter 2.3, Pages 105-115
de Souto, M.CP., Costa, I.G., de Araujo, D.SA., Ludermir, T.B., Schliep, A. (2008)
Clustering cancer gene expression data: a comparative study
BMC Bioinformatics 2008, 9:497 [full text]
de Souto, M.C.P., Prudencio, R.B.C.; Soares, R.G.F.; de Araujo, D.S.A.; Costa, I.G.; Ludermir, T.B.; Schliep, A. (2008)
Ranking and selecting clustering algorithms using a meta-learning approach
IEEE International Joint Conference on Neural Networks (IJCNN) 2008, 1-8 June 2008 Page(s):3729 - 3735 [full text]
de Souto, M.C.P.; de Araujo, D.S.A.; Costa, I.G.; Soares, R.; Ludermir, T.B.; Schliep, A. (2008)
Comparative study on normalization procedures for cluster analysis of gene expression datasets
IEEE International Joint Conference on Neural Networks (IJCNN) 2008, 1-8 June 2008 Page(s):2792 - 2798 [full text]
Duret, L., Arndt, P.F. (2008)
The Impact of Recombination on Nucleotide Substitutions in the Human Genome
PLoS Genet 4(5): e1000071 (2008) [full text]
Giegerich,R., Brazma, A., Jonassen, I., Ukkonen, E., Vingron, M. (2008)
The BREW workshop series: a stimulating experience in PhD education
Briefings in Bioinformatics, VOL 9. NO 3. 250-253 [full text]
Grafahrend-Belau, E., Schreiber, F., Heiner, M., Sackmann, A., Junker, B.H., Grunwald, S., Speer, A., Winder, K., Koch, I. (2008)
Modularization of biochemical networks based on classification of Petri net t-invariants
BMC Bioinformatics 9:90(2008) [full text]
Grunwald, S., Speer, A., Ackermann J, Koch, I. (2008)
Petri net modelling of gene regulation of the Duchenne muscular dystrophy
Biosystems 2008, Mar 10 [full text]
Hain,T., Hossain,H., Chatterjee,S.S., Machata,S., Volk,U., Wagner,S., Brors,B., Haas,S., Kuenne,C.T., Billion,A., Otten,S., Pane-Farre,J., Engelmann,S. and Chakraborty,T. (2008)
Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e sigmaB regulon
BMC Microbiology, 8:20 [full text]
Hufton, A.L., Groth, D., Vingron, M., Lehrach, H., Poustka, A.J., Panopoulou, G. (2008)
Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement
Genome Res, vol. 18, no. 10, pp. 1582--1591, 2008 [full text]
Jacob, J., Jentsch, M., Kostka, D., Bentink, S., Spang, R. (2008)
Detecting hierarchical structure in molecular characteristics of disease using transitive approximations of directed graphs
Bioinformatics 2008 24(7):995-1001 [full text]
Kaluza, P., Vingron, M., Mikhailov, A.S. (2008)
Self-correcting networks: Function, robustness, and motif distributions in biological signal processing
Chaos 18, 026113 (2008) [full text]
Kielbasa, S., Vingron, M. (2008)
Transcriptional Autoregulatory Loops Are Highly Conserved in Vertebrate Evolution
PLoS ONE 3(9): e3210 [full text]
Koch,I. Fuellen, G. (2008)
A review of bioinformatics education in Germany
Briefings in Bioinformatics Advance Access published on March 1, 2008 [full text]
Koch, I., Heiner, M. (2008)
Petri nets
Analysis of Biological Networks, Wiley Book Series in Bioinformatics, chapter 7:139-180 (2008)
Koestner, U., Shnitsar, I., Linnemannstoens, K., Hufton, A.L., Borchers, A. (2008)
Semaphorin and neuropilin expression during early morphogenesis of Xenopus laevis.
Dev Dyn, vol. 237, no. 12, pp. 3853--3863, 2008 [full text]
Kostka D, Spang R (2008)
Microarray Based Diagnosis Profits from Better Documentation of Gene Expression Signatures
PLoS Comput Biol 4(2): e22. [full text]
Lee, J.S., Krause, R., Schreiber, J., Mollenkopf, H.-J., Kowall, J., Stein, R., Jeon, B.-Y., Kwak, J.-Y., Song, M.-K., Patron, J.P., Jorg, S., Roh, K., Cho, S.-N., Kaufmann, S.H.E. (2008)
Mutation in the Transcriptional Regulator PhoP Contributes to Avirulence of Mycobacterium tuberculosis H37Ra Strain
Cell Host & Microbe, Volume 3, Issue 2, Pages 97-103 [full text]
Lee, H.J., Manke, T., Bringas, R., Vingron, M. (2008)
Prioritization of gene regulatory interactions from large-scale modules in yeast
BMC Bioinformatics. 2008; 9: 32 [full text]
Lorena, A.C.; Costa, I.G.; de Souto, M.C.P. (2008)
On the Complexity of Gene Expression Classification Data Sets
Eighth International Conference on Hybrid Intelligent Systems (HIS) 2008, 10-12 Sept. 2008 Page(s):825 - 830 [full text]
Manke, T., Roider, H.G., Vingron, M. (2008)
Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
PLoS Comput Biol. 2008 March; 4(3): e1000039 [full text]
Manke, T., Roider, H.G., Vingron, M. (2008)
A biophysical approach to large-scale protein-DNA binding data
Modern Genome Annotation. The BioSapiens Network. Springer, Chapter 2.2, Pages 91-102
Michael S, Trav G, Chenna R, Chica C, Gibson TJ (2008)
Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.
Bioinformatics. 2008 Feb 15;24(4):453-7 [full text]
Mueller, F.J., Laurent, L., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Rao, M.S., Shamir, R., Schwartz, P.H., Schmidt, N.O., Loring, J.F. (2008)
Regulatory networks define phenotypic classes of human stem cell lines
Nature, 2008, 455, 401-105 [full text]
Pape, U., Rahmann, S., Vingron, M. (2008)
Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering
Bioinformatics 2008 [full text]
Pape, U.J., Klein, H., Vingron, M. (2008)
Statistical detection of co-operative transcription factors with similarity adjustment
Lecture Notes in Informatics: Proc. of German Conference for Bioinformatics (GCB), 2008, 96-105 [full text]
Pape, U.J., Vingron, M. (2008)
Statistics for Co-Occurrence of DNA Motifs
Proc. of International Workshop for Applied Probability (IWAP), 2008
Pape, U.J., Rahmann, S., Sun, F., Vingron, M. (2008)
Compound Poisson approximation of DNA motif counts on both strands
Journal of Computational Biology, 2008, 15 (6), 547-564 [full text]
Polak, P., Arndt, P.F. (2008)
Transcription induces strand-specific mutations at the 5? end of human genes
Genome Res. August 2008 18:1216-1223 [full text]
Rausch, T., Emde, A.K., Weese, D., Doering, A., Notredame, C., Reinert, K. (2008)
Segment-based multiple sequence alignment
Bioinformatics 2008 24(16):i187-i192 [full text]
Rödelsperger C, Dieterich C. (2008)
Syntenator: Multiple gene order alignments with a gene-specific scoring function
Algorithms Mol Biol. 2008 Nov 6;3:14 [full text]
Roytberg, M.A., Gambin, A., Noe, L., Lasota, S., Furletova, E., Szczurek, E., Kucherov, G. (2008)
Efficient Seeding Techniques for Protein Similarity Search
BIRD 2008: 466-478 [full text]
Schliep, A., Krause, R. (2008)
Efficient Algorithms for the Computational Design of Optimal Tiling Arrays
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 4, October-December 2008 [full text]
Schulz, M.H.*, Bauer, S.*, Robinson, P.N. (2008)
The generalised k-Truncated Suffix Tree for time- and space-efficient searches in multiple DNA or protein sequences
International Journal of Bioinformatics Research and Applications 2008, Vol. 4, Nr .1, pp. 81--95 [full text]
*shared first authorship
Schulz, M.H., Weese, D., Rausch, T., Doering, A., Reinert, K., Vingron, M. (2008)
Fast and adaptive variable order Markov chain construction
WABI 2008: 306-317 [full text]
Squartini, F., Arndt, P.F. (2008)
Quantifying the Stationarity and Time Reversibility of the Nucleotide Substitution Process
Molecular Biology and Evolution 2008 25(12):2525-2535 [full text]
Sultan, M.*, Schulz, M.H.*, Richard, H.*, Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., Schmidt, D., O'Keeffe, S., Haas, S., Vingron, M., Lehrach, H., Yaspo, ML (2008)
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
Science, Vol. 321. no. 5891, pp. 956 - 960 [full text]
*shared first authorship
Tegha-Dunghu, J., Neumann, B., Reber, S., Krause, R., Erfle, H., Walter, T., Held, M., Rogers, P., Hupfeld, K., Ruppert, T., Ellenberg, J., Gruss, O.J. (2008)
EML3 is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase
J Cell Sci 2008 121: 1718-1726 [full text]
Toenjes, M., Schueler, M., Hammer, S., Pape, U.J., Fischer, J.J., Berger, F., Vingron, M., Sperling, S. (2008)
Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes
Mol. BioSyst., 2008, 4, 589 - 598 (2008) [full text]
Ulitsky, I., Gat-Viks, I., Shamir, R. (2008)
MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data
Genome Biology 2008, 9:R1 [full text]
Weese, D., Schulz, M.H. (2008)
Efficient string mining under constraints via the deferred frequency index
Industrial Conference for Data Mining (ICDM 2008), LNAI 5077, pp. 374-388 [full text]
Winter, J., Roepcke, S., Krause, S., Mueller, EC., Otto, A., Vingron, M., Schweiger, S.
Comparative 3'UTR analysis allows identification of regulatory clusters that drive Eph/ephrin expression in cancer cell lines
PLoS ONE. 2008; 3(7): e2780 [full text]
Zhang, J., Vingron, M., Roepcke, S. (2008) Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast
BMC Research Notes 2008, 1:109 [full text]

2007

Arndt, P.F., Vingron, M. (2007)
The Otto Warburg International Summer School and Workshop on Networks and Regulation
BMC Bioinformatics 2007, 8(Suppl 6):S1 [full text]
Bais,A.S., Grossmann, S., Vingron, M. (2007)
Simultaneous alignment and annotation of cis-regulatory regions
Bioinformatics 2007 23(2):e44-e49 [full text]
Bais,A.S., Grossmann, S., Vingron, M. (2007)
Incorporating evolution of transcription factor binding sites into annotated alignments
Journal of Biosciences, Vol.32, Suppl.1, 841-850 [full text]
Beisel,C., Buness,A., Roustan-Espinosa,I.M., Koch,B., Schmitt,S., Haas,S.A., Hild,M., Katsuyama,T., Paro,R. (2007)
Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins
Proc. Natl. Acad. Sci., 104(42):16615-16620 [full text]
Bozek, K., Kielbasa, S., Kramer, A., Herzel, HP. (2007)
Promotor Analysis of Mammalian Clock Controlled Genes
Genome Informatics Series Vol. 18 (pp 65-74) [full text]
Costa, I.G., Roepcke, S., Schliep, A. (2007)
Gene expression trees in lymphoid development
BMC Immunology 2007, 8:25 [full text]
Costa, I.G., Krause, R., Opitz, L., Schliep, A. (2007)
Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data
BMC Bioinformatics 2007, 8(Suppl 10):S3 [full text]
Costa, I.G., de Souto, M.C.P., Schliep, A. (2007)
Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information
Lecture Notes in Computer Science, Advances in Bioinformatics and Computational Biology, Vol.4643/2007, 81-92 [full text]
Chung, H.-R., Kostka, D., Vingron, M., (2007)
A physical model for tiling array analysis
Bioinformatics 2007 23(13):i80-i86 [full text]
Chung, HR., Loehr, U., Jaeckle, H. (2007)
Lineage-specific expansion of the zinc finger associated domain ZAD
Mol Biol Evol. 2007 Sep;24(9):1934-1943 [full text]
de la Chaux, N., Messer, P.W., Arndt, P.F. (2007)
DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage
BMC Evol Biol. 2007; 7: 191 [full text]
Demetrius, L., Gundlach, V.M., Ziehe, M. (2007)
Darwinian fitness and the intensity of natural selection: Studies in sensitivity analysis
Journal of Theoretical Biology, Volume 249, Issue 4, 21 December 2007, Pages 641-653 [full text]
Demetrius, L., Ziehe, M. (2007)
Darwinian fitness
Theoretical Population Biology, Volume 72, Issue 3, November 2007, Pages 323-345 [full text]
Dieterich C, Franz MW, Vingron M. (2007)
Developments in CORG: a gene-centric comparative genomics resource
Nucleic Acids Res. 2007 Jan;35(Database issue):D32-5
Georgi, B., Spence, M.A., Flodman, P., Schliep, A. (2007)
Mixture model based group inference in fused genotype and phenotype data
Studies in Classification, Data Analysis, and Knowledge Organization, 2007
Georgi, B., Schultz, J., Schliep, A. (2007)
Context-Specific Independence Mixture Modelling for Protein Families
Lecture Notes in Computer Science, PKDD 2007, Vol. 4702/2007, p.79-90 [full text]
Georgi, B., Schliep, A. (2007)
Partially-supervised context-specific independence mixture modeling
Workshop on Data Mining in Functional Genomics and Proteomics, ECML 2007
Gambin, A., Szczurek, E. (2007)
No-regret boosting
International Conference on Adaptive and Natural Computing Algorithms (ICANNGA 2007), LNCS 4431:422-431 [full text]
Grossmann, S., Bauer, S., Robinson, P.N., Vingron, M. (2007)
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
Bioinformatics 2007 Nov 15;23(22):3024-31
Guo, G., Bauer, S., Hecht, J., Schulz, M.H., Busche, A., Robinson, P.N. (2007)
A short ultraconserved sequence drives transcription from an alternate FBN1 promoter
The International Journal of Biochemistry & Cell Biology, [full text]
Haesler, S., Rochefort, C., Licznerski, P., Georgi, B., Osten, P., Scharff, C. (2007)
Knockdown of FoxP2 in Songbird Basal Ganglia Impairs Song Learning
PloS Biology 2007, Vol. 5, Number 12, Pages e321
Hooper, S.D., Boué, S., Krause, R., Jensen, L. J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E. E. M., Bork, P. (2007)
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
Molecular Systems Biology 3 Article number: 72 (2007) [full text]
Kaluza, P., Ipsen, M.,Vingron, M.,, Mikhailov, A.S. (2007)
Design and statistical properties of robust functional networks: A model study of biological signal transduction
PHYSICAL REVIEW E 75, pp. 015101 (R), 2007 [full text]
Kielbasa, S., Herzel, HP., Axmann, I.M. (2007)
Regulatory Elements of Marine Cyanobacteria
Genome Informatics Series Vol. 18 (pp 1-11) [full text]
Klau, G.W., Rahmann, S.,Schliep A., Vingron, M., and K. Reinert (2007)
Integer linear programming approaches for non-unique probe selection
Discrete Applied Mathematics, Vol.155, Iss.6-7, p.840-856 [full text]
Klein, H., Vingron, M. (2007)
Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions
Genome Informatics Vol. 18, 109-118, (2007)
Lichtenauer U.D., Duchniewicz M., Kolanczyk M., Hoeflich A., Hahner S., Else T., Bicknell A.B., Zemojtel T., Stallings N.R., Schulte D.M., Kamps M.P., Hammer G.D., Scheele J.S., Beuschlein F. (2007)
Pre-B-Cell Transcription Factor 1 and Steroidogenic Factor 1 Synergistically Regulate Adrenocortical Growth and Steroidogenesis
Endocrinology. 2007, 148(2):693-704 [full text]
Mao,L., Zabel, C., Herrmann,M., Nolden, T., Mertes,F., Magnol, L., Chabert, C., Hartl, D., Herault, Y., Delabar, J.M., Manke, T. , Himmelbauer,H., Klose, J. (2007)
Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks
PLoS ONE. 2007; 2(11): e1218 [full text]
Markowetz, F., Kostka, D., Troyanskaya, O.G., Spang, R. (2007)
Nested effects models for high-dimensional phenotyping screens
Bioinformatics 2007 23(13):i305-i312 [full text]
Markowetz, F., Spang, R. (2007)
Inferring cellular networks – a review
BMC Bioinformatics 2007, 8(Suppl 6):S5 [full text]
Messer, P.W., Bundschuh, R., Vingron, M., Arndt, P.F. (2007)
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics
Journal of Computational Biology. 2007, 14(5): 655-668 [full text]
Messer, P.W., Arndt, P.F. (2007)
The Majority of Recent Short DNA Insertions in the Human Genome Are Tandem Duplications
Molecular Biology and Evolution 2007 24(5):1190-1197 [full text]
Opitz, L., Schliep, A.,Posch, A. (2007)
Analysis of fused in-situ hybridization and gene expression data
Advances in Data Analysis, p. 577-584
Roider, H.G., Kanhere, A., Manke, T., Vingron, M. (2007)
Predicting transcription factor affinities to DNA from a biophysical model
Bioinformatics, Vol. 23 no. 2, pages 134–141 (2007) [full text]
Rungsarityotin, W., Krause, R., Schodl, A., Schliep (2007)
Identifying protein complexes directly from high-throughput TAP data with Markov random fields
BMC Bioinformatics 2007, 8:482 [full text]
Schliep, A., Krause, R. (2007)
Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach
Algorithms in Bioinformatics,p. 383-394
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 2007, 8:392 [full text]

2006

Ayerdi-Izquierdo, A., Stavrides, G., Selles-Martinez, J. J., Larrea, L., Bovo, G., de Munain, A. L., Bisulli, F., Marti-Masso, J. F., Michelucci, R., Poza, J. J., Tinuper, P., Stephani, U., Striano, P., Striano, S., Staub, E., Sarafidou, T., Hinzmann, B., Moschonas, N., Siebert, R., Deloukas, P., Nobile, C., & Perez-Tur, J. (2006)
Genetic analysis of the LGI/Epitempin gene family in sporadic and familial lateral temporal lobe epilepsy
Epilepsy Res. 70, 118-126, 2006 [full text]
Behzadi, B. and Vingron, M. (2006)
An Improved Algorithm for the Macro-evolutionary Phylogeny Problem
CPM 2006, LNCS 4009, pp. 177-187 [full text]
Behzadi, B., Vingron, M. (2006)
Reconstructing Domain Compositions of Ancestral Multi-Domain Proteins
Comparative Genomics RECOMB 2006, LNBI 4205, pp. 1-10, 2006 [full text]
Costa, I.G., Schliep, A. (2006)
On the feasibility of Heterogeneous Analysis of Large Scale Biological Data
Proceedings of ECML/PKDD 2006 Workshop on Data and Text Mining for Integrative Biology, Pages 55-60, 2006
Dieterich, C., Vingron, M. (2006)
Comparative promoter analysis in vertebrate genomes with the CORG workbench
Methods Mol Biol. 2006;338:105-18
Dohm, J. C., Vingron, M., Staub, E. (2006)
Horizontal Gene Transfer in Aminoacyl-tRNA Synthetases Including Leucine-Specific Subtypes
J. Mol. Evol., 63:4, 437-447, 2006 [full text]
Duchniewicz M and Zemojtel T, Kolanczyk M, Grossmann S, Scheele JS, Zwartkruis FJ (2006)
Rap1A-deficient T and B cells show impaired integrin-mediated cell adhesion.
Mol Cell Biol. 2006 Jan, 26(2), 643-53 [full text]
Groene, J., Mansmann, U., Meister, R., Staub, E., Roepcke, S., Heinze, M., Klaman, I., Brummendorf, T., Hermann, K., Loddenkemper, C., Pilarsky, C., Mann, B., Adams, H. P., Buhr, H. J., & Rosenthal, A. (2006)
Transcriptional census of 36 microdissected colorectal cancers yields a gene signature to distinguish UICC II and III
Int. J. Cancer 119, 1829-1836, 2006 [full text]
Hecht,H., Kuhl,H., Haas,S.A., Bauer,S., Poustka,A.J., Lienau,J., Schell,H., Stiege,V., Seitz,V., Reinhardt,R., Duda,G.N., Mundlos,S. and Robinson,P.N. (2006)
Gene Identification and Analysis of Transcripts Differentially Regulated in Fracture Healing by EST Sequencing in the Domestic Sheep
BMC Genomics, 7:172 [full text]
Hummel, M., Bentink, S., Berger,H., Klapper, W., Wessendorf,S., Barth, T.F.E., Bernd,H.-W., Cogliatti, S.B., Dierlamm, J., Feller,A.C., Hansmann, M.L., Haralambieva, E., Harder, L., Hasenclever, D., Kühn, M., Lenze, D., Lichter, P., Martin-Subero, J.I., Möller, P., Müller-Hermelink, H.K., Ott, G., Parwaresch, R.M., Pott, C., Rosenwald, A., Rosolowski, M., Schwaenen, C., Stürzenhofecker, B., Szczepanowski, M., Trautmann, H., Wacker, H.-H., Spang, R., Loeffler, M., Trümper, L., Stein, H., Siebert, R. (2006)
A Biologic Definition of Burkitt's Lymphoma from Transcriptional and Genomic Profiling
NEJM June 2006, 354:2419-2430
Lipatov,M., Arndt, P.F., Hwa, T., Petrov, D.A. (2006)
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution
Journal of Molecular Evolution 62 (2006) 168-75 [full text]
Luz H , Vingron M (2006)
Family specific rates of protein evolution
Bioinformatics 2(10):1166-1171.
[full text]
Luz H, Staub S, and Vingron M (2006)
About the interrelation of evolutionary rate and protein age
Genome Informatics 17(1): 240-250.
[full text]
Manke, T., Demetrius, L., Vingon, M. (2006)
An Entropic Characterization of Protein Interaction Networks and Cellular Robustness
Royal Soc. Interface 2006 (to be published) [abstract]
Messer, P.W., Arndt, P.F. (2006)
CorGen-measuring and generating long-range correlations for DNA sequence analysis
W692-W695 Nucleic Acids Research, 2006, Vol. 34 [full text]
Messer, P.W., Bundschuh, R., Vingron, M., Arndt, P.F. (2006)
Alignment Statistics for Long-Range Correlated Genomic Sequences
RECOMB 2006, LNBI 3909, pp. 426-440, 2006 [full text]
Oberthuer,A., Berthold,F., Warnat,P., Hero,B., Kahlert,Y., Spitz,R., Ernestus,K., Koenig,R., Haas,S., Eils,R., Schwab,M., Brors,B., Westermann,F., Fischer,M. (2006)
Gene-expression based classification of neuroblastoma patients using a customized oligonucleotide-microarray outperforms current clinical risk stratification
J. Clin. Oncol., 24:5070-5078, 2006 [abstract]
Pape, U.J., Grossmann, S., Hammer, S., Sperling, S., Vingron, M. (2006)
A new statistical model to select target sequences bound by transcription factors
Genome Inform. 2006 ;17 (1):134-40 17503363
Qin, Y., Polacek, N., Vesper, O., Wilson, D. N., Staub, E., Einfeldt, E., & Nierhaus, K. H. (2006)
The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome and is essential for viability at high ionic strength
Cell, Volume 127, Issue 4, 17 November 2006, Pages 721-733 2006 [full text]
Roepcke, S., Zhi, D., Vingron, M., Arndt, P.F. (2006)
Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters
Gene 365 (2006) 48-56 [full text]
Schoenhuth,A., Costa, I.G., Schliep, A. (2006)
Semi-supervised Clustering of Yeast Gene Expression
Japanese-German Workshop on data analysis and classification, Springer, 2006
Schulz, W.A., Steinhoff, C., Florl, A.R.
Methylation of Endogenous Human Retroelements in Health and Disease
CTMI(2006) 310:211-250
Schwecke T, Göttling K, Durek P, Duenas I, Käufer NF, Zock-Emmenthal S, Staub E, Neuhof T, Dieckmann R, von Döhren H
Nonribosomal peptide synthesis in S. pombe and the architecture of ferrichrome-type siderophore synthetases in fungi
ChemBioChem 2006. Vol. 7, Issue 4, pp. 612-622 [full text]
Staub, E., Mackowiak, S., Vingron, M. (2006)
An inventory of yeast proteins that are associated with nucleoli and ribosomal components
Genome Biology 2006; 7(10): R98 [full text]
Staub, E., Grone, J., Mennerich, D., Roepcke, S., Klamann, I., Hinzmann, B., Castanos-Velez, E., Mann, B., Pilarsky, C., Brummendorf, T., Weber, B., Buhr, H. J., & Rosenthal, A. (2006)
A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer
Mol. Cancer 5, 37, 2006 [full text]
Steinhoff C., Vingron M. (2006)
Review: Normalization and Quantification of Differential Expression
Briefings in Bioinformatic, Advance Access published on March 7, 2006
Yang, X., Bentink, S., Scheid, S., Spang, R. (2006)
Similarities of Ordered Gene Lists
Journal of Bioinformatics and Computational Biology, Vol. 4, No. 3 (2006) 693–708 [full text]
Yeang, Chen-Hsiang, Vingron, Martin
A joint model of regulatory and metabolic networks
BMC Bioinformatics 2006, 7:332 [full text]
Zemojtel T, Kolanczyk M, Kossler N, Stricker S, Lurz R, Mikula I, Duchniewicz M, Schuelke M, Ghafourifar P, Martasek P,Vingron M, Mundlos S. (2006)
Corrigendum to “Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate” [FEBS Lett. 580 (2006) 455–462]
FEBS Lett. 581(10):2072-2073 [full text]
Zemojtel T, Penzkofer T, Duchniewicz M, Zwartkruis FJT (2006)
hRap1B-retro: a novel human processed Rap1B gene blurs the picture?
Leukemia 2006 Jan, 20, 145-146 [full text]
Zemojtel T and Kolanczyk M, Kossler N, Stricker S, Lurz R, Mikula I, Duchniewicz M, Schuelke M, Ghafourifar P, Martasek P, Vingron M, Mundlos S. (2006)
Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate.
FEBS Lett. 2006 Jan, 580(2), 455-462 [full text]
Zemojtel T, Frohlich A, Palmieri MC, Kolanczyk M, Mikula I, Wyrwicz LS, Wanker EE, Mundlos S, Vingron M, Martasek P, Durner J. (2006)
Plant nitric oxide synthase: a never-ending story?
Trends Plant Sci. 2006 Nov, 11 [full text]

2005

Alldinger I, Dittert D, Peiper M, Fusco A, Chiappetta G, Staub E, Lohr M, Jesnowski R, Baretton G, Ockert D, Saeger HD, Grutzmann R, Pilarsky C. (2005)
Gene expression analysis of pancreatic cell lines reveals genes overexpressed in pancreatic cancer.
Pancreatology. 2005;5(4-5):370-9
Arndt PF, Hwa T, Petrov DA (2005)
Substantial Regional Variation in Substitution Rates in the Human Genome: Importance of GC Content, Gene Density, and Telomere-Specific Effects.
J Mol Evol. 2005 Jun;60(6):748-63.
Nadia D Singh, Peter F Arndt, Dmitri A Petrov (2005)
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster
Genetics 2005 169: 709-22 [Fulltext]
Arndt PF, Hwa T (2005)
Identification and measurement of neighbor-dependent nucleotide substitution processes
Bioinformatics 2005 21: 2322-2328.
Belyakin SN, Christophides GK, Alekseyenko AA, Kriventseva EV, Belyaeva ES, Nanayev RA, Makunin IV, Heidelberg FlyArray Consortium, Kafatos FC, Zhimulev IF (2005)
Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories.
PNAS, 102, 8269-8274
Batolla U, Demetrius L (2005)
Stability constraints and protein evolution: the role of chain length, composition and disulfide
Protein Engineering Design and Selection 2005, 38:405-415
Costa IG, Schönhuth A, Schliep A (2005)
The Graphical Query Language: a tool for analysis of gene expression time-courses
Bioinformatics 2005 21: 2544-2545.
Costa IG, Schliep A (2005)
On external indices for mixtures: validating mixtures of genes
Proceedings of the GfKl 2005 Conference, accepted
Demetrius L, Manke T (2005)
Robustness and network evolution--an entropic principle
Physica A: Statistical and Theoretical Physics, 346(3-4):682-696
Demetrius L (2005)
Of mice and men
E MBO reports 6, 39-44
Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M (2005)
Comparative promoter region analysis powered by CORG
BMC Genomics 2005, 6:24
Dyczkowski J, Vingron M (2005)
Comparative analysis of cell cycle regulated genes in eukaryotes
Genome Inform Ser Workshop Genome Inform. 2005;16(1):125-31 [Abstract]
Gupta S, Vingron M, Haas SA (2005)
T-STAG: resource and web-interface for tissue-specific transcripts and genes
Nucleic Acids Research 2005 33(Web Server issue):W654-W658 [Abstract]
Hui J, Hung LH, Heiner M, Schreiner S, Neumuller N, Reither G, Haas SA, Bindereif A (2005)
Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing.
EMBO J., 24(11), 1988-1998
Irlbacher H, Franke J, Manke T, Vingron M, Ehrenhofer-Murray AE. (2005)
Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression
Genes Dev. 2005 Aug 1;19(15):1811-22 [Abstract]
Jaeger J, Weichenhan D, Ivandic B, Spang R (2005)
Early diagnostic marker panel determination for microarray based clinical studies
Statistical Applications in Genetics and Molecular Biology: Vol. 4: No. 1, Article 9
Kasper G, Vogel A, Klaman I, Grone J, Petersen I, Weber B, Castanos-Velez E, Staub E, Mennerich D. (2005)
The human LAPTM4b transcript is upregulated in various types of solid tumours and seems to play a dual functional role during tumour progression.
Cancer Lett. 2005 Jun 16;224(1):93-103
Kowald A, Demetrius L (2005)
Directionaliry theory: a computational study of an entropic principle in evolutionary processes
Proc R Soc B, 2005, 272:741-749
Krause A, Stoye J, Vingron M (2005)
Large Scale Hierarchical Clustering of Protein Sequences
BMC Bioinformatics 6:15, 2005 [Fulltext]
Kristiansen G, Pilarsky C, Wissmann C, Kaiser S, Bruemmendorf T, Roepcke S, Dahl E, Hinzmann B, Specht T, Pervan J, Stephan C, Loening S, Dietel M, Rosenthal A. (2005)
Expression profiling of microdissected matched prostate cancer samples reveals CD166/MEMD and CD24 as new prognostic markers for patient survival
J Pathol. 2005 Feb;205(3):359-76 [Abstract]
Lottaz C, Spang R (2005)
stam - a Bioconductor compliant R package for structured analysis of microarray data
BMC Bioinformatics. 2005 Aug 25;6(1):211
Lottaz C, Spang R (2005)
Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data
Bioinformatics 2005 21(9):1971-1978
Luz H , Vingron M (2005)
Family specific rates of protein evolution
Proceedings of the German Conference on Bioinformatics 2005: 103-108
Manke, T. Dieterich, C. Vingron, M. (2005)
Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome
Lecture Notes in Computer Science, Vol.3318, p.14-21 [Fulltext]
Manke T, Demetrius L, Vingron M. (2005)
Lethality and entropy of protein interaction networks
Genome Inform Ser Workshop Genome Inform. 2005;16(1):159-63 [Abstract]
Markowetz F, Bloch J, Spang R (2005)
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
Bioinformatics 2005 21: 4026-4032.
Markowetz F, Grossmann S, Spang R (2005)
Probabilistic soft interventions in Conditional Gaussian networks
Proc. Tenth International Workshop on Artificial Intelligence and Statistics (AISTATS)
Markowetz F, Spang R (2005)
Molecular diagnosis: classification, model selection, and performance evaluation
Methods of Information in Medicine 2005, 44: 438-43.
Meinel T, Krause A, Luz H, Vingron M, Staub E (2005)
The SYSTERS Protein Family Database in 2005
Nucleic Acids Research, 2005, Vol. 33, Database issue D226-D229
Messer PW, Lässig M, Arndt PF (2005)
Universality of long-range correlations in expansion-randomization systems
Journal of Statistical Mechanics: Theory and Experiment, 10:P10004, 2005.
Messer PW, Arndt PF, Lässig M (2005)
Solvable Sequence Evolution Models and Genomic Correlations
Phys. Rev. Lett. 94, 138103 (2005)
Morris M, Dieterich C, Vingron M (2005)
SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors
Bioinformatics 2005 21: 2093-2094.
Nuber UA, Kriaucionis S, Roloff TC, Guy J, Selfridge J, Steinhoff C, Schulz R, Lipkowitz B, Ropers HH, Holmes MC, Bird A.
Up-regulation of glucocorticoid-regulated genes in a mouse model of Rett syndrome
Hum Mol Genet. 2005 Aug 1;14(15):2247-56. Epub 2005 Jul 7. [Fulltext]
Oostendorp RA, Robin C, Steinhoff C, Marz S, Brauer R, Nuber UA, Dzierzak EA, Peschel C. (2005)
Long-term maintenance of hematopoietic stem cells does not require contact with embryo-derived stromal cells in cocultures.
Stem Cells. 2005 Jun;23(6):842-51. [Fulltext]
Penzkofer T, Dandekar T, Zemojtel T (2005)
L1Base: from functional annotation to prediction of active LINE-1 elements.
Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D498-500.
Roepcke S, Grossmann S, Rahmann S, Vingron M. (2005)
T-Reg Comparator: an analysis tool for the comparison of position weight matrices
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W438-41 [Abstract]
Roepcke S, Fiziev P, Seeburg PH, Vingron M. (2005)
SVC: structured visualization of evolutionary sequence conservation
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W271-3 [Abstract]
Scheid S, Spang R (2005)
twilight; a Bioconductor package for estimating the local false discovery rate.
Bioinformatics 2005 21(12):2921-2922
Scheid S, Spang R (2005)
Data Analysis: Differential gene expression, Chapter 6.2
in: Nuber U (ed), BIOS Advanced Methods: DNA Microarrays Garland Science Publishing 2005
A. Schliep, I. G. Costa, C. Steinhoff, A. A. Schoenhuth. (2005)
Analyzing Gene Expression Time-Courses IEEE/ACM Transactions on Computational Biology and Bioinformatics
(Special Issue on Machine Learning for Bioinformatics), 2005, 2(3):179-193
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU (2005)
A gene expression map of Arabidopsis development
Nat Genet. 2005 May;37(5):501-6.
Seemann P, Schwappacher R, Kjaer KW, Krakow D, Lehmann K, Dawson K, Stricker S, Pohl J, Ploger F, Staub E, Nickel J, Sebald W, Knaus P, Mundlos S.(2005)
Activating and deactivating mutations in the receptor interaction site of GDF5 cause symphalangism or brachydactyly type A2.
J Clin Invest. 2005 Sep;115(9):2373-81. Epub 2005 Aug 25
Sültmann H, von Heydebreck A, Huber W, Kuner R, Buness A, Vogt M, Gunawan B, Vingron M, Fuzesi L, Poustka A (2005)
Gene Expression in Kidney Cancer Is Associated with Cytogenetic Abnormalities, Metastasis Formation, and Patient Survival
Clin Cancer Res 2005 11: 646-655
Steinhoff C, Vingron M (2005)
Normalization strategies for microarray data analysis, Chapter 6.1
in: Nuber U (ed), BIOS Advanced Methods: DNA Microarrays Garland Science Publishing 2005
Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S (2005)
MACAT--microarray chromosome analysis tool.
Bioinformatics. 2005 May 1;21(9):2112-3
Webster MT, Smith NGC, Hultin-Rosenberg L, Arndt PF, Ellegren H (2005)
Male-Driven Biased Gene Conversion Governs the Evolution of Base Composition in Human Alu Repeats
Molecular Biology and Evolution 2005 22(6):1468-1474;
Yang X, Bentink S, Scheid S, Spang R (2005)
Detecting common gene expression patterns in multiple cancer outcome entities
Biomedical Microdevices, Sep 2005, 7(3):247-251.
Zhang J, Vingron M, Hoehe MR (2005)
Haplotype Reconstruction for Diploid Populations
Hum Hered. 2005 May 26;59(3):144-156
Ziehe M, Demetrius L (2005)
Directionality theory: an empirical study of an entropic principle for life-history evolution
Proc. R. Soc. B 2005, 272:1185-1194

2004

Arndt PF, Hwa T (2004)
Regional and time-resolved mutation patterns of the human genome
Bioinformatics 2004 20: 1482-1485. [Fulltext]
Boutros, M., Kiger, A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S., Heidelberg FlyArray, Paro, R. and Perrimon, N. (2004)
Genome-wide RNAi Analysis of Cell Growth and Viability in Drosophila Cells.
Science Feb 6 2004: 832-835.
Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.-H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J. O., Lengauer, T., Liebich, I., van der Linden, M., Luz, H., Meissner, K., von Mering, C., Mevissen, H.-T., Mewes, H.-W., Michael, H., Mokrejs, M., Müller, T., Pospisil, H., Rarey, M., Reich, J. G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E., Zimmer, R. (2004)
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
Bioinformatics 2004 20: 268-270
Demetrius L. (2004)
Caloric Restriction, Metabolic Rate, and Entropy
The Journals of Gerontology Series A: Biological Sciences, 59A, 902-915
Demetrius L., Gundlach M, Ochs G
Complexity and demographic stability in population models
Theoretical Population Biology 2004 May; 65(3):211-225
Dieterich C, Rahmann S, Vingron M (2004)
Functional inference from non-random distributions of conserved predicted transcription factor binding sites
Bioinformatics 20(Suppl.1) 2004: i109-i115 (Proceedings of ISMB 2004)
Florl AR, Steinhoff C, Muller M, Seifert HH, Hader C, Engers R, Ackermann R, Schulz WA
Coordinate hypermethylation at specific genes in prostate carcinoma precedes LINE-1 hypomethylation.
Br J Cancer. 2004 Aug 31;91(5):985-94
Ginalski K and Zemojtel T (2004)
ECEPE proteins: a novel family of eukaryotic cysteine proteinases
Trends in Biochemical Sciences Vol.29(10), 524-526
Grossmann S and Yakir B (2004)
Large deviations for global maxima of independent superadditive processes with negative drift and an application to optimal sequence alignments
Bernoulli 10(5), 2004, 829-845
Gunawan B, Schulten HJ, von Heydebreck A, Schmidt B, Enders C, Höer J, Langer C, Schüler P, Schindler CG, Kuhlgatz J, Füzesi L (2004)
Site-Independent Prognostic Value of 9q Loss in Primary Gastrointestinal Stromal Tumors.
Journal of Pathology 202, 421-429, 2004.
Gupta S, Zink D, Korn B, Vingron M, Haas S (2004)
Genome wide identification and classification of alternative splicing based on EST data.
Bioinformatics 2004 20(16):2579-2585
Gupta S, Zink D, Korn B, Vingron M, Haas S (2004)
Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing.
BMC Genomics, 5:72.
Gurok U, Steinhoff C, Lipkowitz B, Ropers HH, Scharff C, Nuber UA (2004)
Gene Expression Changes in the Course of Neural Progenitor Cell Differentiation
J. Neurosci. 24 2004: 5982-6002
Haller F., Kulle B., Schwager S., Gunawan B., Heydebreck A.v., Sültmann H., Füzesi L. (2004)
Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization.
Analytical Biochemistry, in press
Heydebreck, A. v., Sperling, S., Kaynak, B., Lehrach, H., Vingron, M. (2004)
Genexpressionsanalyse komplexer klinischer Phänotypen mittels cDNS-Arrays - Gene Expression Profiling of Complex Clinical Phenotypes using cDNA-Arrays
it - Information Technology 46 (2004), Oldenbourg Verlag, pages 26-30
Heydebreck, A. v., Bastian Gunawan, László Füzesi (2004)
Maximum likelihood estimation of oncogenetic tree models
Biostat 5: 545-556
Heydebreck A.v., Huber W., Gentleman R. (2004)
Differential Expression with the Bioconductor Project
Bioconductor Project Working Paper 7. To appear in Wiley Encyclopedia of Genomics, Proteomics and Bioinformatics.
Himmelfarb M, Klopocki E, Grube S, Staub E, Klaman I, Hinzmann B, Kristiansen G, Rosenthal A, Durst M, Dahl E. (2004).
ITIH5, a novel member of the inter-alpha-trypsin inhibitor heavy chain family is downregulated in breast cancer.
Cancer Letters, Vol.204(1):69-77.
Huber W., Heydebreck A.v., Vingron M. (2004)
Error models for microarray intensities
Bioconductor Project Working Paper 6. To appear in Wiley Encyclopedia of Genomics, Proteomics and Bioinformatics.
Jaeger J, Spang R (2004)
Vom Biochip zur maßgeschneiderten Therapie
BIOforum 6/2004, pp 50-51
Klau, G.W., Rahmann, S., Schliep, A., Vingron, M., Reinert, K. (2004)
Optimal robust non-unique probe selection using Integer Linear Programming
Bioinformatics 20(Suppl.1) 2004: i186-i193 (Proceedings of ISMB 2004)
Kostka, D. and Spang, R. (2004)
Finding disease specific alterations in the co-expression of genes
Bioinformatics 20(Suppl.1) 2004: i194-i199 (Proceedings of ISMB 2004)
Kunz M, Ibrahim SM, Koczan D, Scheid S, Thiesen HJ, and Gross G (2004)
DNA microarray technology and its applications in dermatology
Experimental Dermatology 13(10):593-606.
Mulvihill ER, Jaeger J, Sengupta R, Ruzzo WL, Reimer C, Lukito S, Schwartz SM (2004)
Atherosclerotic plaque smooth muscle cells have a distinct phenotype.
Arterioscler Thromb Vasc Biol. 2004 Jul;24(7):1283-9.
Philippar U, Schratt G, Dieterich C, Muller JM, Galgoczy P, Engel FB, Keating MT, Gertler F, Schule R, Vingron M, Nordheim A (2004)
The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF.
Mol Cell 16, 867-880.
Pils B, Schultz J. (2004)
Evolution of the multifunctional protein tyrosine phosphatase family.
Mol Biol Evol. 2004 Apr;21(4):625-31.
Rateitschak K, Müller T, Vingron M (2004)
Annotating significant pairs of transcription factor binding sites in regulatory DNA
In Silico Biology 4, 0040 (2004)
Rieker R.J., Penzel R., Aulmann S., Blaeker H., Morresi-Hauf A., Hecker E., Otto H.F., Mechtersheimer G., Heydebreck A.v. (2004)
Oncogenetic tree models based on cytogenetic data: new insights into the development of epithelial tumors of the thymus
Cancer Genetics and Cytogenetics, in press
Scheid S (2004)
GfKl 2004 Contest: Correspondence clustering of Dortmund city districts.
Proceedings of the 28th Annual Conference of the GfKl, accepted.
Scheid S, Spang R (2004)
A stochastic downhill search algorithm for estimating the local false discovery rate
IEEE Transactions on Computational Biology and Bioinformatics 1(3):98-108, 2004.
Schliep A, Steinhoff C, Schönhuth A (2004)
Robust inference of groups in gene expression time-courses using mixtures of HMMs.
Bioinformatics 20(Suppl.1) 2004: i283-i289 (Proceedings of ISMB 2004) [Fulltext]
Singh U, Fohn LE, Wakayama T, Ohgane J, Steinhoff C, Lipkowitz B, Schulz R, Orth A, Ropers HH, Behringer RR, Tanaka S, Shiota K, Yanagimachi R, Nuber UA, Fundele R. (2004)
Different molecular mechanisms underlie placental overgrowth phenotypes caused by interspecies hybridization, cloning, and Esx1 mutation.
Dev Dyn. 2004 May;230(1):149-64.
Staub E, Fiziev P, Rosenthal A, Hinzmann B (2004)
Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.
Bioessays, Vol.26(5):567-81.
Staub E, Fiziev P, Rosenthal A, Hinzmann B (2004).
The nucleolar proteome and the (endosymbiotic) origin of the nucleus. Reply to Moreira et al.
Bioessays, Vol.26(10):1145-47.
Staub E, Rosenthal A, Hinzmann B. (2004).
Systematic identification of immunoreceptor tyrosine-based inhibitory motifs in the human proteome.
Cell Signalling, Vol.16(4):435-56.
Wellmann S, Guschmann M, Griethe W, Eckert C, von Stackelberg A, Lottaz C, Moderegger E, Einsiedel HG, Eckardt KU, Henze G, Seeger K, Stackelberg A. (2004)
Activation of the HIF pathway in childhood ALL, prognostic implications of VEGF.
Leukemia. 2004 May;18(5):926-33.Erratum in: Leukemia. 2004 Jun;18(6):1164
Xue Y, Haas SA, Brino L, Gusnanto A, Reimers M, Talibi D, Vingron M, Ekwall K, Wright APH. (2004)
A DNA microarray for fission yeast: minimal changes after a temperature shift to 36 C.
Yeast, 21(1), 25-39
Zemojtel T, Penzkofer T, Dandekar T, Schultz J (2004)
A novel conserved family of nitric oxide synthase?
Trends in Biochemical Sciences, Vol 29/5 pp 224-226, 2004

2003

Arndt PF (2003)
The History of Nucleotide Substitution Pattern in Human
Biophysics (Moscow). Vol. 48, Suppl. 1, 2003, pp. 1-6.
Beißbarth, T., Borisevich, I., Hörlein, A., Kenzelmann, M., Hergenhahn, M., Klewe-Nebenius, A., Klären, R., Korn, B., Schmidt, W., Vingron, M., Schütz, G. (2003)
Analysis of CREM-dependent gene expression during mouse spermatogenesis.
Molecular and Cellular Endocrinology, 212(1-2): 29-39
Birck, R., Krzossok, S., Markowetz, F., Schnülle, P., van der Woude, F., Braun, C. (2003)
Acetylcysteine for prevention of contrast nephropathy: meta-analysis
Lancet, 362(9384):598-603
Demetrius L (2003)
Bookreview on "Statistics in Genetics and in the Environmental Sciences"
Bulletin of Mathematical Biol, 2003, 19:451
Demetrius, L (2003)
Quantum statistics and allometric scaling of organisms
Physica A, 322:477-490
Dieterich, C., Herwig, R., Vingron M. (2003)
Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites
Bioinformatics 2003 19: ii50-ii56. (Proc. ECCB 2003, Paris)
Dieterich, C., Wang, H., Rateitschak, K., Luz, H.G., Vingron, M. (2003)
CORG: A database for Comparative Regulatory Genomics.
Nucleic Acids Research 31 (1), 55-57.
Fellenberg, K., Vingron, M., Hauser, N.C., Hoheisel, J.D. (2003)
Correspondence analysis with microarray data
In: K. Appasani (ed.), Perspectives in Gene Expression, 2003 Eaton Publishing, Westborough, MA, pp 307-343.
Grimm, M.O., Steinhoff, C., Simon, X., Spiegelhalder, P., Ackermann, R., Vögeli, T.A. (2003)
Effect of routine repeated transurethral resection (ReTURB) of superficial bladder cancer
J Urol. 170(2 Pt 1):433-7
Grzeskowiak, R., Witt, H., Drungowski, M., Thermann, R., Hennig, S., Perrot, A., Osterziel, K.J., Klingbiel, D., Scheid, S., Spang, R., Lehrach, H., Ruiz, P. (2003)
Expression profiling of human idiopathic dilated cardiomyopathy
Cardiovasc Res. 2003 Aug 1;59(2):400-11.
Gunawan, B., Heydebreck, A. v., Fritsch, T., Huber, W.,Ringert, R.-H., Jakse, G., Füzesi, L. (2003)
Cytogenetic and Morphologic Typing of 58 Papillary Renal Cell Carcinomas: Evidence for a Cytogenetic Evolution of Type 2 from Type 1 Tumors.
Cancer Research 63, 6200-6205, 2003
Haas, S.A., Hild, M., Wright, A.P.H., Hain, T., Talibi, D., Vingron, M. (2003)
Genome-scale design of PCR primers and long oligomers for DNA microarrays.
Nucleic Acids Res., 31 (19), 5576-5581
Heydebreck, A. v., Gunawan, B., Huber, W., Vingron, M., Füzesi, L. (2003)
Mathematical tree models for cytogenetic development in solid tumors.
Proceedings of the German Society for Pathology, 2003.
Hild, M., Beckmann, B., Haas, S.A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F., Hoheisel, J.D. and Paro, R. (2003)
An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.
GenomeBiology, 5:R3
Huber, W., Heydebreck, A. v., Sültmann, H., Poustka, A. and Vingron, M. (2003)
Parameter estimation for the calibration and variance stabilization of microarray data.
Statistical Applications in Genetics and Molecular Biology: Vol. 2: No. 1, Article 3. (online publication)
Huber, W., Heydebreck, A. v., Vingron, M. (2003)
Analysis of microarray gene expression data.
In: Handbook of Statistical Genetics, 2nd edition, Wiley (2003).
Jäger, J., Sengupta, R., Ruzzo, W.L. (2003)
Improved Gene Selection for Classification of Microarrays
Biocomputing - Proceedings of the 2003 Pacific Symposium, 53-64.
Kalscheuer, V., Freude, K., Musante, L., Jensen, L.R., Yntema, H.G., Gecz, J., Sefiani, A., Hoffmann, K., Moser, B., Haas, S., Gurok, U., Haesler, S., Aranda, B., Nshedjan, A., Tzschach, A., Hartmann, N., Roloff, T.-C., Shoichet, S., Hagens, O., Tao,J., van Bokhoven, H., Turner, G., Chelly, J., Moraine, C., Fryns, J.-P., Nuber, U., Hoeltzenbein, M., Scharff, C., Scherthan, H., Lenzner, S., Hamel, B.C.J., Schweiger, S. and Ropers, H.-H. (2003)
Mutations in the polyglutamine-binding protein 1 gene cause X-linked mental retardation.
Nature Genetics, 35 (4), 313-315.
Kaynak, B., Heydebreck, A. v., Mebus, S., Seelow, D., Hennig, S., Vogel, J., Sperling, H.-P., Pregla, R., Alexi-Meskishvili, V., Hetzer, R., Lange, P.E., Vingron, M., Lehrach, H., Sperling, S. (2003)
Genome-wide array analysis of normal and malformed human hearts.
Circulation 2003, 107:2467-2474.
Kleiber, C., Scheid, S. (2003)
The generalized lognormal distribution as an income distribution
Bulletin of the International Statistical Institute 60:643-644.
Klempa, B., Schmidt, H.A., Ulrich, R., Kaluz, S., Labuda, M., Meisel, H., Hjelle, B., Krüger, D.H. (2003)
Genetic Interaction between Distinct Dobrava Hantavirus Subtypes in Apodemus agrarius and A. flavicollis in Nature.
J. Virol., 77, 804-809.
Klempa, B., Ulrich, R., Meisel, H., Krüger, D.H., Schmidt, H.A., Kaluz, S., Labuda, M., Hjelle, B. (2003)
Letter to the Editor: Genetic Interaction between Dobrava and Saaremaa Hantaviruses: Now or Millions of Years Ago? (Authors' Reply)
J. Virol., 77, 7157-7158.
Knab, B., Schliep, A., Steckemetz, B., Wichern, B. (2003)
Model-based clustering with Hidden Markov Models and its application to financial times series data.
Proceedings of the GfKl 2002 conference.
Kriventseva, E.V., Koch, I., Apweiler, R., Vingron, M., Bork, P., Gelfand, M.S., Sunyaev, S. (2003)
Increase of functional diversity by alternative splicing.
Trends in Genetics 19 (3), 124-128.
Lottaz, C., Iseli, C., Jongeneel, C.V., Bucher, P. (2003)
Modeling sequencing errors by combining Hidden Markov models
Bioinformatics 2003 19: ii103-ii112 (Proc. ECCB 2003, Paris)
Manke, T., Bringas, R., Vingron, M. (2003)
Correlating Protein-DNA and Protein-Protein Interaction Networks.
J Mol Biol 333:75-85
Marchfelder, U., Rateitschak, K., Ehrenhofer-Murray, A.E. (2003)
SIR-dependet repression of non-telomeric genes in Saccharomyces cerevisiae?
Yeast Vol.20, 797-801
Markowetz, F., Spang, R. (2003)
Evaluating the Effect of Perturbations in Reconstructing Network Topologies.
Proceedings of the 3rd International Workshop on Distributed Statistical Computing.
Markowetz, F., Edler, L., Vingron, M. (2003)
Support Vector Machines for Protein Fold Class Prediction.
Biometrical Journal 45 (3), 377-389.
Meinel, T., Vingron, M., Krause, A. (2003)
The SYSTERS Protein Family Database: Taxon-Related Protein Family Size Distributions and Singleton Frequencies.
In Proceedings of the German Conference on Bioinformatics. Belleville, Munich, Germany, pp. 103-108.
Müller, T., Rahmann, S., Dandekar, T., Wolf, M. (2003)
Robust estimation of the phylogeny of chlorophyceae (chlorophyta) based on profile distances.
In H.-W. Mewes, D. Frishman, V. Heun, and S. Kramer, editors, Proceedings of the German Conference on Bioinformatics (GCB'03), volume 1, pages 97-101, Munich, October 2003.
Panopoulou, G., Hennig, S., Groth, D., Krause, A., Herwig, R., Vingron, M., Lehrach, H. (2003)
New evidence for genome wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes.
Genome Research Vol.13, 1056-1066.
Rahmann, S., Müller, T., Vingron, M. (2003)
On the power of profiles for transcription factor binding site detection.
Statistical Applications in Genetics and Molecular Biology, 2(1):Article 7, 2003.
Rahmann, S. (2003)
The shortest common supersequence problem in a microarray production setting
Bioinformatics 2003 19: ii156-ii161. (Proc. ECCB 2003, Paris)
Rahmann, S. (2003)
Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach.
Journal of Bioinformatics and Computational Biology, 1(2):343-361, 2003.
Rahmann, S., Rivals, E. (2003)
On the Distribution of the Number of Missing Words in Random Texts.
Combinatorics, Probability and Computing 12, 73-87.
Rahmann, S. (2003)
Fast and Sensitive Probe Selection for DNA Chips using Jumps in Matching Statistics.
In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pages 57--64. IEEE, 2003.
Rahmann, S. (2003)
Dynamic programming algorithms for two statistical problems in computational biology.
In Proceedings of the 3rd Workshop of Algorithms in Bioinformatics (WABI), LNCS, pages 151--164. Springer, 2003.
Scheid, S., Spang, R. (2003)
A False Discovery Rate Approach to Separate the Score Distributions of Induced and Non-induced Genes.
Proceedings of the 3rd International Workshop on Distributed Statistical Computing.
Ratsch, E., Schultz, J., Saric, J., Lavin, P.C., Wittig, U., Reyle, U., Rojas, I. (2003)
Developing a protein-interactions ontology.
Comparative and Functional Genomics 4, 85-89.
Rivals, E., Rahmann, S. (2003)
Combinatorics of periods in strings.
Journal of Combinatorial Theory Series A, 2003. In press.
Schliep, A., Schönhuth, A., Steinhoff, C. (2003)
Using Hidden Markov Models to Analyze Gene Expression Time Course Data.
Bioinformatics. 2003 Jul;19 Suppl 1:I255-I263 (Proceedings of the ISMB 2003)
Schliep, A., Torney, D. C., Rahmann, S. (2003)
Group Testing With DNA Chips: Generating Designs and Decoding Experiments.
In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pages 84--93. IEEE, 2003.
Schmidt, H. A., von Haeseler, A. (2003)
Maximum Likelihood Analysis using TREE-PUZZLE.
In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.) Current Protocols in Bioinformatics, Unit 6.6, Wiley and Sons, New York. ISBN 0-471-25093-7
Schmidt, H.A., Petzold, E., Vingron, M., von Haeseler, A. (2003)
Molecular phylogenetics: parallelized parameter estimation and quartet puzzling
Journal of Parallel and Distributed Computing, Volume 63, Issues 7-8 , July-August 2003, Pages 719-727
Schwikowski, B., Vingron, M. (2003)
Weighted sequence graphs: Boosting iterated dynamic programming using locally suboptimal solutions.
Discrete Applied Mathematics 127, 95-117.
Spang, R. (2003)
Diagnostic signatures from microarrays: a bioinformatics concept for personalized medicine
Biosilico May 2003 Volume 1 No. 2.
Steinhoff, C., Müller, T., Nuber, U.A., Vingron, M. (2003)
Gaussian Mixture Density Estimation applied to Microarray Data,
LNCS (Lecture Notes in Computer Sciences) 2810, 418-429
Steinhoff, C., Schulz, W.A. (to appear)
Transcriptional Regulation of the human LINE-1 Retrotransposon L1.2B and its biological activity,
Molecular and General Genetics MGG
Wieczorek, G., Steinhoff, C., Schulz, R., Scheller, M., Vingron, M., Ropers, H.H., Nuber, U. (2003)
Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis.
Cell Tissue Res. 2003 Feb;311(2):227-37.

2002

Beckers, J., Hoheisel, J., Mewes, W., Vingron, M., Hrabé de Angelis, M.(2002)
Molecular phenotyping of mouse mutant resources by RNA expression profiling.
Current Genomics 3 (3), 121-129.
Boué, S., Vingron, M., Kriventsevea, E., Koch, I. (2002)
Theoretical analysis of alternative splice forms using computational methods.
Bioinformatics 18 suppl.2, eds. T. Lengauer, H.-P. Lenhof, 65-73.
Brazma, A., Sarkans, U., Robinson, A., Vilo, J., Vingron, M., Hoheisel, J., Fellenberg,K. (2002)
Microarray data representation, annotation and storage.
Adv Biochem Eng Biotechnol.77,113-39.
Cieliebak, M., Erlebach, T., Lipták, Z., Stoye, J., Welzl, E. (2002)
Algorithmic Complexity of Protein Identification: Searching in Weighted Strings.
Proceedings of the 2nd IFIP International Conference on Theoretical Computer Science 2002, 143-156.
Coward, E., Haas, S. A. and Vingron, M. (2002)
SpliceNest: visualization of gene structure and alternative splicing based on EST clusters.
Trends Genet. 18 (1), 53-55.
Dieterich, C., Cusack, B., Wang, H., Rateitschak, K., Krause, A., Vingron, M. (2002)
Annotating regulatory DNA based on man-mouse genomic comparison.
Bioinformatics 18 suppl.2, eds. T. Lengauer, H.-P. Lenhof, 84-90.
Fellenberg, K., Hauser, N., Brors, B., Neutzner, A., Hoheisel, J., Vingron, M. (2002)
Microarray Data Warehouse Allowing for Inclusion of Experiment Annotations in Statistical Analysis.
Bioinformatics 18 (3), 423-433.
Heber, S., Stoye, J., Frohme, M., Hoheisel, J., Vingron, M. (2002) Resampling Methods in Physical Mapping.
Proceedings of GfKl 2000, 437-444.
Heydebreck, A.v., Huber, W., Poustka, A., Vingron, M. (2002)
Variance stabilization and robust normalization for microarray gene expression data.
Proceedings in Computational Statistics (COMPSTAT), 623-628.
Huber, W., Boer, J., Heydebreck, A.v., Gunawan, B., Vingron, M., Füzesi, L., Poustka, A., Sültmann, H. (2002)
Transcription Profiling of Renal Cell Carcinoma.
Proceedings of the German Society for Pathology 86, 153-64.
Huber, W., Heydebreck, A. v., Sültmann, H., Poustka, A., Vingron, M. (2002)
Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression.
Bioinformatics18 Suppl 1, 96-S104.
Kaderali, L., Schliep, A.. (2002)
An algorithm to select target specific probes for DNA chips.
Bioinformatics. 2002 Oct;18(10):1340-9.
Knab, B., Schliep, A., Steckemetz, B., Wichern, B. (2002)
Model-based clustering with Hidden Markov Models and its application to financial times series data.
Proceedings of the GfKl 2002 conference.
Krause, A., Haas, S. A., Coward, E., Vingron, M. (2002)
SYSTERS, GeneNest, SpliceNest: Exploring sequence space from genome to protein.
Nucleic Acids Res., 30 (1), 299-300.
Markowetz, F., Heydebreck, A. v. (2002)
Class discovery in gene expression data: characterizing splits by support vector machines.
Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation 2002, 377-389.
Mott, R., Schultz, J., Bork, P., Ponting, C.P. (2002)
Predicting Protein Cellular Localisation Using a Domain Projection Method.
Genome Res. 12, 1168-74.
Müller, T., Spang, R., Vingron, M. (2002)
Estimating amino acid substitution models: a comparison of Dayhoff's Estimator, the resolvent approach and a maximum likelihood method.
Mol. Biol. Evol. 19(1), 8-13.
Nicodeme, P., Doerks, T., Vingron, M. (2002)
Proteome Analysis Based on Motif Statistics.
Bioinformatics 8 suppl.2, eds. T. Lengauer, H.-P. Lenhof, 161-171.
Pipenbacher, P., Schliep, A., Schneckener, S., Schönhuth, A., Schomburg, D.,Schrader, R. (2002)
ProClust: Improved clustering of Protein Sequences with an extended graph-based approach.
Proceedings of the ECCB 2002.
Rahmann, S. (2002)
Rapid Large-Scale Selection of Oligonucleotides for Microarrays.
Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB 2002), pp. 54-63. IEEE Press.
Scheideler, M. Schlaich, NL, Fellenberg, K., Beißbarth, T., Hauser, N., Vingron, M., Slusarenko, AJ, Hoheisel, JD (2002)
Monitoring the switch from housekeeping to pathogen defence metabolism in Arabidopsis thaliana.
J. Biol. Chem.277 (12), 10555-10561.
Schliep, A., Hochstättler, W. (2002)
Developing Gato and CATBox with Python: Teaching graph algorithms through visualization and experimentation.
Multimedia Tools for Communicating Mathematics. Springer Verlag, 2002, 291-310
Schmidt, H. A., Strimmer, K., Vingron, M., von Haeseler, A. (2002)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
Bioinformatics 18, 502-504.
Schmidt, H. A., von Haeseler, A. (2002)
Quartet Trees as a Tool to Reconstruct Large Trees from Sequences
in Data Analysis, Classification, and Related Methods (Proceedings of the 9th Conference of the International Federation of Classification Societies - IFCS-2002, Krakow). Edited by Jajuga, K. et. al. Springer Verlag, New York, 379-388.
Schultz, J., Pils, B. (2002)
Prediction of structure and functional residues for O-GlcNAcase, a divergent homologue of Acetyltransferases.
FEBS Letters, 529, 179-182.
Schultz, J. (2002) Mouse Genome Sequencing Consortium
Initial sequencing and comparative analysis of the mouse genome.
Nature 420(6915), 520-562.
Schuster, S., Pfeiffer, T., Koch, I., Moldenhauer, F., Dandekar, T. (2002)
Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma pneumoniae.
Bioinformatics 18 suppl.2, eds. T. Lengauer, H.-P. Lenhof, 351-361.
Spang, R., Blanchette, C., Zuzan, H., Marks, J.R., Nevins, J., West, M. (2002)
Prediction and uncertainty in the analysis of gene expression profiles
In Silico Biol 2 (2002)
Spang, R., Rehmsmeier, M., Stoye, J.(2002)
A Novel Approach to Remote Homology Detection: Jumping Alignments.
J. Comp. Biol. 9(5), 747-760.
Steinhoff, C., Prior, A., Reichmann, G., Seifert, H.H., Schulz, W.A. (2002)
Activity of E2F-dependent promoters in bladder carcinoma cells and their use for tumor-specific targeting of p53-induced apoptosis.
Int J Oncol 21(5), 1033-400
Stoye, J. and Gusfield, D. (2002)
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree.
Theor. Comput. Sci. 270(1-2), 843-856.
Schultz, J. (2002) Mouse Genome Sequencing Consortium
Initial sequencing and comparative analysis of the mouse genome.
Nature 420(6915), 520-562.

2001

Boer, JM, Huber, W., Sültmann, H., Wilmer, F., Heydebreck, A.v., Haas, S., Korn, B.,Gunawan, B., Vente, A., Füzesi, L., Vingron, M, Poustka, A. (2001)
Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500 element cDNA array.
Genome Res. 11 (11), 1861-1870.
Cieliebak, M., Erlebach, T., Lipták, Z., Stoye, J., Welzl, E. (2001)
Algorithmic complexity of protein identification: combinatorics of weighted strings.
Technical Report no. 361, ETH Zürich, Dept. of Computer Science,2001.
Fellenberg, K., Hauser, N., Brors, B., Neutzner, A., Hoheisel, J., Vingron, M. (2001)
Correspondence Analysis Applied to Microarray Data.
Proc. Natl. Acad. Sci. USA 98, 10781-10786.
Gunawan, B., Huber, W., Holtrup, M., Heydebreck, A.v. , Efferth, T., Poustka, A., Ringert, R.-H., Jaske, G.,Füzesi, L. (2001)
Prognostic Impacts of Cytogenetic Findings in Clear Cell Renal Cell Carcinoma: Gain of 5q31-qter Predicts a Distinct Clinical Phenotype with Favorable Prognosis.
Cancer Research 61(21), 7731-7738.
Heber, S., Stoye, J. (2001)
Algorithms for Finding Gene Clusters.
Proceedings of the 1st Workshop on Algorithms in BioInformatics (WABI) 2001,254-265.
Heber, S., Stoye, J. (2001)
Finding all Common Intervals of k Permutations.
Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM) 2001, 207-218.
Heiner, M., Koch, I., Voss, K. (2001)
Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets.
CPN'01-Third Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools (2001) University of Aarhus, Denmark, ed.K. Jensen, ISSN 0105-8517, 15-34.
Heydebreck, A.v., Huber, W., Poustka, A., Vingron, M. (2001)
Identifying splits with clear separation: a new class discovery method for gene expression data.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB)2001, Bioinformatics 17 (1), 107-114, Oxford University Press, London.
Ishida S., Huang E., Zuzan H., Spang R., Leone G., West M., Nevins J.R.
Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis
Mol Cell Biol. 2001 Jul; 21(14):4684-99
Koch, I. (2001)
Fundamental Study: Enumerating all connected maximal common subgraphs in two graphs.
Theoretical Computer Science 250, 1-30.
Kurtz, S., Choudhuri, JV, Ohlebusch, E., Schleiermacher, C., Stoye, J.,Giegerich, R. (2001)
REPuter: the Manifold Applications of Repeat Analysison a Genomic Scale.
Nucleic Acids Res. 29 (22), 4643-4653.
Laprevotte, I., Pupin, M.,Coward, E.,Didier, G., Terzian, C., Devauchelle, C., Hénaut, A. (2001)
HIV-1 and HIV-2 LTR Nucleotide Sequences: Assessment of the Alignment by N-block Presentation, "Retroviral Signatures" of Overrepeated Oligonucleotides, and a Probable Important Role of Scrambled Stepwise Duplications/Deletions in Molecular Evolution.
Mol. Biol. Evol. 18 (7), 1231-1245.
Müller, T., Rahmann, S., Rehmsmeier, M. (2001)
Non-symmetric Score Matrices and the Detection of Homologous Transmembrane Proteins.
In: Søren Brunak et al. (eds), Proceedings of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Bioinformatics 17 (1),182-189, Oxford University Press, London.
Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J., Völker, U., Hecker, M. (2001)
Global analysis of the general stress response of Bacillus subtilis.
J. Bacteriol. 183 (19), 5617-5631.
Prum, B., de Turckheim, E., Vingron, M. (2001)
Statistical tools for discovering pseudo-periodicities in biological sequences,
ESAIM: P&S 5, 171-181.
Rehmsmeier, M., Vingron, M. (2001)
Phylogenetic information improves homology detection.
Proteins: Structure, Function & Genetics 45(4), 360-371.
Rivals, E., Rahmann, S. (2001)
Combinatorics of Periods in Strings.
In: P. Orejas, P. G. Spirakis, J. van Leuween (eds.), Proceedings of the 28th International Colloquium on Automata, Languages, and Programming (ICALP 2001), Lecture Notes in Computer Science 2076,615-626. Springer-Verlag, Berlin.
Spang, R., Vingron, M. (2001)
Limits of homology detection by pairwise sequence comparison.
Bioinformatics 17(4), 338-42.
Sunyaev, S., Ramensky, V., Koch, I., Lathe III, W. Kondrashov, AS,Bork, P. (2001)
Prediction of Deleterious Human Alleles.
Human Molecular Genetics 10 (6), 591-597.
Vingron, M. (2001)
Bioinformatics needs to adopt statistical thinking.
Bioinformatics 17 (5), 389-390.
Vingron, M. (2001)
Sequence Analysis.
In: Bioinformatics: From Genomes to Drugs, edited by Thomas Lengauer. John Wiley & Sons, New York.
West M., Blanchette C., Dressman H., Huang E., Ishida S., Spang R., Zuzan H., Olson J.A. Jr, Marks J.R., Nevins J.R. (2001)
Predicting the clinical status of human breast cancer by using gene expression profiles
Proc Natl Acad Sci U S A. 2001 Sep 25; 98(20):11462-7

Birgit Löhmner

Last modified: Thu Jan 18 14:40:02 CET 2007