List of Publications

|in 2012 |in 2011 |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.

2012

• Ni S, Vingron M, . (2012)
  R2KS: a novel measure for comparing gene expression based on ranked gene lists. J Comput Biol. 2012 Jun;19(6):766-75. [full text]
• Matthäus F, Schmidt JP, Banerjee A, Schulze TG, Demirakca T, Diener C. (2012)
  Effects of age on the structure of functional connectivity networks during episodic and working memory demand. Brain Connect. 2012;2(3):113-24. Epub 2012 Jul 19. [full text]
• Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K. (2012)
  Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics. 2012 Mar 1;28(5):619-27. Epub 2012 Jan 11. [full text]
• Huppke P, Brendel C, Kalscheuer V, Korenke GC, Marquardt I, Freisinger P, Christodoulou J, Hillebrand M, Pitelet G, Wilson C, Gruber-Sedlmayr U, Ullmann R, Haas S, Elpeleg O, Nürnberg G, Nürnberg P, Dad S, Møller LB, Kaler SG, Gärtner J. (2012)
  Mutations in SLC33A1 cause a lethal autosomal-recessive disorder with congenital cataracts, hearing loss, and low serum copper and ceruloplasmin. Am J Hum Genet. 2012 Jan 13;90(1):61-8. [full text]
• Banerjee A. (2012)
  Structural distance and evolutionary relationship of networks. Biosystems. 2012 Mar;107(3):186-96. doi: 10.1016/j.biosystems.2011.11.004. Epub 2011 Nov 23. [full text]
• Göke J, Schulz MH, Lasserre J, Vingron M. (2012)
  Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics. 2012 Mar 1;28(5):656-63. Epub 2012 Jan 12. [full text]
• My�icková A, Vingron M. (2012)
  Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. BMC Genomics. 2012;13 Suppl 1:S2. Epub 2012 Jan 17. [full text]
• Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.(2012)
  Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics. 2012 Apr 1;28(7):1024-5. Epub 2012 Feb 1. [full text]
• Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S.(2012)
  BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012 Mar 7;30(3):224-6. [full text]
• Zemojtel T, Vingron M. (2012)
  P53 binding sites in transposons. Front Genet. 2012;3:40. Epub 2012 Mar 20. [full text]
• Schulz MH, Zerbino DR, Vingron M, Birney E.(2012)
  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012 Apr 15;28(8):1086-92. Epub 2012 Feb 24. [full text]

2011

• Göke J, Jung M, Behrens S, Chavez L, O'Keeffe S, Timmermann B, Lehrach H, Adjaye J, Vingron M. (2012)
  Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Comput Biol. 2011 Dec;7(12):e1002304. Epub 2011 Dec 22. [full text]
• Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J.(2011)
  RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res. 2011 Dec 8. [Epub ahead of print] [full text]
• Thomas-Chollier M, Hufton A, Heinig M, O'Keeffe S, Masri NE, Roider HG, Manke T, Vingron M. 2011)
  Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat Protoc. 2011 Nov 3;6(12):1860-9. doi: 10.1038/nprot.2011.409. [full text]
• Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J.(2011)
  RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. [full text]
• Cusack BP, Arndt PF, Duret L, Roest Crollius H. (2011)
  Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes. PLoS Genet. 2011 Oct;7(10):e1002276. Epub 2011 Oct 13. [full text]
• Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P, Zecha A, Mohseni M, Püttmann L, Vahid LN, Jensen C, Moheb LA, Bienek M, Larti F, Mueller I, Weissmann R, Darvish H, Wrogemann K, Hadavi V, Lipkowitz B, Esmaeeli-Nieh S, Wieczorek D, Kariminejad R, Firouzabadi SG, Cohen M, Fattahi Z, Rost I, Mojahedi F, Hertzberg C, Dehghan A, Rajab A, Banavandi MJ, Hoffer J, Falah M, Musante L, Kalscheuer V, Ullmann R, Kuss AW, Tzschach A, Kahrizi K, Ropers HH. (2011)
  Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature. 2011 Sep 21;478(7367):57-63. doi: 10.1038/nature10423. [full text]
• Love, MI, Mysickova A, Sun R, Kalscheuer V, Vingron M; Haas SA. (2011)
  Modeling Read Counts for CNV Detection in Exome Sequencing Data. Statistical Applications in Genetics and Molecular Biology: Vol. 10: Iss. 1, Article 52. [full text]
• Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M. (2011)
  CpG deamination creates transcription factor binding sites with high efficiency. Genome Biol Evol. 2011 Oct 19. [Epub ahead of print] [full text]
• Heise F, Chung HR, Weber JM, Xu Z, Klein-Hitpass L, Steinmetz LM, Vingron M, Ehrenhofer-Murray AE. (2011)
  Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange.
  Nucleic Acids Res. 2011 Sep 9. [Epub ahead of print] [full text]
• Lasserre J, Arnold S, Vingron M, Reinke P, Hinrichs C. (2011)
  Predicting the outcome of renal transplantation. J Am Med Inform Assoc. 2011 Aug 28. [Epub ahead of print] [full text]
• Wiedenhoeft J, Krause R, Eulenstein O. (2011)
  The plexus model for the inference of ancestral multidomain proteins. IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):890-901. [full text]
• Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M. (2011)
  Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. BMC Bioinformatics. 2011 Jun 21;12:249. [full text]
• Serin A, Vingron M. (2011)
  DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach. Algorithms Mol Biol. 2011 Jun 23;6(1):18. [full text]
• Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R. (2011)
  Cocos: Constructing multi-domain protein phylogenies. PLoS Curr. 2011 Jun 9;3:RRN1240. [full text]
• Schraders M, Haas SA, Weegerink NJ, Oostrik J, Hu H, Hoefsloot LH, Kannan S, Huygen PL, Pennings RJ, Admiraal RJ, Kalscheuer VM, Kunst HP, Kremer H. (2011)
  Next-Generation Sequencing Identifies Mutations of SMPX, which Encodes the Small Muscle Protein, X-Linked, as a Cause of Progressive Hearing Impairment. Am J Hum Genet. 2011 May 13;88(5):628-34. Epub 2011 May 5. [full text]
• Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. (2011)
  Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93. Epub 2011 Jan 5. [full text]
• Lin S, Haas S, Zemojtel T, Xiao P, Vingron M, Li R. (2011)
  Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. Gene. 2011 Mar 1;473(2):139-49. Epub 2010 Dec 13. [full text]
• Hafemeister C, Krause R , Schliep A. (2011)
  Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential.
  IEEE/ACM Trans Comput Biol Bioinform. 2011 Feb 24. [Epub ahead of print] [full text]
• Kolanczyk M, Pech M, Zemojtel T, Yamamoto H, Mikula I, Calvaruso MA, van den Brand M, Richter R, Fischer B, Ritz A, Kossler N, Thurisch B, Spoerle R, Smeitink J, Kornak U, Chan D, Vingron M, Martasek P, Lightowlers RN, Nijtmans L, Schuelke M, Nierhaus KH, Mundlos (2011)
  NOA1 is an essential GTPase required for mitochondrial protein synthesis. Mol Biol Cell. 2011 Jan 1;22(1):1-11. [full text]
• Clement Y, Arndt P.F. (2011)
  Substitution Patterns Are Under Different Influences in Primates and Rodents.
  Genome Biol Evol. 2011 Jan;3:236-45. Epub 2011 Feb 21. [full text]
• Hallen L, Klein H, Stoschek C, Wehrmeyer S, Nonhoff U, Ralser M, Wilde J, Röhr C, Schweiger MR, Zatloukal K, Vingron M, Lehrach H, Konthur Z, Krobitsch S. (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. 2011 Jan 1;20(1):104-14. [full text]
• Pfenninger CV., Steinhoff C., Hertwig F., Nuber UA. (2011)
  Prospectively isolated CD133/CD24-positive ependymal cells from the adult spinal cord and lateral ventricle wall differ in their long-term in vitro self-renewal and in vivo gene expression. Glia. 2011 Jan;59(1):68-81. [full text]

2010

• Behrens S., Vingron M., (2010)
  Studying the evolution of promoter sequences: a waiting time problem.
  J Comput Biol. 2010 Dec;17(12):1591-606. [full text]
• 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]
• Chung HR., Dunkel I., Heise F., Linke C., Krobitsch S., Ehrenhofer-Murray AE., Sperling SR., Vingron M. (2010)
  The effect of micrococcal nuclease digestion on nucleosome positioning data.
  PLoS One. 2010 Dec 29;5(12):e15754. [full text]
• DeKelver RC., Choi VM., Moehle EA., Paschon DE., Hockemeyer D., Meijsing S., Sancak Y., Cui X., Steine EJ., Miller JC., Tam P., Bartsevich VV., Meng X., Rupniewski I., Gopalan SM., Sun HC., Pitz KJ., Rock JM. Zhang L., Davis GD., Rebar EJ., Cheeseman IM., Yamamoto KR., Sabatini DM., Jaenisch R., Gregory PD., Urnov FD.(2010)
  Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome
  Genome Res. 2010 August; 20(8): 1133�1142 [full text]
• Emde AK., Grunert M., Weese D., Reinert K., Sperling SR.(2010)
  MicroRazerS: rapid alignment of small RNA reads
  Bioinformatics (2010) 26 (1): 123-124 [full text]
• Heinig M., Petretto E., Wallace C., Bottolo L., Rotival M., Lu H., Li Y., Sarwar R., Langley SR., Bauerfeind A., Hummel O., Lee YA., Paskas S., Rintisch C., Saar K., Cooper J., Buchan R., Gray EE., Cyster JG.; Cardiogenics Consortium, Erdmann J., Hengstenberg C., Maouche S., Ouwehand WH., Rice CM., Samani NJ., Schunkert H., Goodall AH., Schulz H., Roider HG., Vingron M., Blankenberg S., Münzel T., Zeller T., Szymczak S., Ziegler A., Tiret L, Smyth DJ., Pravenec M., Aitman TJ., Cambien F., Clayton D., Todd JA., Hubner N., Cook SA. (2010)
  A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk
  Nature. 2010 Sep 23;467(7314):460-4 [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]
• Kielbasa SM, Klein H, Roider HG, Vingron M,, Blüthgen N., (2010)
  TransFind--predicting transcriptional regulators for gene sets
  Nucleic Acids Res. 2010 Jul 1;38 Suppl:W275-80 [full text]
• Kielbasa SM, Blüthgen N, Fähling M, Mrowka R. N., (2010)
  Targetfinder.org: a resource for systematic discovery of transcription factor target genes
  Nucleic Acids Res. 2010 Jul 1;38 Suppl:W275-80 [full text]
• Kolanczyk M, Pech M, Zemojte T, Yamamoto H, Mikula I, Calvaruso MA, van den Brand M, Richter R, Fischer B, Ritz A, Kossler N, Thurisch B, Spoerle R, Smeitink J, Kornak U, Chan D, Vingron M, Martasek P, Lightowlers RN, Nijtmans L, Schuelke M, Nierhaus KH, Mundlos S. (2010)
  NOA1 is an essential GTPase required for mitochondrial protein synthesis
  Mol Biol Cell. 2010 Nov 30. [Epub ahead of print] [full text]
• Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S, Robinson PN (2010)
  Microindel detection in short-read sequence data
  Bioinformatics. 2010 Mar 15;26(6):722-9. Epub 2010 Feb 9. [full text]
• Löhr U, Chung HR, Beller M, Jäckle H. (2010)
  Bicoid: Morphogen function revisited
  Fly (Austin). 2010 Jul 18;4(3)236 - 240 [full text]
• Luksza M, Lässig M, Berg J. (2010)
  Significance analysis and statistical mechanics: an application to clustering.
  Phys Rev Lett. 2010 Nov 26;105(22):220601. Epub 2010 Nov 23. [full text]
• Manke, T., Heinig, M., Vingron, M. (2010)
  Quantifying the effect of sequence variation on regulatory interactions
  Hum Mutat. 2010 Feb 2. [full text]
• May, P., Kreuchwig, A., Steinke, T., Koch, I. (2010)
  PTGL: A database for secondary structure-based protein topologies
  Nucleic Acids Research [full text]
• Meng G., Mosig A., Vingron M. (2010)
  A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes BMC Bioinformatics. 2010 May 20;11:267 [full text]
• Polak P., Querfurth R. Arndt PF. (2010)
  The evolution of transcription-associated biases of mutations across vertebrates BMC Evol Biol. 2010 Jun 18;10:187 [full text]
• Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML. (2010)
  Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments Nucleic Acids Res. 2010 Jun;38(10):e112 [full text]
• Rödelsperger C, Dieterich C. (2010)
  CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PLoS One. 2010 Jan 28;5(1):e8861 [full text]
• Rödelsperger C, Guo G, Kolanczyk M, Pletschacher A, Köhler S, Bauer S, Schulz MH, Robinson PN. (2010)
  Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions Nucleic Acids Res. 2010 Nov 24. [Epub ahead of print] [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]
• Schütze T., Arndt PF., Menger M., Wochner A., Vingron M., Erdmann VA., Lehrach H., Kaps C., Glökler J. (2010)
  A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides
  Nucleic Acids Res. 2010 Mar;38(4):e23 [full text]
• Szczurek E, Biecek P, Tiuryn J, Vingron M. (2010)
  Introducing knowledge into differential expression analysis
  J Comput Biol. 2010 Aug;17(8):953-67 [full text]
• Warnatz HJ., Querfurth R., Guerasimova A., Cheng X., Haas SA., Hufton AL., Manke T., Vanhecke D., Nietfeld W., Vingron M., Janitz M., Lehrach H., Yaspo ML. (2010)
  Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters
  Nucleic Acids Res. 2010 Oct;38(18):6112-23 [full text]
• Wiedenhoeft J., Krause R., Eulenstein O. (2010)
  Inferring Evolutionary Scenarios for Protein Domain Compositions
  Lecture Notes in Computer Science, 2010, Volume 6053/2010 [book]
• Zackay A, Steinhoff C. (2010)
  MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing.
  BMC Res Notes. 2010 Dec 15;3:337. [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 (2009)
  KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
  Bioinformatics, Vol 25,1-5 [full text]
• 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]
• Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M, Van Bokhoven H, Chelly J, Ropers H, Chen W. (2010)
  Erratum to: Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing
  Hugo J. 2009 December; 3(1-4): 83. [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) [book]
• 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]
• Rausch T., Koren S., Denisov G., Weese D., Emde AK. Döring A., Reinert K.(2010)
  A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads Bioinformatics (2009) 25 (9): 1118-1124 [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]
• Weese D., Emde AK., Rausch T., Döring A., Reinert K. (2009)
  RazerS--fast read mapping with sensitivity control
  Genome Res. 2009 19: 1646-1654 [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 [book]
• 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) [book]
• 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 [book]
• 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 [conference]
• 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
• Bastolla 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)
• Michael 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