Genomatix

Martini S, Nair V, Patel SR, Eichinger F, Nelson RG, Weil EJ, Pezzolesi MG, Krolewski AS, Randolph A, Keller BJ, Werner T, Kretzler M (2013)
From SNP to Transcriptional Mechanism: A Model for FRMD3 in Diabetic Nephropathy.
Diabetes. 2013 Feb 22. [Epub ahead of print]
» PMID 23434934


Supper J, Gugenmus C, Wollnik J, Drueke T, Scherf M, Hahn A, Grote K, Bretschneider N, Klocke B, Zinser C, Cartharius K, Seifert M (2013)
Detecting and visualizing gene fusions.
Methods. 2013 Jan;59(1):S24-8
» PMID 23036331


Riedmaier I, Benes V, Blake J, Bretschneider N, Zinser C, Becker C, Meyer HH, Pfaffl MW (2012)
RNA-Sequencing as Useful Screening Tool in the Combat against the Misuse of Anabolic Agents.
Anal Chem. 2012 Aug 7;84(15):6863-8. Epub 2012 Jul 13
» PMID 22861009


Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A (2012)
Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis.
PLoS Genet. 8(4): Epub 2012 Apr 12
» PMID 22511886


DeRosa CA, Furusato B, Shaheduzzaman S, Srikantan V, Wang Z, Chen Y, Seifert M, Ravindranath L, Young D, Nau M, Dobi A, Werner T, McLeod DG, Vahey MT, Sesterhenn IA, Srivastava S, Petrovics G (2011)
Elevated osteonectin/SPARC expression in primary prostate cancer predicts metastatic progression.
Prostate Cancer and Prostatic Diseases, Epub 2011 Nov 29
» PMID 22343836


Mah N, Wang Y, Liao MC, Prigione A, Jozefczuk J, Lichtner B, Wolfrum K, Haltmeier M, Flöttmann M, Schaefer M, Hahn A, Mrowka R, Klipp E, Andrade-Navarro MA, Adjaye J (2011)
Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network.
PLoS One. 2011;6(8):e24351. Epub 2011 Aug 31
» PMID 21909390


Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BH, Langmann T (2010)
CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.
Genome Res. 2010 Nov;20(11):1512-25. Epub 2010 Aug 6
» PMID 20693478


Hestand MS, Klingenhoff A, Scherf M, Ariyurek Y, Ramos Y, van Workum W, Suzuki M, Werner T, van Ommen GJ, den Dunnen JT, Harbers M, 't Hoen PA (2010)
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.
Nucleic Acids Res. 2010 Sep;38(16):e165. Epub 2010 Jul 7
» PMID 20615900


Martin Seifert, Robert Schneider (2010)
Chromatin Immunoprecipitation ChIP: Wet Lab Meets In Silico - Epigenetic Targets in Drug Discovery
Book Series: Methods and Principles in Medicinal Chemistry
Published Online: 25 Feb 2010


Frisch M, Klocke B, Haltmeier M, Frech K (2009)
LitInspector: literature and signal transduction pathway mining in PubMed abstracts.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W135-40. Epub 2009 May 5.
» PMID 19417065


Werner T (2009)
The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection.
Textbook article in Bioinformatics for Systems Biology (Ed. Stephen A. Krawetz),
Humana Press, (ISBN: 978-1-934115-02-2), 339-52


Hadian K, Vincendeau M, Mäusbacher N, Nagel D, Hauck SM, Ueffing M, Loyter A, Werner T, Wolff H, Brack-Werner R (2009)
Identification of a heterogeneous nuclear ribonucleoprotein-recognition region in the HIV Rev protein.
J Biol Chem. 284(48), 33384-91
» PMID 19808671


Schaefer A, Unterberger C, Frankenberger M, Lohrum M, Staples KJ, Werner T, Stunnenberg H, Ziegler-Heitbrock L (2009)
Mechanism of interferon-gamma mediated down-regulation of interleukin-10 gene expression.
Mol Immunol. 46, 1351-9
» PMID 19124156

Sultan M, Schulz MH, 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 321(5891), 956-60
» PMID 18599741


Harbers M, Werner T, Carninci P (2008)
From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis.
Textbook article in The Handbook of Plant Functional Genomics: Concepts and Protocols (Eds. Günther Kahl, Khalid Meksem), Wiley-VCH, Weinheim (ISBN: 978-3-527-31885-8)


Palmieri MC, Sell S, Huang X, Scherf M, Werner T, Durner J, Lindermayr C (2008)
Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach.
J Exp Bot. 59, 177-186
» PMID 18272923

Unterberger C, Hanson S, Klingenhoff A, Oesterle D, Frankenberger M, Endo Y, Matsushita M, Fujita T, Schwaeble W, Weiss EH, Ziegler-Heitbrock L, Stover C (2007)
Stat3 is involved in control of MASP2 gene expression.
Biochem Biophys Res Commun. 364, 1022-5
» PMID 17971300


Mutch DM, Klocke B, Morrison P, Murray CA, Henderson CJ, Seifert M, Williamson G (2007)
The Disruption of Hepatic Cytochrome P450 Reductase Alters Mouse Lipid Metabolism.
J Proteome Res. 6, 3976-3984
» PMID 17722906


Werner T (2007)
Regulatory networks: Linking microarray data to systems biology.
Mech Ageing Dev. 128, 168-72
» PMID 17113628


Del Mastro RG, Turenne L, Giese H, Keith TP, Van Eerdewegh P, May KJ, Little RD (2007)
Mechanistic role of a disease-associated genetic variant within the ADAM33 asthma susceptibility gene.
BMC Medical Genetics 8, 46
» PMID 17640346


Turk BE, Lee DH, Yamakoshi Y, Klingenhoff A, Reichenberger E, Wright JT, Simmer JP, Komisarof JA, Cantley LC, Bartlett JD (2006)
MMP-20 Is Predominately a Tooth-Specific Enzyme with a Deep Catalytic Pocket that Hydrolyzes Type V Collagen.
Biochemistry 45, 3863-3874
» PMID 16548514


Cohen C, Klingenhoff A, Boucherot A, Nitsche A, Henger A, Brunner B, Schmid H, Merkle M, Saleem M, Koller KP, Werner T, Gröne HJ, Nelson PJ, Kretzler M (2006)
Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins.
Proc Natl Acad Sci U S A. 103(15), 5682-7
» PMID 16581909


Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T (2005)
MatInspector and beyond: promoter analysis based on transcription factor binding sites.
Bioinformatics 21, 2933-42
» PMID 15860560


Scherf M, Epple A, Werner T (2005)
The next generation of literature analysis: integration of genomic analysis into text mining.
Brief Bioinform. 6, 287-97
» PMID 16212776


Kramer-Hämmerle S, Ceccherini-Silberstein F, Bickel C, Wolff H, Vincendeau M, Werner T, Erfle V, Brack-Werner R (2005)
Identification of a novel Rev-interacting cellular protein.
BMC Cell Biology 6, 20
» PMID 15847701


Masuda K, Werner T, Maheshwari S, Frisch M, Oh S, Petrovics G, May K, Srikantan V, Srivastava S, Dobi A (2005)
Androgen Receptor Binding Sites identified by a GREF_GATA model.
J. Mol. Biol. 353, 763-71
» PMID 16213525


Maier H, Döhr S, Grote K, O'Keeffe S, Werner T, Hrabé de Angelis M, Schneider R (2005)
LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W779-82.
» PMID 15980584


Atchley WR, Zhao J, Fernandes AD, Drüke T (2005)
Solving the protein sequence metric problem.
Proc Natl Acad Sci 102:6395
» PMID 15851683


Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC (2005)
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bioinformatics. 2005 Apr 1;21(7):853-9
» PMID 15514001


Tasheva ES, Klocke B, Conrad GW (2004)
Analysis of transcriptional regulation of the small leucine rich proteoglycans.
Molecular Vision 10, 758-72
» PMID 15496828


Rudd S, Frisch M, Grote K, Meyers BC, Mayer K, Werner T (2004)
Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression.
Plant Physiol. 135, 715-22
» PMID 15208419


Werner T (2004)
Proteomics and regulomics: The yin and yang of functional genomics.
Mass Spectrom Rev. 23, 25-33
» PMID 14625890


Bourdeau V, Deschênes J, Métivier R, Nagai Y, Nguyen D, Bretschneider N, Gannon F, White JH, Mader S. (2004)
Genome-wide identification of high-affinity estrogen response elements in human and mouse.
Mol Endocrinol. 2004 Jun;18(6):1411-27
» PMID 15001666


Brazma A, Freeman T, Gardiner K, Weissman S, Werner T, Korn B (2004)
Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop.
Cytogenet Genome Res. 105(1), 11-7
» PMID 15218252


Wolff H, Brack-Werner R, Neumann M, Werner T, Schneider R (2003)
Integrated functional and bioinformatics approach for the identification and experimental verification of RNA signals: application to HIV-1 INS.
Nucleic Acids Res. 31, 2839-51
» PMID 12771211


Ziegler-Heitbrock L, Lötzerich M, Schaefer A, Werner T, Frankenberger M, Benkhart E (2003)
IFN-alpha induces the human IL-10 gene by recruiting both IFN regulatory factor 1 and Stat3.
J. Immunol. 171, 285-90
» PMID 12817009


Werner T, Fessele S, Maier H, Nelson PJ (2003)
Computer modeling of promoter organization as a tool to study transcriptional coregulation.
FASEB J. 2003 Jul;17(10):1228-37
» PMID 12832287


Werner T (2003)
Yeast expression-array analysis goes molecular.
Trends in Genetics 19, 467-9
» PMID 12957536


Klingenhoff A, Frech K, Werner T (2002)
Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach.
In Silico Biol. 2, S17-S26
» PMID 11808874


Frisch M, Frech K, Klingenhoff A, Cartharius K, Liebich I, Werner T (2002)
In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences.
Genome Research 12, 349-54
» PMID 11827955


Werner T (2002)
Finding and decrypting of promoters contributes to the elucidation of gene function.
In Silico Biol. 2, 249-55
» PMID 12542410


Fessele S, Böhlk S, Mojaat A, Miyamoto NG, Werner T, Nelson EL, Schlöndorff D, Nelson PJ (2001)
Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells.
FASEB Journal 15, 577-79
» PMID 11259372


Werner T (2001)
Target gene identification from expression array data by promoter analysis.
Biomol. Eng. 17, 87-94
» PMID 11222983


Gailus-Durner V, Scherf M, Werner T (2001)
Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity.
Mammalian Genome 12, 67-72
» PMID 11178746


Santagati F, Gerber JK, Blusch JH, Kokubu C, Peters H, Adamski J, Werner T, Balling R, Imai K (2001)
Comparative analysis of the genomic organization of Pax9 and its conserved physical association with Nkx2-9 in the human, mouse, and pufferfish genomes.
Mamm Genome. 12(3), 232-7
» PMID 11252173


Werner T (2001)
Analyzing regulatory regions in genomes.
Textbook article in Bioinformatics - From Genomes to Drugs (Ed. Thomas Lengauer), Wiley-VCH, Weinheim (ISBN: 3-527-29988-2)


Frisch M, Frech K, Klingenhoff A, Quandt K, Liebich I, Werner T (2000)
A new tool for the in silico prediction of matrix attachment regions in large genomic sequences.
in Proceedings of the German Conference on Bioinformatics, GCB 2000 (Eds. Bornberg-Bauer E, Rost U, Stoye J, Vingron, M.), 27-34, Logos Verlag, Berlin.


Fuchs H, Schlee P, Blusch J, Werner T, Stein H, Rottmann O (2000)
Phylogenetic studies in cyprinid species from central Europe by cytochrome b sequences of mitochondrial DNA.
Journal of Applied Ichthyology 16, 79–82
» doi: 10.1046/j.1439-0426.2000.00162.x


Boehlk S, Fessele S, Mojaat A, Miyamoto NG, Werner T, Nelson EL, Schlöndorff D, Nelson PJ (2000)
ATF and Jun transcription factors, acting through an Ets/CRE promoter module, mediate lipopolysaccharide inducibility of the chemokine RANTES in monocytic Mono Mac 6 cells.
Eur J Immunol. 30(4), 1102-12
» PMID 10760799


Roulet E, Bucher P, Schneider R, Wingender E, Dusserre Y, Werner T, Mermod N (2000)
Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.
J Mol Biol. 297(4), 833-48
» PMID 10736221


Klingenhoff A, Frech K, Quandt K, Werner T (1999)
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.
Bioinformatics 15, 180-6
» PMID 10222404


Werner T (1999)
Computer-Assisted Analysis of Transcription Control Regions.
Textbook article in Bioinformatics - Methods and Protocols (Eds. Stephen Misener, Stephen A. Krawetz),
Humana Press, Totowa, New Jersey (ISBN: 0-89603-732-0)


Gardiner K, Mural R, Werner T (1999)
Report of the eighth international workshop on the identification of transcribed sequences.
Cytogenet Cell Genet. 84(1-2), 2-10
» PMID 10343091


Lavorgna G, Boncinelli E, Wagner A, Werner T (1998)
Detection of potential target genes in silico?
Trends Genet. 14, 375-6
» PMID 9841458


Reuter I, Werner T, Wingender E (1998)
Computer-assisted methods for the identification and characterization of polymerase II promoters.
Genet Eng (N Y). 1998;20:25-40
» PMID 9705623


Blusch JH, Haltmeier M, Frech K, Sander I, Leib-Mösch C, Brack-Werner R, Werner T (1997)
Identification of endogenous retroviral sequences based on modular organization: proviral structure at the SSAV1 locus.
Genomics 43, 52-61
» PMID 9226372


Frech K, Quandt K, Werner T (1997)
Finding protein-binding sites in DNA sequences: the next generation.
Trends Biochem Sci. 22, 103-4
» PMID 9066261


Frech K, Quandt K, Werner T (1997)
A new method to develop highly specific models for regulatory DNA regions.
in Lecture Notes in Computer Science Vol. 1278: Bioinformatics, German Conference on Bioinformatics, GCB'96 (Eds. R. Hofestädt, T. Lengauer, M. Löffler, D. Schomburg), 79-87, Springer Verlag, Berlin Heidelberg


Morgenstern B, Werner T (1997)
DIALIGN 1.0: Multiple alignment by segment rather than by position comparison.
In: Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (Eds. Frishman; D.; Mewes; H.; W.), 69-72.


Frech K, Brack-Werner R, Werner T (1996)
Common modular structure of Lentivirus LTRs.
Virology 224, 256-67
» PMID 8862420


Quandt K, Grote K, Werner T (1996)
GenomeInspector: Basic software tools for analysis of spatial correlations between genomic structures within megabase sequences.
Genomics 33, 301-4
» PMID 8660981


Wolfertstetter F, Frech K, Herrmann G, Werner T (1996)
Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm.
Comp. Appl. Biosci. 12, 71-80
» PMID 8670622


Herrmann G, Schön A, Brack-Werner R, Werner T (1996)
CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering.
Comput Appl Biosci. 12(3), 197-203
» PMID 8872388


Gimbel W, Schmidt J, Erfle V, Werner T (1996)
A new variant of B1 elements, vB1, identified upstream of a retroviral integration site.
DNA Seq. 6(4), 229-32
» PMID 8912925


Quandt K, Frech K, Karas H, Wingender E, Werner T (1995)
MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.
Nucleic Acids Res. 23, 4878-84
» PMID 8532532


Simon M, Haltmeier M, Papakonstantinou G, Werner T, Hehlmann R, Leib-Mösch C (1994)
Transcription of HERV-K-related LTRs in human placenta and leukemic cells.
Leukemia 1994;8 Suppl 1():S12-7
» PMID 8152277


Graw J, Liebstein A, Pietrowski D, Schmitt-John T, Werner T (1993)
Genomic sequences of murine gamma B- and gamma C-crystallin-encoding genes: promoter analysis and complete evolutionary pattern of mouse, rat and human gamma-crystallins.
Gene 136(1-2), 145-56
» PMID 8293998

Stein MF, Lang S, Winkler TH, Deinzer A, Erber S, Nettelbeck DM, Naschberger E, Jochmann R, Stürzl M, Slany RK, Werner T, Steinkasserer A, Knippertz I (2013)
Multiple Interferon Regulatory Factor and NF-κB Sites Cooperate in Mediating Cell-Type- and Maturation-Specific Activation of the Human CD83 Promoter in Dendritic Cells.
Mol Cell Biol. 2013 Apr;33(7):1331-44
» PMID 23339870


Vikström Bergander L, Cai W, Klocke B, Seifert M, Pongratz I (2012)
Tryptamine Serves As a Proligand of the AhR Transcriptional Pathway Whose Activation Is Dependent of Monoamine Oxidases.
Mol Endocrinol. 2012 Aug 3. [Epub ahead of print]
» PMID: 22865928


Coon SL, Munson PJ, Cherukuri PF, Sugden D, Rath MF, Møller M, Clokie SJ, Fu C, Olanich ME, Rangel Z, Werner T; NISC Comparative Sequencing Program, Mullikin JC, Klein DC (2012)
Circadian changes in long noncoding RNAs in the pineal gland.
Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13319-24
» PMID: 22864914


Mittal RA, Hammel M, Schwarz J, Heschl KM, Bretschneider N, Flemmer AW, Herber-Jonat S, Königshoff M, Eickelberg O, Holzinger A (2012)
SFTA2-A Novel Secretory Peptide Highly Expressed in the Lung-Is Modulated by Lipopolysaccharide but Not Hyperoxia.
PLoS One. 2012;7(6):e40011. Epub 2012 Jun 29
» PMID: 22768197


Seitz V, Butzhammer P, Hirsch B, Hecht J, Gütgemann I, Ehlers A, Lenze D, Oker E, Sommerfeld A, von der Wall E, König C, Zinser C, Spang R, Hummel M (2011)
Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma.
PLoS One. 2011;6(11):e26837. Epub 2011 Nov 10
» PMID: 22102868


Grote K, Werner T (2011)
Multidimensional Context of Sequence Tags: Biological Data Integration
Textbook article in Tag-based Next Generation Sequencing (Ed. Matthias Harbers , Guenter Kahl)
Wiley VCH, (ISBN: 3-527-32819-X), 407-15


Werner T. (2010)
Next generation sequencing in functional genomics.
Brief Bioinform. 2010 Sep;11(5):499-511. Epub 2010 May 25
» PMID: 20501549


Albert TK, Grote K, Boeing S, Meisterernst M (2010)
Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.
Genome Biol. 2010;11(3):R33
» PMID 20230619


Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, Zinser C, Chiusano ML, Traini A, De Bortoli M, Weisz A (2010)
Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs.
Am J Pathol. 2010 May;176, 2113-30
» PMID 20348243


Wieczorek D, Pawlik B, Li Y, Akarsu NA, Caliebe A, May KJ, Schweiger B, Vargas FR, Balci S, Gillessen-Kaesbach G, Wollnik B (2009)
A specific mutation in the distant sonic hedgehog (SHH) cis-regulator (ZRS) causes Werner mesomelic syndrome (WMS) while complete ZRS duplications underlie Haas type polysyndactyly and preaxial polydactyly (PPD) with or without triphalangeal thumb.
Hum Mutat. 2010 Jan;31(1):81-9
» PMID 19847792


Epple A, Scherf M (2009)
BiblioSphere - Hypothesis Generation in Regulatory Network Analysis.
Textbook article in Bioinformatics for Systems Biology (Ed. Stephen A. Krawetz),
Humana Press, (ISBN: 978-1-934115-02-2), 401-13


Vidakovic M, Gluch A, Qiao J, Oumard A, Frisch M, Poznanovic G, Bode J. (2009)
PARP-1 expression in the mouse is controlled by an autoregulatory loop: PARP-1 binding to an upstream S/MAR element and to a novel recognition motif in its promoter suppresses transcription.
J Mol Biol. 388, 730-50
» PMID 19303024


Bretschneider N, Kangaspeska S, Seifert M, Reid G, Gannon F, Denger S (2008)
E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements.
Molecular Oncology 2, 182-90
» PMID 19383337


Denger S, Bähr-Ivacevic T, Brand H, Reid G, Blake J, Seifert M, Lin CY, May K, Benes V, Liu ET, Gannon F (2008)
Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast specific regulation of the IGFBP4 gene.
Mol Endocrinol. 22, 361-79
» PMID 17962383

Werner T (2008)
Bioinformatics applications for pathway analysis of microarray data.
Curr Opin Biotechnol. 2008 Feb;19(1):50-4
» PMID 18207385


Bretschneider N, Brand H, Miller N, Lowery AJ, Kerin MJ, Gannon F, Denger S. (2008)
Estrogen induces repression of the breast cancer and salivary gland expression gene in an estrogen receptor alpha-dependent manner.
Cancer Res. 2008 Jan 1;68(1):106-14.
» PMID 18172302


Cohen CD, Lindenmeyer MT, Eichinger F, Hahn A, Seifert M, Moll AG, Schmid H, Kiss E, Gröne E, Gröne HJ, Kretzler M, Werner T, Nelson PJ (2008)
Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis.
PLoS ONE. 3(8), e2937
» PMID 18698414

Werner T (2007)
Analyzing regulatory regions in genomes.
Textbook article in Bioinformatics - From Genomes to Therapies (Ed. Thomas Lengauer), Wiley-VCH, Weinheim (ISBN: 3-527-31278-1)


Albert TK, Grote K, Boeing S, Stelzer G, Schepers A, Meisterernst M (2007)
Global distribution of negative cofactor 2 subunit-α on human promoters.
Proc Natl Acad Sci U S A. 104, 10000-5
» PMID 17548813


Furusato B, Shaheduzzaman S, Petrovics G, Dobi A, Seifert M, Ravindranath L, Nau ME, Werner T, Vahey M, McLeod DG, Srivastava S, Sesterhenn IA (2007)
Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens.
Prostate Cancer Prostatic Dis. 2008;11(2):194-7
» PMID 17768422


Keller B, Grote K, Adamski J (2006)
In silico Northern blot, an automated method to determine expression patterns from EST databases, reveals tissue specificity of murine 17beta-hydroxysteroid dehydrogenase type 11.
Molecular and cellular endocrinology 2006;248(1-2):242-5
» PMID 16406283


Werner T, Nelson PJ (2006)
Joining high-throughput technology with in silico modelling advances genome-wide screening towards targeted discovery.
Brief Funct Genomic Proteomic. 5, 32-36
» PMID 16769675


Seifert M, Scherf M, Epple A, Werner T (2005)
Multievidence microarray mining.
Trends in Genetics 21, 553-8
» PMID 16098629


Cartharius K (2005)
MatInspector: Analysing Promoters for Transcription Factor Binding Sites
in "Analytical tools for DNA, genes and genomes: nuts & bolts", by Arseni Markoff ed., The nuts & bolts series, DNA Press, 2005,
ISBN 0-9748765-1-8.


Kramer-Hämmerle S, Hahn A, Brack-Werner R, Werner T (2005)
Elucidating effects of long-term expression of HIV-1 Nef on astrocytes by microarray, promoter, and literature analyses.
Gene 26, 31-8
» PMID 15958282


Döhr S, Klingenhoff A, Maier H, Hrabé de Angelis M, Werner T, Schneider R (2005)
Linking disease-associated genes to regulatory networks via promoter organization.
Nucleic Acids Res. 33, 864-72
» PMID 15701758


Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, Do L, Gorospe M, Becker KG (2005)
Stability regulation of mRNA and the control of gene expression.
Ann N Y Acad Sci. 1058, 196-204
» PMID 16394137


Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, Do L, Gorospe M, Becker KG (2005)
Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.
BMC Genomics 6, 75
» PMID 15907206


Alberti M, Kausch U, Haindl S, Leibiger R, Budczies J, Seifert M, Hock B (2005)
Gene expression patterns - a tool for bioanalysis
International Journal of Environmental Analytical Chemistry, 85(9), 589-608.
» doi:10.1080/03067310500145930


Bajic VB, Werner T (2005)
Promoter prediction.
Textbook article in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (Eds. Lynn Jorde , Peter Little , Mike Dunn, Shankar Subramaniam), John Wiley & Sons, 1st ed. (ISBN 0-47084-974-6)


Naschberger E, Werner T, Vicente AB, Guenzi E, Topolt K, Leubert R, Lubeseder-Martellato C, Nelson PJ, Stürzl M (2004)
Nuclear factor-kappaB motif and interferon-alpha-stimulated response element co-operate in the activation of guanylate-binding protein-1 expression by inflammatory cytokines in endothelial cells.
Biochem J. 379, 409-20
» PMID 14741045


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, Gössling 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 (Oxford, England) 2004;20(2):268-70
» PMID 14734319


Seifert M (2004)
Luminescent enzyme-linked receptor assay for estrogenic compounds.
Anal Bioanal Chem. 2004 Feb;378(3):684-7
» PMID 14658031


Werner T (2003)
The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection.
Textbook article in Introduction to Bioinformatics A Theoretical And Practical Approach (Eds. Stephen A. Krawetz, David D. Womble), Humana Press, Totowa, New Jersey (ISBN: 1-58829-241-4)


Wolff H, Brack-Werner R, Neumann M, Werner T, Schneider R (2003)
Integrated functional and bioinformatics approach for the identification and experimental verification of RNA signals: application to HIV-1 INS.
Nucleic acids research 2003;31(11):2839-51
» PMID 12771211


Werner T (2003)
Functional In Silico Analysis of Non-coding SNPs.
in Bioinformatics for Geneticists, 1st ed (Eds. Michael R. Barnes, Ian C. Gray), John Wiley & Sons, England (ISBN: 0-470-84393-4)


Werner T (2003)
Promoters can contribute to the elucidation of protein function.
Trends Biotechnol. 21, 9-13
» PMID 12480345


Werner T (2003)
The state of the art of mammalian promoter recognition.
Brief. Bioinform. 4, 22-30
» PMID 12715831


Liebich I, Bode J, Frisch M, Wingender E (2002)
S/MARt DB: a database on scaffold/matrix attached regions.
Nucleic Acids Res. 30, 372-74
» PMID 11752340


Werner T (2002)
Promoter analysis.
Ernst Schering Research Foundation Workshop 38, 65-82
» PMID 12061007


Fessele S, Maier H, Zischek C, Nelson PJ, Werner T (2002)
Regulatory context is a crucial part of gene function.
Trends in genetics : TIG 2002;18(2):60-3
» PMID 11818130


Werner T, Weissman S, Hedges SB, Gardiner K (2002)
Report on the twelfth international workshop on the identification of transcribed sequences: functional, expression and evolutionary analysis.
Cytogenet Genome Res. 98(2-3), 109-17
» PMID 12697992


Werner T (2001)
The promoter connection.
Nature Genetics 29, 105-6
» PMID 11586286


Gardiner K, Weissman S, Werner T (2001)
Report on the Eleventh International Workshop on the Identification of Transcribed Sequences 2001. November 9-11, 2001. Washington, DC, USA.
Cytogenet Cell Genet. 95(1-2), 1-8
» PMID 11978961


Scherf M, Klingenhoff A, Frech K, Quandt K, Schneider R, Grote K, Frisch M, Gailus-Durner V, Seidel A, Brack-Werner R, Werner T (2001)
First pass annotation of promoters on human chromosome 22.
Genome Research 11, 333-40
» PMID 11230158


Werner T (2001)
Cis-acting Locus.
Textbook article in Encyclopedia of Genetics (Eds. Sydney Brenner, Jeffrey H. Miller), Academic Press (ISBN: 0-12-227080-0)


Werner T (2001)
Cluster analysis and promoter modelling as bioinformatics tools for the identification of target genes from expression array data.
Pharmacogenomics 2, 25-36
» PMID 11258194


Korn B, Weissman S, Werner T, Gardiner K (2001)
Report on the tenth international workshop on the identification of transcribed sequences 2000. Heidelberg, Germany, October 28-31, 2000.
Cytogenet Cell Genet. 92(1-2), 49-58
» PMID 11306796


Scherf M, Klingenhoff A, Werner T (2000)
Highly Specific Localization of Promoter Regions in Large Genomic Sequences by PromoterInspector: A Novel Context Analysis Approach.
J. Mol. Biol. 297 (3), 599-606
» PMID 10731414


Werner T (2000)
Identification and functional modelling of DNA sequence elements of transcription.
Brief. Bioinform. 1, 372-80
» PMID 11465054


Benkhart EM, Siedlar M, Wedel A, Werner T, Ziegler-Heitbrock HW (2000)
Role of Stat3 in lipopolysaccharide-induced IL-10 gene expression.
Journal of Immunology 165(3), 1612-7
» PMID 10903771


Gardiner K, Mural R, Werner T (2000)
Report of the ninth international workshop on the identification of transcribed sequences.
Cytogenet Cell Genet. 88(1-2), 1-10
» PMID: 10773655


Hock B, Seifert M (1999)
Detecting estrogens in food and the environment.
Nat Biotechnol. 1999 Dec;17(12):1162-3
» PMID: 10585710


Werner T (1999)
Models for prediction and recognition of eukaryotic promoters.
Mammalian Genome 10, 168-75
» PMID 9922398


Blusch JH, Brack-Werner R, Werner T (1999)
A pseudoautosomal boundary-like element adjacent to the SSAV1 locus at 18q21.
DNA Seq. 10(2), 115-9
» PMID 10376214


Frech K, Quandt K, Werner T (1998)
Muscle actin genes: A first step towards computational classification of tissue specific promoters.
In Silico Biol. 1, 29-38
» PMID 11471240


Morgenstern B, Frech K, Dress A, Werner T (1998)
DIALIGN : Finding local similarities by multiple sequence alignment.
Bioinformatics 14, 290-4
» PMID 9614273


Frech K, Quandt K, Werner T (1997)
Software for the analysis of DNA sequence elements of transcription.
Comp. Appl. Biosci. 13, 89-97
» PMID 9088714


Frech K, Danescu-Mayer J, Werner T (1997)
A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter.
J. Mol. Biol. 270 (5), 674-87
» PMID 9245596


Frech K, Dietze P, Werner T (1997)
ConsInspector 3.0: new library and enhanced functionality.
Comp. Appl. Biosci. 13, 109-10
» PMID 9088717


Quandt K, Frech K, Werner T (1997)
Analysis of transcription control regions by detecting individual transcription factor binding sites and assessing their spatial organization.
Mol. Biol (Mosk, Engl. Tr.) 31, 638-46
» PMID 9340501


Morgenstern B, Dress A, Werner T (1996)
Multiple DNA and protein sequence alignment based on segment-to-segment comparison.
Proc. Natl. Acad. Sci. USA 93, 12098-103
» PMID 8901539


Frech K, Werner T (1996)
Specific modelling of regulatory units in DNA sequences.
In: Pacific Symposium on Biocomputing 1997 (Eds. R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein), 151-162, World Scientific Publishing Co. Pte. Ltd, Singapore


Quandt K, Grote K, Werner T (1996)
GenomeInspector: A new approach to detect correlation patterns of elements on genomic sequences.
Comp. Appl. Biosci. 12, 405-13
» PMID 8996789


Zarbalis K, Chatterjee B, Löster J, Werner T, Graw J (1996)
Sequence analysis of the beta B2-crystallin cDNA of hamster containing a domain conserved among vertebrates.
Gene 174(1), 181-4
» PMID 8863746


Witter K, Werner T, Blusch JH, Schneider EM, Riess O, Ziegler I, Rödl W, Bacher A, Gütlich M
Cloning, sequencing and functional studies of the gene encoding human GTP cyclohydrolase I.
Gene 171(2), 285-90
» PMID 8666288


Quandt K, Frech K, Herrmann G, Werner T (1995)
A consensus match scoring system that is correlated with biological functionality.
in Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism (Eds. D. Schomburg, U. Lessel), 47-57, GBF Monographs Volume 18, VCH Publishers, Inc, NewYork, NY.


Frech K, Herrmann G, Werner T (1993)
Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids.
Nucleic Acids Res. 21, 1655-64
» PMID 8479918