Genomatix know-how. Many facets. A clear picture.

Genomatix Publications

Here you can find a list of publications from the members of our team as well as customer and collaborative papers. We're always happy to tell you more details if any of the papers has sparked your interest and of course we're also open to new scientific collaborations.

 

Genomatix Publications

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

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


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


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

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


Collaborative publications

Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, Oskolkov N, Fadista J, Ehlers K, Wahl S, Hoffmann C, Qian K, Rönn T, Riess H, Müller-Nurasyid M, Bretschneider N, Schroeder T, Skurk T, Horsthemke B; DIAGRAM+Consortium, Spieler D, Klingenspor M, Seifert M, Kern MJ, Mejhert N, Dahlman I, Hansson O, Hauck SM, Blüher M, Arner P, Groop L, Illig T, Suhre K, Hsu YH, Mellgren G, Hauner H, Laumen H (2014)
Leveraging cross-species transcription factor binding site patterns: from diabetes risk Loci to disease mechanisms.
Cell. 2014 Jan 16;156(1-2):343-58

» PMID 24439387

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 Jul;62(7):2605-12. doi: 10.2337/db12-1416. Epub 2013 Feb 22

» PMID 23434934


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

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 Sep;26(9):1542-51. doi: 10.1210/me.2011-1351
» PMID 22865928


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

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


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

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

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


Customer publications

Tomita S, Abdalla MO, Fujiwara S, Matsumori H, Maehara K, Ohkawa Y, Iwase H, Saitoh N, Nakao M (2015)
A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation.
Nat Commun. 2015 Apr 29;6:6966. doi: 10.1038/ncomms7966.

» PMID 25923108

Masuda T, Endo M, Yamamoto Y, Odagiri H, Kadomatsu T, Nakamura T, Tanoue H, Ito H, Yugami M, Miyata K, Morinaga J, Horiguchi H, Motokawa I, Terada K, Morioka MS, Manabe I, Iwase H, Mizuta H, Oike Y (2015)
ANGPTL2 increases bone metastasis of breast cancer cells through enhancing CXCR4 signaling.
Sci Rep. 2015 Mar 16;5:9170. doi: 10.1038/srep09170.

» PMID 25773070


Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M. (2015)
Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.
Genome Biol. 2015 Jan 29;16:19. doi: 10.1186/s13059-014-0578-9.

» PMID 25631560

Thangapazham R, Saenz F, Katta S, Mohamed AA, Tan SH, Petrovics G, Srivastava S, Dobi A. (2014)
Loss of the NKX3.1 tumorsuppressor promotes the TMPRSS2-ERG fusion gene expression in prostate cancer.
BMC Cancer. 2014 Jan 13;14(1):16. doi: 10.1186/1471-2407-14-16.

» PMID 24418414


Nazir N, Siddiqui K, Al-Qasim S, Al-Naqeb D (2014)
Meta-analysis of diabetic nephropathy associated genetic variants in inflammation and angiogenesis involved in different biochemical pathways.
NBMC Med Genet. 2014 Oct 4;15(1):103. doi: 10.1186/s12881-014-0103-8.

» PMID 25280384

Södersten E, Feyder M, Lerdrup M, Gomes AL, Kryh H, Spigolon G, Caboche J, Fisone G, Hansen K (2014)
Dopamine signaling leads to loss of polycomb repression and aberrant gene activation in experimental parkinsonism.
PLoS Genet. 2014 Sep 25;10(9):e1004574.

» PMID 25254549


Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer MW (2013)
Dynamic association of NUP98 with the human genome.
PLoS Genet. 2013 Feb;9(2), Epub 2013 Feb 28.

» PMID 23468646

Zaade D, Schmitz J, Benke E, Klare S, Seidel K, Kirsch S, Goldin-Lang P, Zollmann FS, Unger T, Funke-Kaiser H (2013)
Distinct Signal Transduction Pathways Downstream of the (P)RR Revealed by Microarray and ChIP-chip Analyses.
PLoS One. 2013;8(3):e57674. doi: 10.1371/journal.pone.0057674. Epub 2013 Mar 4.

» PMID 23469216


Sendler E, Johnson GD, Mao S, Goodrich RJ, Diamond MP, Hauser R, Krawetz SA (2013)
Stability, delivery and functions of human sperm RNAs at fertilization.
Nucleic Acids Res. 2013 Apr 1;41(7):4104-17. doi: 10.1093/nar/gkt132.

» PMID 23471003

Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM, Taubenberger JK (2013)
High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic.
J Pathol. 2013 Mar;229(4):535-45. doi: 10.1002/path.4145.

» PMID 23180419


Pierron G, Tirode F, Lucchesi C, Reynaud S, Ballet S, Cohen-Gogo S, Perrin V,
Coindre JM, Delattre O (2012)
A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.
Nat Genet. 44(4):461-6

» PMID 22387997

Fortschegger K, de Graaf P, Outchkourov NS, van Schaik FM, Timmers HT,
Shiekhattar R (2010)
PHF8 targets histone methylation and RNA polymerase II to activate
transcription.

Mol Cell Biol. 2010 Jul;30(13):3286-98

» PMID 20421419


Prinzen C, Trümbach D, Wurst W, Endres K, Postina R, Fahrenholz F (2009)
Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice.
BMC Genomics 10:66

» PMID 19196476

Weigelt K, Moehle C, Stempfl T, Weber B, Langmann T (2008)
An integrated workflow for analysis of ChIP-chip data.
Biotechniques. 2008 Aug;45(2):131-2

» PMID 18687062


Complete list

List of publications with Genomatix (co-)authors


Liu Y, Duong W, Krawczyk C, Bretschneider N, Borbély G, Varshney M, Zinser C, Schär P, Rüegg J (2016)
Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase.
Epigenetics Chromatin. 2016 Feb 16;9:7
» PMID 26889208

Petrovics G, Li H, Stümpel T, Tan SH, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn I, Freedman M, Dobi A, Srivastava S (2015)
A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men.
EBioMedicine. 2015 Oct 31;2(12):1957-64
» PMID 26844274

Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, Oskolkov N, Fadista J, Ehlers K, Wahl S, Hoffmann C, Qian K, Rönn T, Riess H, Müller-Nurasyid M, Bretschneider N, Schroeder T, Skurk T, Horsthemke B, Spieler D, Klingenspor M, Seifert M, Kern MJ, Mejhert N, Dahlman I, Hansson O, Hauck SM, Blüher M, Arner P, Groop L, Illig T, Suhre K, Hsu YH, Mellgren G, Hauner H, Laumen H (2014)
Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms.
Cell. 2014 Jan 16;156(1-2):343-58
» PMID 24439387

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 Jul;62(7):2605-12
» 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

Werner T, Dombrowski SM, Zgheib C, Zouein FA, Keen HL, Kurdi M, Booz GW (2013)
Elucidating functional context within microarray data by integrated transcription factor-focused gene-interaction and regulatory network analysis.
Eur Cytokine Netw. 2013 Jun;24(2):75-90
» PMID 23822978

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


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

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

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

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

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.
i
n 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

Witter K, Werner T, Blusch JH, Schneider EM, Riess O, Ziegler I, Rödl W, Bacher A, Gütlich M (1996)
Cloning, sequencing and functional studies of the gene encoding human GTP cyclohydrolase I.
Gene 171(2), 285-90
» PMID 8666288

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

Honkela A, Peltonen J, Topa H, Charapitsa I, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M (2015)
Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.
Proc Natl Acad Sci U S A. 2015 Oct 20
» PMID 26438844

Schwartz T, Armant O, Bretschneider N, Hahn A, Kirchen S, Seifert M, Dötsch A (2015)
Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water.
Microb Biotechnol. 2015 Jan;8(1):116-30
» PMID 25186059

Yadav SP, Hao H, Yang HJ, Kautzmann MA, Brooks M, Nellissery J, Klocke B, Seifert M, Swaroop A (2014)
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression.
Hum Mol Genet. 2014 Apr 15;23(8):2132-44
» PMID 24301678

Wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M (2014)
Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data.
PLoS Comput Biol. 2014 May 15;10(5):e1003598
» PMID 24830797

Ovaska K, Matarese F, Grote K, Charapitsa I, Cervera A, Liu C, Reid G, Seifert M, Stunnenberg HG, Hautaniemi S (2013)
Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.
PLoS Comput Biol. 2013 Jun;9(6):e1003100
» PMID 23818839

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

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 Â, 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
» PMID: 22398613

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

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

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

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

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

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