Serving Science since 1997

Since 1997, our analysis middleware offers a complete solution for the study of genetic data. Our world-wide largest transcription factor database MatInspector/MatBase is applied by more than 30,000 researchers around the globe and cited in over 10,000 scientific publications.
Scientific insight is a fundamental step in creating the best technologies for understanding life-science data. Genomatix has been part of the scientific community for more than two decades and continues to be an active player in research activities around the world.

Our unique combination of algorithms and knowledge bases enable the efficient interpretation of life-science data.


In October 2018, Genomatix AG’s assets and business were transferred to Intrexon Bioinformatics Germany GmbH, a newly formed subsidiary of Intrexon Corporation. Concurrent with the renaming of Intrexon Corporation to Precigen, Inc., Intrexon Bioinformatics Germany GmbH changed its name to Precigen Bioinformatics Germany GmbH (PBG) doing business as Genomatix*. Precigen is a dedicated discovery and clinical stage biopharmaceutical company advancing the next generation of gene and cell therapies using precision technology to target the most urgent and intractable diseases in our core therapeutic areas of immuno-oncology, autoimmune disorders, and infectious diseases.

Our technologies enable us to find innovative solutions for affordable biotherapeutics in a controlled manner. Precigen operates as an innovation engine progressing a preclinical and clinical pipeline of well-differentiated unique therapies toward clinical proof-of-concept and commercialization.

* Precigen Bioinformatics Germany GmbH (PBG) is doing business as “Genomatix” and all references to Genomatix herein shall be references to the business of Precigen Bioinformatics Germany GmbH (PBG).


From molecular data to medical relevance, our biological knowledge base will help you answer the complex questions of today’s life science research.

Compiled from a multitude of public and proprietary sources, it provides information from A for Alternative Transcripts to Z for Z-Scores for your individual field of research.


With the ever-increasing amount of biomedical data generated, the need for efficient analysis and comprehendible visualization has quickly become a major issue.

Genomatix offers online software for the analysis and interpretation in context with copious high-quality background data.


With their unique combination of proprietary algorithms and comprehensive data background, our solutions do more than enable you to efficiently and effectively analyze and interpret biological data.

Whether you choose the Genomatix Software Suite hosted on our secure servers, or our renowned TF binding site analysis program MatInspector, you will always get results of unprecedented relevance – ones that answer precise scientific questions.

By complementing our innovative technologies with excellent technical and scientific support, we can help to you to advance your research in every possible way.

Genomatix Software Suite

Gene Regulation
Gene regulation analysis
Complex regulatory patterns
De novo TFBS definition
TFBS overrepresentation
TFBS motif detection
Genes & Genomes
Genome annotation
Genome browser
Orthologous regions
Promoter extraction
Literature & Pathways
Gene networks
Literature analysis
Biological classification


Genomatix’s scientific contributions, collaborations and customer publications have been published in a number of quality scientific journals such as Nature, Cell, Proceedings of the National Academy of Science, Genome Research and many others. Please refer to the expandable menus below for an illustrative list of publications.

Chromatin Immunoprecipitation ChIP: Wet Lab Meets In Silico – Epigenetic Targets in Drug Discovery. Seifert M, Schneider R. (2010) Book Series: Methods and Principles in Medicinal Chemistry

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

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

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

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data. Dzida T, Iqbal M, Charapitsa I, Reid G, Stunnenberg H, Matarese F, Grote K, Honkela A, Rattray M. (2017) PeerJ. 5:e3742. PMID: 28970965.

Serotonin receptor 2C regulates neurite growth and is necessary for normal retinal processing of visual information. Trakhtenberg EF, Pita-Thomas W, Fernandez SG, Patel KH, Venugopalan P, Shechter JM, Morkin MI, Galvao J, Liu X, Dombrowski SM, Goldberg JL. (2017) Dev Neurobiol. 77(4):419-437. PMID: 26999672.

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

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays. Honkela A, Peltonen J, Topa H, Charapitsa I, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M. (2015) Proc Natl Acad Sci U S A. 112(42):13115-20. PMID: 26438844.

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

The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. Yadav SP, Hao H, Yang HJ, Kautzmann MA, Brooks M, Nellissery J, Klocke B, Seifert M, Swaroop A. (2014) Hum Mol Genet. 23(8): 2132 – 2144. PMID: 24301678.

Leveraging cross-species transcription factor binding site patterns: from diabetes risk Loci to disease mechanisms. 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) Cell. 156(1-2):343-58. PMID: 24439387.

From SNP to Transcriptional Mechanism: A Model for FRMD3 in Diabetic Nephropathy. 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) Diabetes. 62(7):2605-12. PMID: 23434934.

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

Tryptamine Serves As a Proligand of the AhR Transcriptional Pathway Whose Activation Is Dependent of Monoamine Oxidases. Vikström Bergander L, Cai W, Klocke B, Seifert M, Pongratz I. (2012) Mol Endocrinol. 26(9):1542-51. PMID: 22865928.

Elevated osteonectin/SPARC expression in primary prostate cancer predicts metastatic progression. 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) Prostate Cancer and Prostatic Diseases. PMID: 22343836.

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma. 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) PLoS One. 6(11):e26837. PMID: 22102868.

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. 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) Genome Res. 20(11):1512-25. PMID: 20693478.

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

Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. 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) Am J Pathol. 176:2113-30. PMID: 20348243.

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. 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) Science. 321(5891):956-60. PMID: 18599741.

Cooperative p16 and p21 action protects female astrocytes from transformation. Kfoury N, Sun T, Yu K, Rockwell N, Tinkum KL, Qi Z, Warrington NM, McDonald P, Roy A, Weir SJ, Mohila CA, Deneen B, Rubin JB. (2018) Acta Neuropathol Commun. 6(1):12. PMID: 18599741.

Cerebral organoids derived from Sandhoff disease induced pluripotent stem cells exhibit impaired neurodifferentiation. Allende ML, Cook EK, Larman BC, Nugent A, Brady JM, Golebiowski D, Sena-Esteves M, Tifft CJ, Proia RL. (2018) J Lipid Res. 59(3):550-563. PMID: 29358305

Transcriptional regulation of CRMP5 controls neurite outgrowth through Sox5. Naudet N, Moutal A, Vu HN, Chounlamountri N, Watrin C, Cavagna S, Malleval C, Benetollo C, Bardel C, Dronne MA, Honnorat J, Meissirel C, Besançon R. (2018) Cell Mol Life Sci. 75(1):67-79. PMID: 28864883.

ABIN1 determines severity of glomerulonephritis via activation of intrinsic glomerular inflammation. Korte EA, Caster DJ, Barati MT, Tan M, Zheng S, Berthier CC, Brosius FC 3rd, Vieyra MB, Sheehan RM, Kosiewicz M, Wysoczynski M, Gaffney PM, Salant DJ, McLeish KR, Powell DW. (2017) Am J Pathol. 187(12):2799-2810. PMID: 28935578.

Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts. Shved N, Warsow G, Eichinger F, Hoogewijs D, Brandt S, Wild P, Kretzler M, Cohen CD, Lindenmeyer MT. (2017) Sci Rep. 7(1):8576. PMID: 28819298.

Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation. Lee H, Qian K, von Toerne C, Hoerburger L, Claussnitzer M, Hoffmann C, Glunk V, Wahl S, Breier M, Eck F, Jafari L, Molnos S, Grallert H, Dahlman I, Arner P, Brunner C, Hauner H, Hauck SM, Laumen H. (2017) Nucleic Acids Res. 45(6):3266-3279. PMID: 28334807.

ANGPTL2 increases bone metastasis of breast cancer cells through enhancing CXCR4 signaling. Lumsden AL, Young RL, Pezos N, Keating DJ. (2016) BMC Evol Biol. 16(1):214. PMID: 27737633.

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation. Tomita S, Abdalla MO, Fujiwara S, Matsumori H, Maehara K, Ohkawa Y, Iwase H, Saitoh N, Nakao M. (2015) Nat Commun. 6:6966. PMID: 25923108.

ANGPTL2 increases bone metastasis of breast cancer cells through enhancing CXCR4 signaling. 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) Sci Rep. 5:9170. PMID: 25773070.

Loss of the NKX3.1 tumorsuppressor promotes the TMPRSS2-ERG fusion gene expression in prostate cancer. Thangapazham R, Saenz F, Katta S, Mohamed AA, Tan SH, Petrovics G, Srivastava S, Dobi A. (2014) BMC Cancer. 14(1):16. PMID: 24418414.

Meta-analysis of diabetic nephropathy associated genetic variants in inflammation and angiogenesis involved in different biochemical pathways. Nazir N, Siddiqui K, Al-Qasim S, Al-Naqeb D (2014) NBMC Med Genet. 15(1):103. PMID: 25280384.

Dopamine signaling leads to loss of polycomb repression and aberrant gene activation in experimental parkinsonism. Södersten E, Feyder M, Lerdrup M, Gomes AL, Kryh H, Spigolon G, Caboche J, Fisone G, Hansen K. (2014) PLoS Genet. 10(9):e1004574. PMID: 25254549.

Dynamic association of NUP98 with the human genome. Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer MW. (2013) PLoS Genet. 9(2). PMID: 23468646.

Distinct Signal Transduction Pathways Downstream of the (P)RR Revealed by Microarray and ChIP-chip Analyses. Zaade D, Schmitz J, Benke E, Klare S, Seidel K, Kirsch S, Goldin-Lang P, Zollmann FS, Unger T, Funke-Kaiser H. (2013) PLoS One. 2013;8(3):e57674. PMID: 23469216.

Stability, delivery and functions of human sperm RNAs at fertilization. Sendler E, Johnson GD, Mao S, Goodrich RJ, Diamond MP, Hauser R, Krawetz SA. (2013) Nucleic Acids Res. 41(7):4104-17. PMID: 23471003.

High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM, Taubenberger JK (2013) J Pathol. 229(4):535-45. PMID: 23180419.

A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion. Pierron G, Tirode F, Lucchesi C, Reynaud S, Ballet S, Cohen-Gogo S, Perrin V, Coindre JM, Delattre O. (2012) Nat Genet. 44(4):461-6. PMID: 22387997.

PHF8 targets histone methylation and RNA polymerase II to activate transcription. Fortschegger K, de Graaf P, Outchkourov NS, van Schaik FM, Timmers HT, Shiekhattar R. (2010) Mol Cell Biol. 30(13):3286-98. PMID: 20421419.

Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice. Prinzen C, Trümbach D, Wurst W, Endres K, Postina R, Fahrenholz F. (2009) BMC Genomics. 10:66. PMID: 19196476.

An integrated workflow for analysis of ChIP-chip data. Weigelt K, Moehle C, Stempfl T, Weber B, Langmann T. (2008) Biotechniques. 45(2):131-2. PMID: 18687062.