“Advanced Gene Control Systems”

About Us

In October 2018, Genomatix AG’s assets and business were transferred to Intrexon Bioinformatics Germany GmbH (IBG), a newly formed subsidiary of Intrexon Corporation doing business as Genomatix*. Intrexon is a US-based NASDAQ publicly-listed company with international business operations. Intrexon designs and engineers living systems to address the world’s greatest challenges in health, energy, food, and environmental sustainability.

Intrexon is a leader in the engineering of biology to improve the quality of life and health of the planet through a diverse portfolio of technological offerings. Intrexon develops unique solutions for 1) precise control of gene expression; 2) design and engineering of biosystems and 3) engineered gene function and delivery.

 

Intrexon’s proprietary technologies in UltraVector®, RheoSwitch®, AdenoVerse™, and AttSite™ platforms, combined with Genomatix’s award winning tools and data content for understanding eukaryotic gene expression, now provide unparalleled solutions for the controlled design, expression and delivery of genetically-modified genes or cells into living systems.

* Intrexon Bioinformatics Germany GmbH is doing business as “Genomatix” and all references to Genomatix herein shall be references to the business of Intrexon Bioinformatics Germany GmbH

Integrated Technology Platforms

Intrexon’s suite of complementary technologies combines the principles of precision biological engineering with statistical modeling, automation, and large-scale production. Intrexon is focused on applying these capabilities to the design and construction of single and multi-gene programs to enable therapeutic development. By integrating data and analysis of gene regulation, signaling pathways, and complex cell functions, Genomatix capabilities are central to Intrexon’s Cell Systems Informatics platform and serve as the foundation for design of gene and cell therapy products. Together, Intrexon’s technology suite offers the potential to advance a diverse spectrum of therapeutic modalities to address unmet medical needs.

Cell Systems Informatics

UltraVector optimized Gene Networks

Protein Engineering

RheoSwitch mediated Transcription Control

AttSite mediated Genome Integration

AdenoVerse mediated Gene Delivery

Scientific Literature

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.

  • Genomatix 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.

  • Collaborative Publications

    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.

  • Customer Publications

    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.

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