Integrating the world's high quality expression data -
For more effective discovery and interpretation
We enable the future of genomic research through precise curation
and advanced analytics of public and private studies

Science


At the heart of NEBION's curated data and products is scientific rigor and many years of research experience. Over 80% of NEBION employees have a PhD in either molecular biology, informatics, statistics, physics or electrical engineering. We strive to develop products and services at the highest level of quality and scientific stringency. Besides applying our scientific skills and curiosity into developing innovative products and services, NEBION participates in various international research projects and publishes novel methods for bioinformatic data analysis and curation.

Research Partnerships


TransCard logo
TransCard is an EU FP7 collaborative project to identify, prioritize and validate therapeutic targets and novel key regulators of lipid and lipoprotein metabolism. As partner of this project, Nebion curates relevant datasets, integrates them for global analysis, and uses its technologies to identify and prioritize novel targets . See also project website.

CTI logo
CTI, the Swiss Commission for Technology and Innovation (CTI), co-funded two projects in partnership with ETH Zurich. The projects led to the development of novel methods for large-scale biological data integration, data curation, the development of ontologies, and tools for target and biomarker discovery.

SystemsX logo
SystemsX co-funded a Bridge-to-Industry Project in which Nebion and ETH Zurich partnered to develop novel methodologies for the integration and visualization of biclustering results. The project is co-funded by SystemsX.ch and Nebion. See also project page at Systems X.

3to4 logo
3to4 is a large EU FP7 collaborative project to uncover mechanisms underlying important aspects of the C4 leaf and study ways to transfer C4 traits to C3 plants. As an SME, Nebion will provide expertise and services to manage the consortium's high-throughput biological data, develop novel tools and support data analysis. See also project website.




Selected publications by Nebion scientists


Bioinformatics and Biocuration


Zimmermann P, Bleuler S, Laule O, Martin F, Ivanov NV, Campanoni P, Oishi K, Lugon-Moulin N, Wyss M, Hruz T and W Gruissem (2014) ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions. BioData Mining 2014, 7:18. [Abstract]


Prasad A, Suresh Kumar S, Dessimoz C, Bleuler S, Laule O, Hruz T, Gruissem W, and P Zimmermann (2013) Global regulatory architecture of human, mouse and rat tissue transcriptomes. BMC Genomics 2013, 14:716. [Abstract]


Meskauskiene R, Laule O, Ivanov NV, Martin F, Wyss M, Gruissem W, and P Zimmermann (2013) Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. Plant Methods 2013, 9:33. [Abstract]


Hruz T, Wyss M, Lucas C, Laule O, von Rohr P, Zimmermann P, and S Bleuler (2013) A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks. Advances in Bioinformatics, vol. 2013, Article ID 920325, 10 pages, 2013. doi:10.1155/2013/920325. [Full text]


Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, Borghi L, Verbrugge P, Kalaydjieva L, Bleuler S, Laule O, Descombes P, Gruissem W and P Zimmermann (2011) RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 2011, 12:156. [Abstract]


Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, and W Gruissem (2008) Genevestigator Transcriptome Meta-Analysis and Biomarker Search Using Rice and Barley Gene Expression Databases. Molecular Plant 1 (5), 851-857. [Abstract]


Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W and P Zimmermann (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 2008, 420747 [Full Text]


Bleuler S, Zimmermann P, Friberg M, and E Zitzler (2007) Discovering Trends in Gene Expression Data Using a Hybrid Evolutionary Algorithm. Algorithmic Operations Research, Vol 3(2)


Grennan AK (2006) Genevestigator. Facilitating web-based gene-expression analysis. Plant Physiology 141(4):1164-6 [PubMed]


Hruz T, Hirsch-Hoffmann M, Gruissem W, and P Zimmermann (2006) Reducing Java Internet project risks: a case study of public measurement of client component functionality in the user community. PPPJ06, pp. 199-202 


Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, and P Zimmermann (2006) Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics 7, 311 [Full text]


Schöner D, Barkow S, Bleuler S, Bühlmann P, Gruissem W, Hennig L, Wille A, Zimmermmann P, and E Zitzler (2006) Network analysis of systems elements. In: Plant Systems Biology (ed. S. Baginsky and A. Fernie), Birkhäuser Verlag.


Hennig L and P Zimmermann (2006) Data warehouses - Your one-stop-shops for microarray data In: European Training and Networking Activity. Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond – a course book (ed. J. Freitag), MPI-MPP 2006, Potsdam-Golm, pp. 211-217


Zimmermann P, Schildknecht B, Garcia-Hernandez M, Gruissem W, Craigon D, Mukherjee G, May S, Parkinson H, Rhee S, Wagner U, and L Hennig (2006) MIAME/Plant - adding value to plant microarrray experiments. Plant Methods  2 , 1 [PubMed]


Prelic A, Bleuler S, Zimmermann P, Wille A, Bühlmann P, Gruissem W, Hennig L, Thiele L, and E Zitzler (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics  22 , 1122-112 [PubMed]


Barkow S, Bleuler S, Prelic A, Zimmermann P, and E Zitzler (2006) BicAT: a biclustering analysis toolbox. Bioinformatics 22(10): 1282-1283 [PubMed]


Zimmermann P, Hennig L, and W Gruissem (2005) Gene expression analysis and network discovery using Genevestigator. Trends in Plant Science 9 10 , 407-409 [PubMed]


Zimmermann P, Hirsch-Hoffmann M, Hennig L, and W Gruissem (2004) GENEVESTIGATOR: Arabidopsis Microarray Database and Analysis Toolbox. Plant Physiology 136 1 , 2621-2632 [PubMed] (most frequently cited GENEVESTIGATOR paper)


Wille A, Zimmermann P, Vranová E, Bleuler S, Fürholz A, Hennig L, Laule O, Prelíc A, von Rohr P, Thiele L, Zitzler E, Gruissem W, and P Bühlmann (2004) Sparse graphical gaussian modeling for genetic regulatory network inference. Genome Biology  5 , R92.1-R92.13 [PubMed]



Red and White Biology


Mermod M, Hiou-Feige A, Bovay E, Roh V, Sponarova J, Bongiovanni M, Vermeer DW, Lee JH, Petrova TV, Rivals JP, Monnier Y, Tolstonog GV, Simon C (2018) Mouse model of postsurgical primary tumor recurrence and regional lymph node metastasis progression in HPV-related head and neck cancer. Int J Cancer. 2018 Jan 4.


Dostalova A, Rommelaere S, Poidevin M, Lemaitre B (2017) Thioester-containing proteins regulate the Toll pathway and play a role in Drosophila defence against microbial pathogens and parasitoid wasps. BMC Biol. 2017 Sep 5;15(1):79.


Macuchova E, Nohejlova K, Sevcikova M, Hrebickova I, Slamberova R (2017) Sex differences in the strategies of spatial learning in prenatally-exposed rats treated with various drugs in adulthood. Behavioural Brain Research; 327:83-93. ]


Jiraskova A, Bortolussi G, Dostalova G, EremiaSova L, Golan L, Danzig V, Linhart A, Vitek L. (2017) Serum Bilirubin Levels and Promoter Variations in HMOX1 and UGT1A1 Genes in Patients with Fabry Disease. Oxid Med Cell Longev 2017:9478946.


Andersson A, Bluwstein A, Kumar N, Teloni F, Traenkle J, Baudis M, Altmeyer M, Hottiger MO (2016) PKCα and HMGB1 antagonistically control hydrogen peroxide-induced poly- ADP-ribose formation. Nucleic Acids Research, 19;44 (16): 7630-45.


Macuchova E, Sevcikova M, Hrebickova I, Nohejlova K, Slamberova R (2016) How various drugs affect anxiety-related behavior in male and female rats prenatally exposed to methamphetamine. International Journal of Developmental Neuroscience; 51:1-11.


Hajkova A, Techlovska S, Dvorakova M, Chambers JN, KumpoSt J, Hubalkova P, Prezeau L, Blahos J. (2016) SGIP1 alters internalization and modulates signaling of activated cannabinoid receptor 1 in a biased manner. Neuropharmacology. 2016 Aug;107:201-214. doi: 10.1016.


Mrizova I, Moserova M, Milichovsky J, Sulc M, Kizek R, Kubackova K, Arlt VM, Stiborova M. (2016) Heterologous expression of human cytochrome P450 2S1 in Escherichia coli and investigation of its role in metabolism of benzo[a]pyrene and ellipticine. Monatsh Chem 147:881-888.


Valny M, Honsa P, Kirdajova D, Kamenik Z, Anderova M. (2016) Tamoxifen in the mouse brain: Implications for fate-mapping studies using the tamoxifen-inducible Cre-loxP system. Frontiers in Cellular Neuroscience 10, 243, DOI: 10.3389/fncel.2016.00243.


Honsa P, Valny M, Kriska J, Matuskova H, Harantova L, Kirdajova D, Valihrach L, Androvic P, Kubista M, Anderova M. (2016) Generation of reactive astrocytes from NG2 cells is regulated by sonic hedgehog. Glia 64 (9), 1518-1531.


Kalferstova L, Vilimovska Dedeckova K, Antuskova M, Melter O, Drevinek P. J (2016) How and why to monitor Pseudomonas aeruginosa infections in the long term at a cystic fibrosis centre. Hosp Infect. 2016 Jan;92(1):54-60.


Polakova E, Illaste A, Niggli E, Sobie EA. (2015) Maximal acceleration of Ca2+ release refractoriness by β-adrenergic stimulation requires dual activation of kinases PKA and CaMKII in mouse ventricular myocytes. J Physiol. 593(6):1495-507.


Andersson A, Minotti R, Hottiger MO (2015) ARTD1 Suppresses Interleukin 6 Expression by Repressing MLL1- Dependent Histone H3 Trimethylation. Molecular and Cellular Biology, 35 (18): 3189-99


Arlt VM, Krais AM, Godschalk RW, Riffo-Vasquez Y, Mrizova I, Roufosse CA, Corbin C, Shi Q, Frei E, Stiborova M, van Schooten FJ, Phillips DH and Spina D. (2015) Pulmonary inflammation impacts on CYP1A1-mediated respiratory tract DNA damage induced by the carcinogenic air pollutant benzo[a]pyrene. Toxicol Sci 146(2):213-25.


Lenicek M, Duricova D, Hradsky O, Dusatkova P, Jiraskova A, Lukas M, Nachtigal P, Vitek L. (2014) The relationship between serum bilirubin and Crohn's disease. Inflamm Bowel Dis 20(3):481-7.


Techlovska S, Chambers JN, Dvorakova M, Petralia RS, Wang YX, Hajkova A, Nova A, Frankova D, Prezeau L, Blahos J (2014) Metabotropic glutamate receptor 1 splice variants mGluR1a and mGluR1b combine in mGluR1a/b dimers in vivo. Neuropharmacology. 2014 Nov;86:329-336. doi: 10.1016.


Honsa P, Pivonkova H, Harantova L, Butenko O, Kriska J, Dzamba D, Rusnakova V, Valihrach L, Kubista M, Anderova M (2014) Increased expression of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in reactive astrocytes following ischemia. Glia. 2014 Jul 14. DOI: 10.1002/glia.22721.


Stiborova M, Cerna V, Moserova M, Mrizova I, Arlt VM and E Frei (2014) The anticancer drug ellipticine activated with cytochrome P450 mediates DNA damage determining its pharmacological efficiencies: studies with rats, Hepatic Cytochrome P450 Reductase Null (HRN) mice and pure enzymes. Int J Mol Sci 16(1): 284-306.


Macuchova E, Nohejlova K, Slamberova R (2014) Gender differences in the effect of adult amphetamine on cognitive functions of rats prenatally exposed to methamphetamine. Behavioural Brain Research; 270: 8-17.


Vitek L, Gbelcova H, Muchova L, Vanova K, Zelenka J, Konickova R, Suk J, Zadinova M, Knejzlik Z, Ahmad S, Fujisawa T, Ahmed A, Ruml T. (2014) Antiproliferative effects of carbon monoxide on pancreatic cancer. Dig Liver Dis 46(4):369-75.


Cuperus FJ, Schreuder AB, van Imhoff DE, Vitek L, Vanikova J, Konickova R, Ahlfors CE, Hulzebos CV, Verkade HJ (2013) Beyond plasma bilirubin: the effects of phototherapy and albumin on brain bilirubin levels in Gunn rats. J Hepatol 58(1):134-40.


Kyrychenko S, Polakova E, Kang C, Pocsai K, Ullrich ND, Niggli E, Shirokova N. (2013) Hierarchical accumulation of RyR post-translational modifications drives disease progression in dystrophic cardiomyopathy. Cardiovasc Res. 97(4):666-75.


Sponarova J, Nuvolone M, Whicher C, Frei N, Kana V, Schwarz P, Westermark GT, Aguzzi A (2013) Efficient amyloid A clearance in the absence of immunoglobulins and complement factors. Am J Pathol. 2013 Apr;182(4):1297-307.


Dostalova A, Kaeser S, Cristodero M, Schimanski B (2013) The nuclear mRNA export receptor Mex67-Mtr2 of Trypanosoma brucei contains a unique and essential zinc finger motif. Mol Microbiol. 2013 May;88(4):728-39


Dedeckova K, Kalferstova L, Strnad H, Vavrova J and Drevinek P (2013) Novel diagnostic PCR assay for Burkholderia cenocepacia epidemic strain ST32 and its utility in monitoring infection in cystic fibrosis patients. Cyst Fibros. 2013 Jan 11.



Dedeckova K, Fila L, Skalicka V, Bartosova J, Kucerova T, Vavrova V, Zemkova D, Kalferstova L, Melter O, Cinek O, Drevinek P. (2012) PCR detection of Burkholderia cepacia complex as one of key factors to handle a longterm outbreak. J Cyst Fibros. 2012 Sep;11(5):440-5.


Jiraskova A, Novotny J, Novotny L, Vodicka P, Pardini B, Naccarati A, Schwertner HA, Hubacek JA, Puncocharova L, Smerhovsky Z, Vitek L. (2012) Association of serum bilirubin and promoter variations in HMOX1 and UGT1A1 genes with sporadic colorectal cancer. Int J Cancer 131(7):1549-55.


O'Connor T, Frei N, Sponarova J, Schwarz P, Heikenwalder M, Aguzzi A (2012) Lymphotoxin, but not TNF, is required for prion invasion of lymph nodes. PLoS Pathog. 2012;8(8):e10028675.


Dostalova A, Votypka J, Favreau AJ, Barbian KD, Volf P, Valenzuela JG, Jochim RC (2011) The midgut transcriptome of Phlebotomus (Larroussius) perniciosus, a vector of Leishmania infantum: comparison of sugar fed and blood fed sand flies. BMC Genomics. 2011 May 10;12:223


Ballmer-Hofer K, Andersson AE, Ratcliffe LE, Berger P (2011) Neuropilin-1 promotes VEGFR-2 trafficking through Rab11 vesicles thereby specifying signal output. Blood, 118 (3): 816-826


Polakova E, Zahradnikova A Jr, Pavelkova J, Zahradnik I, Zahradnikova A. (2008) Local calcium release activation by DHPR calcium channel openings in rat cardiac myocytes. . J Physiol 586(16):3839-54.


Scrima A, Konickova R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP, Thomä NH (2008) Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex. Cell 135(7):1213-23.


Sponarova J, Mustard KJ, Horakova O, Flachs P, Rossmeisl M, Brauner P, Bardova K, Thomason-Hughes M, Braunerova R, Janovska P, Hardie DG, Kopecky J (2005) Involvement of AMP-activated protein kinase in fat depot-specific metabolic changes during starvation. FEBS Lett. 2005 Nov 7;579(27):6105-10


Green Biology


Kucharewicz W, Distelfeld A, Bilger W, Mueller M, Munne-Bosch S, Hensel G, Krupinska K. (2017) Acceleration of leaf senescence is slowed down in transgenic barley plants deficient in the DNA/RNA-binding protein WHIRLY1. J Exp Bot. 68(5):983-996.


Kim C, Meskauskiene R, Zhang S, Lee KP, Lakshmanan Ashok M, Blajecka K, Herrfurth C, Feussner I, Apel K (2012) Chloroplasts of Arabidopsis are the source and a primary target of a plant-specific programmed cell death signaling pathway. Plant Cell. 2012 Jul;24(7):3026-39


Meskauskiene R, Wuersch M, Laloi C, Vidi PA, Coll NS, Kessler F, Baruah A, Kim C, Apel K (2009) A mutation in the Arabidopsis mTERF-related plastid protein SOLDAT10 activates retrograde signaling and suppresses (1)O(2)-induced cell death. Plant J. 2009 Nov;60(3):399-410


Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U and W Gruissem (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320 (5878), 938-941


Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, Langebartels C, Gruissem W, Inze D and F van Breusegem (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiology 139 (2), 806-821 [Abstract]


Zimmermann P, Regierer B, Kossmann J, Frossard E, Amrhein N and M Bucher (2004) Differential expression of three purple acid phosphatases from potato. Plant Biology 6 (05), 519-528 [Abstract]


Zimmermann P, Zardi G, Lehmann M, Zeder C, Amrhein N, Frossard E and M Bucher (2003) Engineering the root–soil interface via targeted expression of a synthetic phytase gene in trichoblasts. Plant Biotechnology Journal 1 (5), 353-360


Meskauskiene R, Nater M, Goslings D, Kessler F, op den Camp R, Apel K (2001) FLU: a negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12826-31