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Benjamin (B) Nota PhD

Department
Blood Cell Research
E-mail
b.nota@sanquin.nl
LinkedIn
http://nl.linkedin.com/pub/benjamin-nota/25/a50/a1/
Training

Biology, VU University Amsterdam, 2005

Thesis

‘Ecotoxicogenomics of springtails’
2010 - VU University, Amsterdam

Research interests
My interests are in genetics and genomics of blood cells and immune disorders. With novel genomics tools, such as next-generation sequencing and bioinformatics, I investigate the relationship between genetic mechanisms and pathophysiology.
Technology
  • Next-generation sequencing
  • Bioinformatics
  • Genomics data analysis
  • Shell scripting (Linux, bash)
  • Statistics in R
  • Mutation analysis
  • RNAseq
Resume
2014-present Bioinformatician, Dept of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, AMC, Amsterdam
2013-2014 Lecturer, BSc Bioinformatics, Hogeschool Leiden
2011-2013 Postdoctoral fellow, Dept of Clinical Chemistry, VU University medical center, Amsterdam
2009-2011 Postdoctoral fellow, Dept of Animal Ecology, VU University, Amsterdam
2005-2009 PhD training, Dept of Animal Ecology, VU University, Amsterdam
Publications
Sanquin publications
Other publications

Nota B, Ndika JD, van de Kamp JM, Kanhai WA, van Dooren SJ, van de Wiel MA, Pals G, Salomons GS. RNA Sequencing of Creatine Transporter (SLC6A8) Deficient Fibroblasts Reveals Impairment of the Extracellular Matrix. Hum Mutat 2014 Jun 24. [Epub ahead of print]

Nota B, Hamilton EM, Sie D, Ozturk S, van Dooren SJ, Ojeda MR, Jakobs C, Christensen E, Kirk EP, Sykut-Cegielska J, Lund AM, van der Knaap MS, Salomons GS. Novel cases of D-2-hydroxyglutaric aciduria with IDH1 or IDH2 mosaic mutations identified by amplicon deep sequencing. J Med Genet 2013; 50(11):754-9.

Nota B, Struys EA, Pop A, Jansen EE, Fernandez Ojeda MR, Kanhai WA, Kranendijk M, van Dooren SJ, Bevova MR, Sistermans EA, Nieuwint AW, Barth M, Ben-Omran T, Hoffmann GF, de Lonlay P, McDonald MT, Meberg A, Muntau AC, Nuoffer JM, Parini R, Read MH, Renneberg A, Santer R, Strahleck T, van Schaftingen E, van der Knaap MS, Jakobs C, Salomons GS. Deficiency in SLC25A1, encoding the mitochondrial citrate carrier, causes combined D-2- and L-2-hydroxyglutaric aciduria. Am J Hum Genet 2013; 92(4):627-31.

Nota B, de Korte M, Ylstra B, van Straalen NM, Roelofs D. Genetic variation in parthenogenetic collembolans is associated with differences in fitness and cadmium-induced transcriptome responses. Environ Sci Technol 2013;47(2):1155-62.

Struys EA, Nota B, Bakkali A, Al Shahwan S, Salomons GS, Tabarki B. Pyridoxine-dependent epilepsy with elevated urinary α-amino adipic semialdehyde in molybdenum cofactor deficiency. Pediatrics 2012; 130(6):e1716-9.

Hawliczek A, Nota B, Cenijn P, Kamstra J, Pieterse B, Winter R, Winkens K, Hollert H, Segner H, Legler J. Developmental toxicity and endocrine disrupting potency of 4-azapyrene, benzo[b]fluorene and retene in the zebrafish Danio rerio. Reprod Toxicol 2012; 33(2):213-23.

Nota B, Vooijs R, van Straalen NM, Roelofs D. Expression of mtc in Folsomia candida indicative of metal pollution in soil. Environ Pollut 2011; 159(5):1343-7.

Nota B, Verweij RA, Molenaar D, Ylstra B, van Straalen NM, Roelofs D. Gene expression analysis reveals a gene set discriminatory to different metals in soil. Toxicol Sci 2010; 115(1):34-40.

Nota B, van Straalen NM, Ylstra B, Roelofs D. Gene expression microarray analysis of heat stress in the soil invertebrate Folsomia candida. Insect Mol Biol 2010; 19(3):315-22.

Timmermans MJ, Roelofs D, Nota B, Ylstra B, Holmstrup M. Sugar sweet springtails: on the transcriptional response of Folsomia candida (Collembola) to desiccation stress. Insect Mol Biol 2009; 18(6):737-46.

Roelofs D, Janssens TK, Timmermans MJ, Nota B, Mariën J, Bochdanovits Z, Ylstra B, van Straalen NM. Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta. Mol Ecol 2009; 18(15):3227-39.

de Boer ME, de Boer TE, Mariën J, Timmermans MJ, Nota B, van Straalen NM, Ellers J, Roelofs D. Reference genes for QRT-PCR tested under various stress conditions in Folsomia candida and Orchesella cincta (Insecta, Collembola). BMC Mol Biol 2009; 10:54.

Nota B, Bosse M, Ylstra B, van Straalen NM, Roelofs D. Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene. BMC Genomics 2009; 10:236.

Nota B, Timmermans MJ, Franken O, Montagne-Wajer K, Mariën J, de Boer ME, de Boer TE, Ylstra
B, van Straalen NM, Roelofs D. Gene expression analysis of collembola in cadmium containing soil. Environ Sci Technol 2008; 42(21):8152-7.

Timmermans MJ, de Boer ME, Nota B, de Boer TE, Mariën J, Klein-Lankhorst RM, van Straalen NM, Roelofs D. Collembase: a repository for springtail genomics and soil quality assessment. BMC Genomics 2007; 8:341.

Muris JJ, Ylstra B, Cillessen SA, Ossenkoppele GJ, Kluin-Nelemans JC, Eijk PP, Nota B, Tijssen M, de Boer WP, van de Wiel M, van den Ijssel PR, Jansen P, de Bruin PC, van Krieken JH, Meijer GA, Meijer CJ, Oudejans JJ. Profiling of apoptosis genes allows for clinical stratification of primary nodal diffuse large B-cell lymphomas. Br J Haematol 2007; 136(1):38-47.

Last edited on: 23 May 2016
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