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My research

My main interest in the past 5 years has been the interaction of micro-organisms (either pathogenic or commensal) within their community and with their host. I have a keen interest in translating results from 'big data' approaches to meaningful biological information using bioinformatics approaches.

I am involved in projects concerning genome sequencing for comparative genomics, molecular epidemiology and phenotype-genotype linking, prokaryotic and eukaryotic expression analysis, disease severity signature gene detection and immunoinformatics.

Other interests are the development of bioinformatics tools (Perl, Python, R) and statistics and machinelearning techniques (mostly in R)

h and i10 indices and number of citations are automatically pulled from Google Scholar:

H - indices

https://scholar.google.nl/citations?user=VHHhpoAAAAAJ&hl=nl

 

 

2014-current Assistant Professor at Utrecht University

Analysis of bacterial (meta-)genomes for comparative genomics, molecular epidemiology and linking bacterial genotype to clinical manifestation of disease. Staff member of the WHO-Collaborating Center for Campylobacter, WHO consultant on genomics for antimicrobial resistance detection. 

November 2012 - Current Bioinformatics Consultant Bacterial Vaccine Development

Bioinformatics Consultant Bacterial Vaccine Development for a large pharmaceutical company

2010 - 2014 Postdoctoral researcher at Radboudumc

Late 2010 I started working at Radboud University Nijmegen Medical Centre, Laboratory of Pediatric Infectious Diseases for which I received funding from a Marie Curie IEF fellowship. My current research focuses on essential gene discovery of respiratory pathogens with next generation sequencing techniques such as Tn-seq and analyzing resulting data using smart bioinformatics methods. In addition I am involved in projects concerning genome sequencing, prokaryotic and eukaryotic microarray analysis, disease severity signature gene detection, biomarker discovery and immunoinformatics.

My tool for essential gene detection is available online:

http://bamics2.cmbi.ru.nl/websoftware/essentials/essentials_start.php

Publications:

  1. ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data. Aldert Zomer, Peter Burghout, Hester J Bootsma, Peter WM Hermans, Sacha AFT van Hijum. PLoS ONE 7(8): e43012. doi:10.1371/journal.pone.0043012
  2. For more please see http://www.zomeronline.net/joomla/index.php/publications

 

2006-2010 Postdoctoral researcher at University College Cork.

Late 2006 I started as a postdoc in the group of Prof. van Sinderen at University College Cork in Ireland where I worked on gut health and Bifidobacterium genomics. My work was funded by an IRCSET Embark postdoctoral grant which I received in 2007.

My research included transcriptome analysis of B. breve , Lactococcus and lactobacillus grown both in vitro and in vivo under various relevant conditions, host transcriptomics, genome sequencing and analysis of novel probiotic strains. Furthermore I supervised students performing microbiology, genetics or bioinformatics projects. In addition I was responsible for running the BioIT and gene array platform of the Alimentary Pharmabiotics Centre. My work resulted in several publications listed below.

  1. A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003. Alvarez-Martin P, Fernández M, O'Connell-Motherway M, O'Connell KJ, Sauvageot N, Fitzgerald GF, Macsharry J, Zomer A, van Sinderen D; Appl Environ Microbiol. 2012 May 25.
  2. Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Cronin M, Zomer A, Fitzgerald G, van Sinderen D; Bioengineered bugs. 2012 May 1;3(3)
  3. A bile-inducible membrane protein mediates bifidobacterial bile resistance. Ruiz L, O'Connell-Motherway M, Zomer A, de Los Reyes-Gavilán CG, Margolles A, van Sinderen D; Microbial biotechnology. 2012 Feb 1
  4. Discovering Novel Bile Protection Systems in Bifidobacterium breve UCC2003 through Functional Genomics. Ruiz L, Zomer A, O'Connell-Motherway M, van Sinderen D, Margolles A; Applied and environmental microbiology. 2012 Feb;78(4):1123-31
  5. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Fanning S, Hall LJ, Cronin M, Zomer A, Macsharry J, Goulding D, O'Connell Motherway M, Shanahan F, Nally K, Dougan G, van Sinderen D; Proceedings of the National Academy of Sciences of the United States of America. 2012 Jan 23
  6. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Motherway MO, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Moreno Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D; Proceedings of the National Academy of Sciences of the United States of America. 2011 Jul 5;108(27):11217-22
  7. Cellodextrin utilization by bifidobacterium breve UCC2003.Pokusaeva K, O'Connell-Motherway M, Zomer A, Macsharry J, Fitzgerald GF, van Sinderen D; Applied and environmental microbiology. 2011 Mar;77(5):1681-90
  8. Complete genome sequence of Bifidobacterium bifidum S17.Zhurina D, Zomer A, Gleinser M, Brancaccio VF, Auchter M, Waidmann MS, Westermann C, van Sinderen D, Riedel CU; Journal of bacteriology. 2011 Jan;193(1):301-2
  9. The stress response of bifidobacteriaMarco Ventura, Abelardo Margolles, Francesca Turroni, Aldert L. Zomer, G de los Reyes-Gavilan, Douwe van Sinderen; Stress response of Lactic Acid Bacteria. 2011
  10. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Turroni F, Bottacini F, Foroni E, Mulder I, Kim JH, Zomer A, Sánchez B, Bidossi A, Ferrarini A, Giubellini V, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Fitzgerald GF, Mills D, Margolles A, Kelly D, van Sinderen D, Ventura M; Proceedings of the National Academy of Sciences of the United States of America. 2010 Nov 9;107(45):19514-9
  11. Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Turroni F, Foroni E, O'Connell Motherway M, Bottacini F, Giubellini V, Zomer A, Ferrarini A, Delledonne M, Zhang Z, van Sinderen D, Ventura MApplied and environmental microbiology. 2010 May;76(10):3206-19
  12. Ribose utilization by the human commensal Bifidobacterium breve UCC2003. Pokusaeva K, Neves AR, Zomer A, O'Connell-Motherway M, MacSharry J, Curley P, Fitzgerald GF, van Sinderen D; Microbial biotechnology. 2010 May;3(3):311-23
  13. Acid and bile resistance and stress response in bifidobacteria.Borja Sanchez, Lorena Ruiz, Douwe van Sinderen, Abelardo Margolles, Aldert L. Zomer; Bifidobacteria: Genomics and Molecular Aspects. 2010:71-96
  14. Intertwinement of stress response regulons in Bifidobacterium breve UCC2003.Zomer A, van Sinderen D; Gut microbes. 2010 3;1(2):100-102
  15. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. Ventura M, Turroni F, Zomer A, Foroni E, Giubellini V, Bottacini F, Canchaya C, Claesson MJ, He F, Mantzourani M, Mulas L, Ferrarini A, Gao B, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Gupta RS, Zhang Z, Beighton D, Fitzgerald GF, O'Toole PW, van Sinderen D; PLoS genetics. 2009 Dec;5(12):e1000785
  16. An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. Zomer A, Fernandez M, Kearney B, Fitzgerald GF, Ventura M, van Sinderen D; Journal of bacteriology. 2009 Nov;191(22):7039-49
  17. Comparative analyses of prophage-like elements present in bifidobacterial genomes. Ventura M, Turroni F, Lima-Mendez G, Foroni E, Zomer A, Duranti S, Giubellini V, Bottacini F, Horvath P, Barrangou R, Sela DA, Mills DA, van Sinderen D; Applied and environmental microbiology. 2009 Nov;75(21):6929-36
  18. Characterization of two novel alpha-glucosidases from Bifidobacterium breve UCC2003. Pokusaeva K, O'Connell-Motherway M, Zomer A, Fitzgerald GF, van Sinderen D Applied and environmental microbiology. 2009 Feb;75(4):1135-43

 

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