dr. A.L. (Aldert) Zomer
A.L.Zomer@uu.nl
Gegenereerd op 2018-06-23 23:17:19


Profile

Assistant Professor at Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine. Associated with Theoretical Biology and Bioinformatics, both at Utrecht University. Bioinformatics consultant for Janssen Pharmaceuticals on bacterial vaccine development.

My interests are the analysis of bacterial (meta)genomes for comparative genomics, molecular epidemiology and linking the bacterial genotype to a phenotype such as host association or clinical manifestation of disease.

For a list of publications and my citations, please see:

http://scholar.google.com/citations?hl=nl&user=VHHhpoAAAAAJ&view_op=list_works&pagesize=100

 

Gegenereerd op 2018-06-23 23:17:19

Details about all my publications and my citations can be found on Google Scholar . For some reason publications disappear from this profile page  once in a while (or it only shows one specific year) due to bugs in the UU publication software. 

 

Key publications

Gilbert, Maarten J, Duim, Birgitta, van der Graaf-van Bloois, Linda, Wagenaar, Jaap A & Zomer, Aldert L (2018). Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation. Genome Biology and Evolution, 10 (3), (pp. 716-722) (7 p.).

Mobegi, Fredrick M, Cremers, Amelieke J H, de Jonge, Marien I, Bentley, Stephen D, van Hijum, Sacha A F T & Zomer, Aldert (16.02.2017). Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data. Scientific Reports, 7 (13 p.).

Tunjungputri, Rahajeng N, Mobegi, Fredrick M, Cremers, Amelieke J, van der Gaast-de Jongh, Christa E, Ferwerda, Gerben, Meis, Jacques F, Roeleveld, Nel, Bentley, Stephen D, Pastura, Alexander S, van Hijum, Sacha A F T, van der Ven, Andre J, de Mast, Quirijn, Zomer, Aldert & de Jonge, Marien I (17.01.2017). Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease. mBio, 8 (1) (10 p.). Copyright © 2017 Tunjungputri et al..

van der Graaf-van Bloois, Linda, Duim, Birgitta, Miller, William G, Forbes, Ken J, Wagenaar, Jaap A & Zomer, Aldert (06.09.2016). Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production. BMC Genomics, 17 (10 p.).

Cremers, Amelieke J H, Mobegi, Fredrick M, de Jonge, Marien I, van Hijum, Sacha A F T, Meis, Jacques F, Hermans, Peter W M, Ferwerda, Gerben, Bentley, Stephen D & Zomer, Aldert L (2015). The post-vaccine microevolution of invasive Streptococcus pneumoniae. Scientific Reports, 5 (8 p.).

Cremers, Amelieke Jh, Zomer, Aldert L, Gritzfeld, Jenna F, Ferwerda, Gerben, van Hijum, Sacha Aft, Ferreira, Daniela M, Shak, Joshua R, Klugman, Keith P, Boekhorst, Jos, Timmerman, Harro M, de Jonge, Marien I, Gordon, Stephen B & Hermans, Peter Wm (15.12.2014). The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. Microbiome, 2, (pp. 44).

Mobegi, Fredrick M, van Hijum, Sacha Aft, Burghout, Peter, Bootsma, Hester J, de Vries, Stefan Pw, Jongh, Christa E van der Gaast-de, Simonetti, Elles, Langereis, Jeroen D, Hermans, Peter Wm, de Jonge, Marien I & Zomer, Aldert (2014). From microbial gene essentiality to novel antimicrobial drug targets. BMC Genomics, 15 (1).

Zomer, Aldert, Burghout, Peter, Bootsma, Hester J, Hermans, Peter W M & van Hijum, Sacha A F T (2012). ESSENTIALS - software for rapid analysis of high throughput transposon insertion sequencing data. PLoS One, 7 (8), (pp. e43012).

O'Connell Motherway, Mary, Zomer, Aldert, Leahy, Sinead C, Reunanen, Justus, Bottacini, Francesca, Claesson, Marcus J, O'Brien, Frances, Flynn, Kiera, Casey, Patrick G, Munoz, Jose Antonio Moreno, Kearney, Breda, Houston, Aileen M, O'Mahony, Caitlin, Higgins, Des G, Shanahan, Fergus, Palva, Airi, de Vos, Willem M, Fitzgerald, Gerald F, Ventura, Marco, O'Toole, Paul W & van Sinderen, Douwe (05.07.2011). Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proceedings of the National Academy of Sciences of the United States of America, 108 (27), (pp. 11217-22) (6 p.).

Zomer, Aldert L, Buist, Girbe, Larsen, Rasmus, Kok, Jan & Kuipers, Oscar P (2007). Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. Journal of Bacteriology, 189 (4), (pp. 1366-81) (16 p.).

Wegmann, Udo, O'Connell-Motherway, Mary, Zomer, Aldert, Buist, Girbe, Shearman, Claire, Canchaya, Carlos, Ventura, Marco, Goesmann, Alexander, Gasson, Michael J, Kuipers, Oscar P, van Sinderen, Douwe & Kok, Jan (2007). Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. Journal of Bacteriology, 189 (8), (pp. 3256-70) (15 p.).

van Hijum, Sacha A F T, Zomer, Aldert L, Kuipers, Oscar P & Kok, Jan (15.11.2003). Projector - automatic contig mapping for gap closure purposes. Nucleic Acids Research, 31 (22), (pp. e144).

All publications
  Articles - 2018
Lavelle, Katherine, Murphy, James, Fitzgerald, Brian, Lugli, Gabriele Andrea, Zomer, Aldert, Neve, Horst, Ventura, Marco, Franz, Charles M, Cambillau, Christian, van Sinderen, Douwe & Mahony, Jennifer (09.03.2018). A decade of <i>Streptococcus thermophilus</i> phage evolution in an Irish dairy plant. Applied and Environmental Microbiology, (pp. AEM.02855-17).
Lavelle, Katherine, Murphy, James, Fitzgerald, Brian, Lugli, Gabriele Andrea, Zomer, Aldert, Neve, Horst, Ventura, Marco, Franz, Charles M, Cambillau, Christian, van Sinderen, Douwe & Mahony, Jennifer (2018). A decade ofphage evolution in an Irish dairy plant. Applied and Environmental Microbiology Copyright © 2018 American Society for Microbiology..
van Beek, Lucille L F, Gouw, Daan de, Eleveld, Marc J, Bootsma, Hester J, de Jonge, Marien I, Mooi, Frits R, Zomer, Aldert A & Diavatopoulos, Dimitri A (2018). Adaptation of Bordetella pertussis to the respiratory tract. Journal of Infectious Diseases
Zomer, Aldert, Otsuka, Nao, Hiramatsu, Yukihiro, Kamachi, Kazunari, Nishimura, Naoko, Ozaki, Takao, Poolman, Jan Theunis & Geurtsen, Jeroen (2018). Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines. Microbial genomics
Gilbert, Maarten J, Zomer, Aldert L, Timmerman, Arjen J, Spaninks, Mirlin P, Rubio García, Ana, Rossen, John W A, Duim, Birgitta & Wagenaar, Jaap A (06.04.2018). Campylobacter blaseri sp. nov., isolated from common seals (Phoca vitulina). International Journal of Systematic and Evolutionary Microbiology
Gilbert, Maarten J, Duim, Birgitta, van der Graaf-van Bloois, Linda, Wagenaar, Jaap A & Zomer, Aldert L (2018). Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation. Genome Biology and Evolution, 10 (3), (pp. 716-722) (7 p.).
Cuperus, Tryntsje, Kraaij, Marina D, Zomer, Aldert L, van Dijk, Albert & Haagsman, Henk P (2018). Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2. PLoS One, 13 (6), (pp. e0198188).
van der Maten, Erika, van den Broek, Bryan, de Jonge, Marien I, Rensen, Kim J W, Eleveld, Marc J, Zomer, Aldert L, Cremers, Amelieke J H, Ferwerda, Gerben, de Groot, Ronald, Langereis, Jeroen D & van der Flier, Michiel (29.01.2018). Streptococcus pneumoniae PspC-subgroup prevalence in invasive disease and difference in contribution to complement evasion. Infection and Immunity Copyright © 2018 American Society for Microbiology..
Cremers, Amelieke J H, Mobegi, Fredrick M, van der Gaast-de Jongh, Christa E, van Weert, Michelle, van Opzeeland, Fred J, Vehkala, Minna, Knol, Mirjam J, Bootsma, Hester J, Välimäki, Niko, Croucher, Nicholas J, Meis, Jacques F, Bentley, Stephen D, van Hijum, Sacha A F T, Corander, Jukka, Zomer, Aldert L, Ferwerda, Gerben & de Jonge, Marien I (2018). The Contribution of Genetic Variation of Streptococcus Pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease. Clinical Infectious Diseases
  Articles - 2017
Mobegi, Fredrick M, Zomer, Aldert, de Jonge, Marien I & van Hijum, Sacha A F T (2017). Advances and perspectives in computational prediction of microbial gene essentiality. Briefings in Functional Genomics, 16 (2), (pp. 70-79). © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com..
Mobegi, Fredrick M, Cremers, Amelieke J H, de Jonge, Marien I, Bentley, Stephen D, van Hijum, Sacha A F T & Zomer, Aldert (16.02.2017). Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data. Scientific Reports, 7 (13 p.).
Koppenaal, H, Groenendijk, F, van den Berge, M., Verkade, E., Verduin, K, Zomer, A L, Duim, B, Wagenaar, J A, Tijsma, A S L, Spierenburg, M A H & Te Wierik, Margreet J M (2017). Een uitbraak met Campylobacter fetus na het eten van rauwmelkse schapenkaas - Hoe traceer je de bron van een uitbraak?. Nederlands Tijdschrift voor Geneeskunde, 161 (7 p.).
Vries, Stefan P W de, Gupta, Srishti, Baig, Abiyad, Wright, Elli, Wedley, Amy, Jensen, Annette Nygaard, Lora, Lizeth LaCharme, Humphrey, Suzanne, Skovgård, Henrik, Macleod, Kareen, Pont, Elsa, Wolanska, Dominika P, L'Heureux, Joanna, Mobegi, Fredrick M, Smith, David G E, Everest, Paul, Zomer, Aldert, Williams, Nicola, Wigley, Paul, Humphrey, Thomas, Maskell, Duncan J & Grant, Andrew J (28.04.2017). Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models. Scientific Reports, 7 (1) (17 p.).
Bottacini, Francesca, Zomer, Aldert, Milani, Christian, Ferrario, Chiara, Lugli, Gabriele Andrea, Egan, Muireann, Ventura, Marco & van Sinderen, Douwe (28.12.2017). Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003. BMC Genomics, 18 (1).
Capel, Elena, Barnier, Jean-Philippe, Zomer, Aldert L, Bole-Feysot, Christine, Nussbaumer, Thomas, Jamet, Anne, Lécuyer, Hervé, Euphrasie, Daniel, Virion, Zoé, Frapy, Eric, Pélissier, Philippe, Join-Lambert, Olivier, Rattei, Thomas, Bourdoulous, Sandrine, Nassif, Xavier & Coureuil, Mathieu (2017). Peripheral blood vessels are a niche for blood-borne meningococci. Virulence, 8 (8), (pp. 1808-1819).
Tunjungputri, Rahajeng N, Mobegi, Fredrick M, Cremers, Amelieke J, van der Gaast-de Jongh, Christa E, Ferwerda, Gerben, Meis, Jacques F, Roeleveld, Nel, Bentley, Stephen D, Pastura, Alexander S, van Hijum, Sacha A F T, van der Ven, Andre J, de Mast, Quirijn, Zomer, Aldert & de Jonge, Marien I (17.01.2017). Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease. mBio, 8 (1) (10 p.). Copyright © 2017 Tunjungputri et al..
Rozwandowicz, Marta, Brouwer, Michael S.M., Zomer, Aldert L., Bossers, Alex, Harders, Frank, Mevius, Dik J., Wagenaar, Jaap A. & Hordijk, Joost (2017). Plasmids of distinct IncK lineages show compatible phenotypes. Antimicrobial Agents and Chemotherapy, 61 (3) (5 p.).
Ahout, Inge M L, Brand, Kim H, Zomer, Aldert, van den Hurk, Wilhelma H, Schilders, Geurt, Brouwer, Marianne L, Neeleman, Chris, de Groot, Ronald & Ferwerda, Gerben (30.06.2017). Prospective observational study in two Dutch hospitals to assess the performance of inflammatory plasma markers to determine disease severity of viral respiratory tract infections in children. BMJ Open, 7 (6) (8 p.). © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted..
Kuipers, Kirsten, Jong, Wouter S P, van der Gaast-de Jongh, Christa E, Houben, Diane, van Opzeeland, Fred, Simonetti, Elles, van Selm, Saskia, de Groot, Ronald, Koenders, Marije I., Azarian, Taj, Pupo, Elder, van der Ley, Peter, Langereis, Jeroen D, Zomer, Aldert, Luirink, Joen & de Jonge, Marien I (2017). Th17-Mediated Cross Protection against Pneumococcal Carriage by Vaccination with a Variable Antigen. Infection and Immunity, 85 (10) (13 p.). Copyright © 2017 American Society for Microbiology..
Nebenzahl-Guimaraes, Hanna, van Laarhoven, Arjan, Farhat, Maha R, Koeken, Valerie Acm, Mandemakers, Jornt, Zomer, Aldert, van Hijum, Sacha Aft, Netea, Mihai G, Murray, Megan, van Crevel, Reinout & van Soolingen, Dick (01.06.2017). Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes. American Journal of Respiratory and Critical Care Medicine, 195 (11), (pp. 1519-1527).
Gilbert, Maarten J, Duim, Birgitta, Timmerman, Arjen J, Zomer, Aldert L & Wagenaar, Jaap A (21.08.2017). Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host. Scientific Reports, 7 (8 p.).
  Articles - 2016
Graaf-van Bloois, Linda van der, Miller, William G, Yee, Emma, Gorkiewicz, Gregor, Forbes, Ken J, Zomer, Aldert L, Wagenaar, Jaap A & Duim, Birgitta (2016). Campylobacter fetus Subspecies Contain Conserved Type IV Secretion Systems on Multiple Genomic Islands and Plasmids. PLoS One, 11 (4).
Murphy, James, Bottacini, Francesca, Mahony, Jennifer, Kelleher, Philip, Neve, Horst, Zomer, Aldert, Nauta, Arjen & van Sinderen, Douwe (2016). Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages. Scientific Reports, 6.
Gilbert, Maarten J, Miller, William G, Yee, Emma, Zomer, Aldert L, van der Graaf-van Bloois, Linda, Fitzgerald, Collette, Forbes, Ken J, Méric, Guillaume, Sheppard, Samuel K, Wagenaar, Jaap A & Duim, Birgitta (2016). Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages. Genome Biology and Evolution, 8 (6), (pp. 2006-2019) (14 p.). © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution..
Gilbert, Maarten J, Miller, William G, Yee, Emma, Kik, Marja, Zomer, Aldert L, Wagenaar, Jaap A & Duim, Birgitta (2016). Comparative genomics of Campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts. Genome Biology and Evolution, 8 (9), (pp. 3022-3029) (8 p.). © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution..
Capel, Elena, Zomer, Aldert L, Nussbaumer, Thomas, Bole, Christine, Izac, Brigitte, Frapy, Eric, Meyer, Julie, Bouzinba-Ségard, Haniaa, Bille, Emmanuelle, Jamet, Anne, Cavau, Anne, Letourneur, Franck, Bourdoulous, Sandrine, Rattei, Thomas, Nassif, Xavier & Coureuil, Mathieu (2016). Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. mBio, 7 (4) (13 p.). Copyright © 2016 Capel et al..
Jong, Victor L, Ahout, Inge M L, van den Ham, Henk-Jan, Jans, Jop, Zaaraoui-Boutahar, Fatiha, Zomer, Aldert, Simonetti, Elles, Bijl, Maarten A, Brand, H Kim, van IJcken, Wilfred F J, de Jonge, Marien I, Fraaij, Pieter L, de Groot, Ronald, Osterhaus, Albert D M E, Eijkemans, Marinus J, Ferwerda, Gerben & Andeweg, Arno C (2016). Transcriptome assists prognosis of disease severity in respiratory syncytial virus infected infants. Scientific Reports, 6.
van der Graaf-van Bloois, Linda, Duim, Birgitta, Miller, William G, Forbes, Ken J, Wagenaar, Jaap A & Zomer, Aldert (06.09.2016). Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production. BMC Genomics, 17 (10 p.).
  Articles - 2015
Kuipers, Kirsten, Gallay, Clement, Martínek, Václav, Rohde, Manfred, Martínková, Markéta, van der Beek, Samantha L, Jong, Wouter S P, Venselaar, Hanka, Zomer, Aldert, Bootsma, Hester, Veening, Jan-Willem & de Jonge, Marien I (21.12.2015). Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae. Molecular Microbiology © 2015 John Wiley & Sons Ltd..
Cremers, Amelieke J H, Mobegi, Fredrick M, de Jonge, Marien I, van Hijum, Sacha A F T, Meis, Jacques F, Hermans, Peter W M, Ferwerda, Gerben, Bentley, Stephen D & Zomer, Aldert L (2015). The post-vaccine microevolution of invasive Streptococcus pneumoniae. Scientific Reports, 5 (8 p.).
  Articles - 2014
Short, Kirsty R, Vissers, Marloes, de Kleijn, Stan, Zomer, Aldert L, Kedzierska, Katherine, Grant, Emma, Reading, Patrick C, Hermans, Peter W M, Ferwerda, Gerben & Diavatopoulos, Dimitri A (2014). Bacterial lipopolysaccharide inhibits influenza virus infection of human macrophages and the consequent induction of CD8+ T cell immunity. Journal of Innate Immunity, 6 (2), (pp. 129-139) (11 p.). Copyright © 2013 S. Karger AG, Basel..
Bottacini, Francesca, O'Connell Motherway, Mary, Kuczynski, Justin, O'Connell, Kerry Joan, Serafini, Fausta, Duranti, Sabrina, Milani, Christian, Turroni, Francesca, Lugli, Gabriele Andrea, Zomer, Aldert, Zhurina, Daria, Riedel, Christian, Ventura, Marco & van Sinderen, Douwe (2014). Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics, 15, (pp. 170).
de Gouw, Daan, Hermans, Peter W M, Bootsma, Hester J, Zomer, Aldert, Heuvelman, Kees, Diavatopoulos, Dimitri A & Mooi, Frits R (2014). Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally. PLoS One, 9 (1), (pp. e84523).
Mobegi, Fredrick M, van Hijum, Sacha Aft, Burghout, Peter, Bootsma, Hester J, de Vries, Stefan Pw, Jongh, Christa E van der Gaast-de, Simonetti, Elles, Langereis, Jeroen D, Hermans, Peter Wm, de Jonge, Marien I & Zomer, Aldert (2014). From microbial gene essentiality to novel antimicrobial drug targets. BMC Genomics, 15 (1).
Verhagen, Lilly M, de Jonge, Marien I, Burghout, Peter, Schraa, Kiki, Spagnuolo, Lorenza, Mennens, Svenja, Eleveld, Marc J, van der Gaast-de Jongh, Christa E, Zomer, Aldert, Hermans, Peter W M & Bootsma, Hester J (2014). Genome-wide identification of genes essential for the survival of Streptococcus pneumoniae in human saliva. PLoS One, 9 (2).
Wilson, Charlotte M, Loach, Diane, Lawley, Blair, Bell, Tracey, Sims, Ian M, O'Toole, Paul W, Zomer, Aldert & Tannock, Gerald W (2014). Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach. Applied and Environmental Microbiology, 80 (19), (pp. 6104-13) (10 p.). Copyright © 2014, American Society for Microbiology. All Rights Reserved..
van den Kieboom, Corné H, Ahout, Inge M L, Zomer, Aldert, Brand, Kim H, de Groot, Ronald, Ferwerda, Gerben & de Jonge, Marien I (26.09.2014). Nasopharyngeal gene expression, a novel approach to study the course of respiratory syncytial virus infection. European Respiratory Journal ©ERS..
Gouw, Daan de, Jonge, Marien I de, Hermans, Peter W M, Wessels, Hans J C T, Zomer, Aldert, Berends, Alinda, Pratt, Catherine, Berbers, Guy A, Mooi, Frits R & Diavatopoulos, Dimitri A (2014). Proteomics-identified Bvg-activated autotransporters protect against bordetella pertussis in a mouse model. PLoS One, 9 (8), (pp. e105011).
Cremers, Amelieke Jh, Zomer, Aldert L, Gritzfeld, Jenna F, Ferwerda, Gerben, van Hijum, Sacha Aft, Ferreira, Daniela M, Shak, Joshua R, Klugman, Keith P, Boekhorst, Jos, Timmerman, Harro M, de Jonge, Marien I, Gordon, Stephen B & Hermans, Peter Wm (15.12.2014). The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. Microbiome, 2, (pp. 44).
de Gouw, Daan, Serra, Diego O, de Jonge, Marien I, Hermans, Peter Wm, Wessels, Hans Jct, Zomer, Aldert, Yantorno, Osvaldo M, Diavatopoulos, Dimitri A & Mooi, Frits R (2014). The vaccine potential of Bordetella pertussis biofilm-derived membrane proteins. Emerging Microbes and Infections, 3 (8), (pp. e58).
O'Connell, Kerry Joan, Motherway, Mary O'Connell, Liedtke, Andrea, Fitzgerald, Gerald F, Paul Ross, R, Stanton, Catherine, Zomer, Aldert & van Sinderen, Douwe (2014). Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators. Applied and Environmental Microbiology, 80 (12), (pp. 3604-14) (11 p.).
  Articles - 2013
Verhagen, Lilly M, Zomer, Aldert, Maes, Mailis, Villalba, Julian A, Del Nogal, Berenice, Eleveld, Marc, van Hijum, Sacha Aft, de Waard, Jacobus H & Hermans, Peter Wm (2013). A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children. BMC Genomics, 14, (pp. 74).
Ainsworth, Stuart, Zomer, Aldert, de Jager, Victor, Bottacini, Francesca, van Hijum, Sacha A F T, Mahony, Jennifer & van Sinderen, Douwe (2013). Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. Genome Announcements, 1 (1).
de Vries, Stefan P W, Burghout, Peter, Langereis, Jeroen D, Zomer, Aldert, Hermans, Peter W M & Bootsma, Hester J (2013). Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions. Molecular Microbiology, 87 (1), (pp. 14-29) (16 p.). © 2012 Blackwell Publishing Ltd..
Short, Kirsty R, Reading, Patrick C, Brown, Lorena E, Pedersen, John, Gilbertson, Brad, Job, Emma R, Edenborough, Kathryn M, Habets, Marrit N, Zomer, Aldert, Hermans, Peter W M, Diavatopoulos, Dimitri A & Wijburg, Odilia L (2013). Influenza-induced inflammation drives pneumococcal otitis media. Infection and Immunity, 81 (3), (pp. 645-52) (8 p.).
Ainsworth, Stuart, Zomer, Aldert, Mahony, Jennifer & van Sinderen, Douwe (2013). Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Applied and Environmental Microbiology, 79 (16), (pp. 4786-98) (13 p.).
Johnston, Calum, Caymaris, Stéphanie, Zomer, Aldert, Bootsma, Hester J, Prudhomme, Marc, Granadel, Chantal, Hermans, Peter W M, Polard, Patrice, Martin, Bernard & Claverys, Jean-Pierre (2013). Natural genetic transformation generates a population of merodiploids in Streptococcus pneumoniae. PLoS Genetics, 9 (9), (pp. e1003819).
Langereis, Jeroen D, Zomer, Aldert, Stunnenberg, Hendrik G, Burghout, Peter & Hermans, Peter W M (2013). Nontypeable Haemophilus influenzae carbonic anhydrase is important for environmental and intracellular survival. Journal of Bacteriology, 195 (12), (pp. 2737-46) (10 p.).
Burghout, Peter, Zomer, Aldert, van der Gaast-de Jongh, Christa E, Janssen-Megens, Eva M, Françoijs, Kees-Jan, Stunnenberg, Hendrik G & Hermans, Peter W M (2013). Streptococcus pneumoniae folate biosynthesis responds to environmental CO2 levels. Journal of Bacteriology, 195 (7), (pp. 1573-82) (10 p.).
de Stoppelaar, Sacha F, Bootsma, Hester J, Zomer, Aldert, Roelofs, Joris J T H, Hermans, Peter W M, van 't Veer, Cornelis & van der Poll, Tom (2013). Streptococcus pneumoniae serine protease HtrA, but not SFP or PrtA, is a major virulence factor in pneumonia. PLoS One, 8 (11), (pp. e80062).
  Articles - 2012
Ruiz, Lorena, O'Connell-Motherway, Mary, Zomer, Aldert, de los Reyes-Gavilán, Clara G, Margolles, Abelardo & van Sinderen, Douwe (2012). A bile-inducible membrane protein mediates bifidobacterial bile resistance. Microbial Biotechnology, 5 (4), (pp. 523-35) (13 p.). © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd..
Alvarez-Martin, Pablo, Fernández, Matilde, O'Connell-Motherway, Mary, O'Connell, Kerry Joan, Sauvageot, Nicolas, Fitzgerald, Gerald F, MacSharry, John, Zomer, Aldert & van Sinderen, Douwe (2012). A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003. Applied and Environmental Microbiology, 78 (15), (pp. 5258-69) (12 p.).
Fanning, Saranna, Hall, Lindsay J, Cronin, Michelle, Zomer, Aldert, MacSharry, John, Goulding, David, Motherway, Mary O'Connell, Shanahan, Fergus, Nally, Kenneth, Dougan, Gordon & van Sinderen, Douwe (07.02.2012). Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proceedings of the National Academy of Sciences of the United States of America, 109 (6), (pp. 2108-13) (6 p.).
Ruiz, Lorena, Zomer, Aldert, O'Connell-Motherway, Mary, van Sinderen, Douwe & Margolles, Abelardo (2012). Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics. Applied and Environmental Microbiology, 78 (4), (pp. 1123-31) (9 p.).
Zomer, Aldert, Burghout, Peter, Bootsma, Hester J, Hermans, Peter W M & van Hijum, Sacha A F T (2012). ESSENTIALS - software for rapid analysis of high throughput transposon insertion sequencing data. PLoS One, 7 (8), (pp. e43012).
Zomer, Aldert, de Vries, Stefan P W, Riesbeck, Kristian, Meinke, Andreas L, Hermans, Peter W M & Bootsma, Hester J (2012). Genome sequence of Moraxella catarrhalis RH4, an isolate of seroresistant lineage. Journal of Bacteriology, 194 (24), (pp. 6969).
  Articles - 2011
Pokusaeva, Karina, O'Connell-Motherway, Mary, Zomer, Aldert, Macsharry, John, Fitzgerald, Gerald F & van Sinderen, Douwe (2011). Cellodextrin utilization by bifidobacterium breve UCC2003. Applied and Environmental Microbiology, 77 (5), (pp. 1681-90) (10 p.).
Zhurina, Daria, Zomer, Aldert, Gleinser, Marita, Brancaccio, Vincenco Francesco, Auchter, Marc, Waidmann, Mark S, Westermann, Christina, van Sinderen, Douwe & Riedel, Christian U (2011). Complete genome sequence of Bifidobacterium bifidum S17. Journal of Bacteriology, 193 (1), (pp. 301-2) (2 p.).
O'Connell Motherway, Mary, Zomer, Aldert, Leahy, Sinead C, Reunanen, Justus, Bottacini, Francesca, Claesson, Marcus J, O'Brien, Frances, Flynn, Kiera, Casey, Patrick G, Munoz, Jose Antonio Moreno, Kearney, Breda, Houston, Aileen M, O'Mahony, Caitlin, Higgins, Des G, Shanahan, Fergus, Palva, Airi, de Vos, Willem M, Fitzgerald, Gerald F, Ventura, Marco, O'Toole, Paul W & van Sinderen, Douwe (05.07.2011). Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proceedings of the National Academy of Sciences of the United States of America, 108 (27), (pp. 11217-22) (6 p.).
Cronin, Michelle, Zomer, Aldert, Fitzgerald, Gerald F & van Sinderen, Douwe (20.12.2011). Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression. Bioengineered Bugs, 3 (3), (pp. 157-67) (11 p.).
  Articles - 2010
Turroni, Francesca, Foroni, Elena, O'Connell Motherway, Mary, Bottacini, Francesca, Giubellini, Vanessa, Zomer, Aldert, Ferrarini, Alberto, Delledonne, Massimo, Zhang, Ziding, van Sinderen, Douwe & Ventura, Marco (2010). Characterization of the serpin-encoding gene of Bifidobacterium breve 210B. Applied and Environmental Microbiology, 76 (10), (pp. 3206-19) (14 p.).
Turroni, Francesca, Bottacini, Francesca, Foroni, Elena, Mulder, Imke, Kim, Jae-Han, Zomer, Aldert, Sánchez, Borja, Bidossi, Alessandro, Ferrarini, Alberto, Giubellini, Vanessa, Delledonne, Massimo, Henrissat, Bernard, Coutinho, Pedro, Oggioni, Marco, Fitzgerald, Gerald F, Mills, David, Margolles, Abelardo, Kelly, Denise, van Sinderen, Douwe & Ventura, Marco (09.11.2010). Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proceedings of the National Academy of Sciences of the United States of America, 107 (45), (pp. 19514-9) (6 p.).
Zomer, Aldert & van Sinderen, Douwe (2010). Intertwinement of stress response regulons in Bifidobacterium breve UCC2003. Beneficial microbes, 1 (2), (pp. 100-102) (3 p.).
Pokusaeva, Karina, Neves, Ana Rute, Zomer, Aldert, O'Connell-Motherway, Mary, MacSharry, John, Curley, Peter, Fitzgerald, Gerald F & van Sinderen, Douwe (2010). Ribose utilization by the human commensal Bifidobacterium breve UCC2003. Microbial Biotechnology, 3 (3), (pp. 311-23) (13 p.). © 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd..
  Articles - 2009
Zomer, Aldert, Fernandez, Matilde, Kearney, Breda, Fitzgerald, Gerald F, Ventura, Marco & van Sinderen, Douwe (2009). An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. Journal of Bacteriology, 191 (22), (pp. 7039-49) (11 p.).
Pokusaeva, Karina, O'Connell-Motherway, Mary, Zomer, Aldert, Fitzgerald, Gerald F & van Sinderen, Douwe (2009). Characterization of two novel alpha-glucosidases from Bifidobacterium breve UCC2003. Applied and Environmental Microbiology, 75 (4), (pp. 1135-43) (9 p.).
Ventura, Marco, Turroni, Francesca, Lima-Mendez, Gipsi, Foroni, Elena, Zomer, Aldert, Duranti, Sabrina, Giubellini, Vanessa, Bottacini, Francesca, Horvath, Philippe, Barrangou, Rodolphe, Sela, David A, Mills, David A & van Sinderen, Douwe (2009). Comparative analyses of prophage-like elements present in bifidobacterial genomes. Applied and Environmental Microbiology, 75 (21), (pp. 6929-36) (8 p.).
Ventura, Marco, Turroni, Francesca, Zomer, Aldert, Foroni, Elena, Giubellini, Vanessa, Bottacini, Francesca, Canchaya, Carlos, Claesson, Marcus J, He, Fei, Mantzourani, Maria, Mulas, Laura, Ferrarini, Alberto, Gao, Beile, Delledonne, Massimo, Henrissat, Bernard, Coutinho, Pedro, Oggioni, Marco, Gupta, Radhey S, Zhang, Ziding, Beighton, David, Fitzgerald, Gerald F, O'Toole, Paul W & van Sinderen, Douwe (2009). The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genetics, 5 (12), (pp. e1000785).
  Articles - 2008
van Hijum, Sacha A F T, Baerends, Richard J S, Zomer, Aldert L, Karsens, Harma A, Martin-Requena, Victoria, Trelles, Oswaldo, Kok, Jan & Kuipers, Oscar P (2008). Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons. BMC Bioinformatics, 9, (pp. 93).
  Articles - 2007
Martínez, Beatriz, Zomer, Aldert L, Rodríguez, Ana, Kok, Jan & Kuipers, Oscar P (2007). Cell envelope stress induced by the bacteriocin Lcn972 is sensed by the Lactococcal two-component system CesSR. Molecular Microbiology, 64 (2), (pp. 473-86) (14 p.).
Ventura, Marco, Zomer, Aldert, Canchaya, Carlos, O'Connell-Motherway, Mary, Kuipers, Oscar, Turroni, Francesca, Ribbera, Angela, Foroni, Elena, Buist, Girbe, Wegmann, Udo, Shearman, Claire, Gasson, Michael J, Fitzgerald, Gerald F, Kok, Jan & van Sinderen, Douwe (2007). Comparative analyses of prophage-like elements present in two Lactococcus lactis strains. Applied and Environmental Microbiology, 73 (23), (pp. 7771-80) (10 p.).
Wegmann, Udo, O'Connell-Motherway, Mary, Zomer, Aldert, Buist, Girbe, Shearman, Claire, Canchaya, Carlos, Ventura, Marco, Goesmann, Alexander, Gasson, Michael J, Kuipers, Oscar P, van Sinderen, Douwe & Kok, Jan (2007). Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. Journal of Bacteriology, 189 (8), (pp. 3256-70) (15 p.).
Zomer, Aldert L, Buist, Girbe, Larsen, Rasmus, Kok, Jan & Kuipers, Oscar P (2007). Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. Journal of Bacteriology, 189 (4), (pp. 1366-81) (16 p.).
  Articles - 2005
Kok, Jan, Buist, Girbe, Zomer, Aldert L, van Hijum, Sacha A F T & Kuipers, Oscar P (2005). Comparative and functional genomics of lactococci. FEMS Microbiology Reviews, 29 (3), (pp. 411-33) (23 p.).
van Hijum, Sacha A F T, Zomer, Aldert L, Kuipers, Oscar P & Kok, Jan (01.07.2005). Projector 2 - contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Research, 33 (Web Server issue), (pp. W560-6).
  Articles - 2003
Steen, Anton, Buist, Girbe, Leenhouts, Kees J, El Khattabi, Mohamed, Grijpstra, Froukje, Zomer, Aldert L, Venema, Gerard, Kuipers, Oscar P & Kok, Jan (27.06.2003). Cell wall attachment of a widely distributed peptidoglycan binding domain is hindered by cell wall constituents. Journal of Biological Chemistry, 278 (26), (pp. 23874-81) (8 p.).
van Hijum, Sacha A F T, Zomer, Aldert L, Kuipers, Oscar P & Kok, Jan (15.11.2003). Projector - automatic contig mapping for gap closure purposes. Nucleic Acids Research, 31 (22), (pp. e144).
  Articles - 2002
Kuipers, Oscar P, de Jong, Anne, Baerends, Richard J S, van Hijum, Sacha A F T, Zomer, Aldert L, Karsens, Harma A, den Hengst, Chris D, Kramer, Naomi E, Buist, Girbe & Kok, Jan (2002). Transcriptome analysis and related databases of Lactococcus lactis. Antonie van Leeuwenhoek, 82 (1-4), (pp. 113-22) (10 p.).
  Book parts / chapters - 2011
Ventura, Marco, Margolles, Abelardo, Turroni, Francesca, Zomer, Aldert, Clara, G & van Sinderen, Douwe (2011). Stress Responses of Bifidobacteria - Stress Responses of Lactic Acid Bacteria. Stress Responses of Lactic Acid Bacteria (pp. 323-347) (25 p.). Springer US.
  Book parts / chapters - 2010
Sánchez, Borja, Ruiz, Lorena, van Sinderen, Douwe, Margolles, Abelardo & Zomer, Aldert L (2010). Acid and Bile Resistance and Stress. In Baltasar Mayo & Douwe van Sinderen (Eds.), Bifidobacteria: Genomics and Molecular Aspects (pp. 71). Caister Academic press, Norfolk (UK).
  Patents - 2016
Zomer, A.L. & Poolman, Jan Theunis (06.02.2016). Meningitis b vaccine.
  Editorial activity - 2017
Zomer, A.L. (01.01.2017 01.01.2020) Peer reviewer Scientific Reports (Journal) Editor Scientific Rreports
  Publication peer-review - 2015
Zomer, A.L. (2015) Peer reviewer PLoS Genetics (Journal)
  Publication peer-review - 2014
Zomer, A.L. (2014 2015) Peer reviewer BMC Microbiology [E] (Journal)
Zomer, A.L. (2014 2015) Peer reviewer PLoS Computational Biology (Journal)
Zomer, A.L. (2014) Peer reviewer PLoS One (Journal)
  Consultancy - 2012
Zomer, A.L. (01.10.2012) Advisor Crucell Bioinformatics consultant
  Membership of committee - 2017
Zomer, A.L. (01.06.2017 01.06.2020) Chair Commissie Wetenschap KNVM-NVMM (External organisation) Treasurer Science Committee Royal Microbiology Society/Dutch Medical Microbiology society
Zomer, A.L. (01.01.2017 01.01.2020) Chair KNVM (External organisation) Chair division Microbial Bioinformatics. See https://www.knvm.org/knvm-divisions/microbial-bioinformatics
  Membership of committee - 2015
Zomer, A.L. (2015) Member Danish Council for Independent Research (External organisation) Danish Council for Independent Research International Review 2015
Zomer, A.L. (01.01.2015 01.01.2019) Chair World Health Organization (External organisation) Member WHO-Collaborating Center for Campylobacter
  Membership of committee - 2014
Zomer, A.L. (2014) Member William Harvey Research Institute (External organisation) WHRI Marie Curie cofund
  Membership of network - 2014
Zomer, A.L. (2014 2015) Member Royal Dutch Society for Microbiology (External organisation) Audit committee KNVM
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Gegenereerd op 2018-06-23 23:17:20
Additional functions and activities

All additional functions and activities are performed via my UU appointment. 

2017 - current: Royal Dutch Society for Microbiology (KNVM) / Dutch Society for Medical microbiology - Treasurer Committee Science

2016 - current: Royal Dutch Society for Microbiology (KNVM) - Chair division Microbial Bioinformatics. See https://www.knvm.org/knvm-divisions/microbial-bioinformatics

2014 - 2017: Royal Dutch Society for Microbiology (KNVM) - Audit committee

2012 - current: Bioinformatics Consultant Janssen Pharmaceuticals

2015- current: Member WHO-Collaborating Center for Campylobacter

2016 - current: Consultant WHO - WHO-AMR One Health - Genomics for Foodborne disease and Antimicrobial resistance detection.

Gegenereerd op 2018-06-23 23:17:20
Full name
dr. A.L. Zomer Contact details
Hugo R. Kruytgebouw

Padualaan 8
Room Z532
3584 CH  UTRECHT
The Netherlands


Phone number (direct) +31 30 253 6700
Androclusgebouw

Yalelaan 1
Room W310
3584 CL  UTRECHT
The Netherlands


Phone number (direct) +31 30 253 3603
Phone number (department) +31 30 253 1467

Please use my veterinary faculty contact information (Androclus building)

Gegenereerd op 2018-06-23 23:17:20
Last updated 13.04.2018