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Scientific articles using BIONUMERICS

Since many customers or prospective customers request references dealing with the use of our software in a specific field or application, we maintain a database of peer-reviewed scientific publications that mention the use of BIONUMERICS.

The database of publications we have currently recorded is not complete but impressive enough: over 15,000 research articles in peer-reviewed journals! You can search for articles using Google Scholar with the search function below.


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Articles by scientists from the BIONUMERICS team:

2022

  • Mirsepasi-Lauridsen, Hengameh Chloé, Vranckx, Katleen, Nielsen, Henrik Vedel, Andersen, Lee O’Brien, Archampong, Timothy, Krogfelt, Karen Angeliki, & Petersen, Andreas Munk (2022). Substantial Intestinal Microbiota Differences Between Patients With Ulcerative Colitis From Ghana and Denmark. Frontiers in Cellular and Infection Microbiology, 114. DOI link.

2021

  • Goyal, Manisha, De Bruyne, Katrien, van Belkum, Alex, & West, Brian (2021). Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Infection, Genetics and Evolution, 90, 104730. DOI link.
  • Jamin, Casper, De Koster, Sien, van Koeveringe, Stefanie, De Coninck, Dieter, Mensaert, Klaas, De Bruyne, Katrien, Selva, Natascha Perales, Lammens, Christine, Goossens, Herman, Hoebe, Christian, & others (2021). Harmonization of whole-genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci. Microbial genomics, 7, . DOI link.
  • Nambiar, Remya, Tornheim, Jeffrey A, Diricks, Margo, De Bruyne, Katrien, Sadani, Meeta, Shetty, Anjali, & Rodrigues, Camilla (2021). Linezolid resistance in Mycobacterium tuberculosis isolates at a tertiary care centre in Mumbai, India. The Indian Journal of Medical Research, 154, 85. DOI link.
  • Papić, Bojan, Diricks, Margo, & Kučar, Darja (2021). Analysis of the global population structure of Paenibacillus larvae and outbreak investigation of American foulbrood using a stable wgMLST scheme. Frontiers in veterinary science, 8, 161. DOI link.
  • Rahmani, Alexandra, Vercauteren, Maaike, Vranckx, Katleen, Boyen, Filip, Bidault, Adeline, Pichereau, Vianney, Decostere, Annemie, Paillard, Christine, & Chiers, Koen (2021). MALDI-TOF MS as a promising tool to assess potential virulence of Vibrio tapetis isolates. Aquaculture, 530, 735729. DOI link.
  • Weigand, Michael R, Peng, Yanhui, Pouseele, Hannes, Kania, Dane, Bowden, Katherine E, Williams, Margaret M, & Tondella, M Lucia (2021). Genomic surveillance and improved molecular typing of Bordetella pertussis using wgMLST. Journal of Clinical Microbiology, 59, e02726-20. DOI link.

2020

  • Blanc, Dominique S, Magalhães, Bárbara, Koenig, Isabelle, Senn, Laurence, & Grandbastien, Bruno (2020). Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumericsTM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa. Frontiers in microbiology, 11, 1729. DOI link.
  • Goyal, Manisha, Hauben, Lysiane, Pouseele, Hannes, Jaillard, Magali, De Bruyne, Katrien, van Belkum, Alex, & Goering, Richard (2020). Retrospective Definition of Clostridioides difficile PCR Ribotypes on the Basis of Whole Genome Polymorphisms: A Proof of Principle Study. Diagnostics, 10, 1078. DOI link.
  • Gröschel, Matthias I, Meehan, Conor J, Barilar, Ivan, Diricks, Margo, Gonzaga, Aitor, Steglich, Matthias, Conchillo-Solé, Oscar, Scherer, Isabell-Christin, Mamat, Uwe, Luz, Christian F, & others (2020). The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nature communications, 11, 1-12. DOI link.
  • Jamin, Casper, de Koster, Sien, van Koeveringe, Stefanie, de Coninck, Dieter, Mensaert, Klaas, de Bruyne, Katrien, Selva, Natascha Perales, Lammens, Christine, Goossens, Herman, Hoebe, Christian JPA, & others (2020). Harmonization of whole genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci. bioRxiv, . DOI link.
  • Nouws, Stéphanie, Bogaerts, Bert, Verhaegen, Bavo, Denayer, Sarah, Crombé, Florence, De Rauw, Klara, Piérard, Denis, Marchal, Kathleen, Vanneste, Kevin, Roosens, Nancy HC, & others (2020). The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a National Reference Laboratory in a smaller country. Foods, 9, 1030. DOI link.
  • Rokney, Assaf, Valinsky, Lea, Vranckx, Katleen, Feldman, Noa, Agmon, Vered, Moran-Gilad, Jacob, & Weinberger, Miriam (2020). WGS-based prediction and analysis of antimicrobial resistance in Campylobacter jejuni isolates from Israel. Frontiers in cellular and infection microbiology, 10, 365. DOI link.
  • Slingerland, Bibi CGC, Vos, Margreet C, Bras, Willeke, Kornelisse, René F, De Coninck, Dieter, Van Belkum, Alex, Reiss, Irwin KM, Goessens, Wil HF, Klaassen, Corné HW, & Verkaik, Nelianne J (2020). Whole-genome sequencing to explore nosocomial transmission and virulence in neonatal methicillin-susceptible Staphylococcus aureus bacteremia. Antimicrobial Resistance \& Infection Control, 9, 1-7. DOI link.
  • Vercauteren, Maaike, Rahmani, Alexandra, Vranckx, Katleen, Boyen, Filip, Bidault, Adeline, Pichereau, Vianney, Decostere, Annemie, Paillard, Christine, & Chiers, Koen (2020). MALDI-TOF MS as a promising tool to assess potential virulence of Vibrio tapetis isolates. AQUACULTURE, 530, . DOI link.

2019

  • Gröschel, Matthias I, Meehan, Conor J, Barilar, Ivan, Diricks, Margo, Gonzaga, Aitor, Steglich, Matthias, Conchillo-Solé, Oscar, Scherer, Isabell-Christin, Mamat, Uwe, Luz, Christian F, & others (2019). The global phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. bioRxiv, 748954. DOI link.
  • Heinrichs, Amélie, Argudín, Maria Angeles, De Mendonça, Ricardo, Deplano, Ariane, Roisin, Sandrine, Dodémont, Magali, Coussement, Julien, Filippin, Lorenzo, Dombrecht, Jill, De Bruyne, Katrien, & others (2019). An Outpatient Clinic as a Potential Site of Transmission for an Outbreak of New Delhi Metallo-$\beta$-Lactamase--producing Klebsiella pneumoniae Sequence Type 716: A Study Using Whole-genome Sequencing. Clinical infectious diseases, 68, 993-1000. DOI link.
  • Rossen, John WA, Dombrecht, Jill, Vanfleteren, Diederik, De Bruyne, Katrien, van Belkum, Alex, Rosema, Sigrid, Lokate, Mariette, Bathoorn, Erik, Reuter, Sandra, Grundmann, Hajo, & others (2019). Epidemiological typing of Serratia marcescens isolates by whole-genome multilocus sequence typing. Journal of clinical microbiology, 57, e01652-18. DOI link.

2018

  • Dunne Jr, W Michael, Pouseele, Hannes, Monecke, Stefan, Ehricht, Ralf, & van Belkum, Alex (2018). Epidemiology of transmissible diseases: array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools. Infection, Genetics and Evolution, 63, 332-345. DOI link.
  • Giacometti, Federica, Piva, Silvia, Vranckx, Katleen, De Bruyne, Katrien, Drigo, Ilenia, Lucchi, Alex, Manfreda, Gerardo, & Serraino, Andrea (2018). Application of MALDI-TOF MS for the subtyping of Arcobacter butzleri strains and comparison with their MLST and PFGE types. International journal of food microbiology, 277, 50-57. DOI link.
  • Rokney, Assaf, Valinsky, Lea, Moran-Gilad, Jacob, Vranckx, Katleen, Agmon, Vered, & Weinberger, Miriam (2018). Genomic epidemiology of campylobacter jejuni transmission in Israel. Frontiers in microbiology, 9, 2432. DOI link.
  • Tanmoy, Arif M, Westeel, Emilie, De Bruyne, Katrien, Goris, Johan, Rajoharison, Alain, Sajib, Mohammad SI, van Belkum, Alex, Saha, Samir K, Komurian-Pradel, Florence, & Endtz, Hubert P (2018). Salmonella enterica Serovar Typhi in Bangladesh: exploration of genomic diversity and antimicrobial resistance. MBio, 9, e02112-18. DOI link.

2017

  • Dunne Jr, W Michael, Pouseele, Hannes, Monecke, Stefan, Ehricht, Ralf, & van Belkum, Alex (2017). Epidemiology of transmissible diseases: array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools. Infection, Genetics and Evolution, . DOI link.
  • Mahu, Maxime, Pasmans, Frank, Vranckx, Katleen, De Pauw, Nele, Maele, L Vande, Vyt, Philip, Vandersmissen, Tamara, Martel, An, Haesebrouck, Freddy, & Boyen, Filip (2017). Presence and mechanisms of acquired antimicrobial resistance in Belgian Brachyspira hyodysenteriae isolates belonging to different clonal complexes. Veterinary microbiology, 207, 125-132. DOI link.
  • Michiels, A., Vranckx, K., Piepers, S., Del Pozo Sacristan, R., Arsenakis, I., Boyen, F., Haesebrouck, F., & Maes, D. (2017). Impact of diversity of Mycoplasma hyopneumoniae strains on lung lesions in slaughter pigs. Veterinary Research, 48, 2. DOI link.
  • Moura, Alexandra, Criscuolo, Alexis, Pouseele, Hannes, Maury, Mylène M, Leclercq, Alexandre, Tarr, Cheryl, Björkman, Jonas T, Dallman, Timothy, Reimer, Aleisha, Enouf, Vincent, & others (2017). Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nature microbiology, 2, 16185. DOI link.
  • Rouffaer, Lieze Oscar, Baert, Kristof, Van den Abeele, Anne-Marie, Cox, Ivo, Vanantwerpen, Gerty, De Zutter, Lieven, Strubbe, Diederik, Vranckx, Katleen, Lens, Luc, Haesebrouck, Freddy, & others (2017). Low prevalence of human enteropathogenic Yersinia spp. in brown rats (Rattus norvegicus) in Flanders. PloS one, 12, e0175648. DOI link.
  • Vranckx, Katleen, De Bruyne, Katrien, & Pot, Bruno (2017). Analysis of MALDI-TOF MS Spectra using the BioNumerics Software. MALDI-TOF and Tandem MS for Clinical Microbiology, 539-562. DOI link.
  • Xu, Zhen, Olkun, Ali, Vranckx, Katleen, Mkrtchyan, Hermine V, Shah, Ajit J, Pot, Bruno, Cutler, Ronald R, & Shah, Haroun N (2017). Subtyping of Staphylococcus spp. Based upon MALDI-TOF MS Data Analysis. MALDI-TOF and Tandem MS for Clinical Microbiology, 563-578. DOI link.

2016

  • Cools, Piet, Ho, Erwin, Vranckx, Katleen, Schelstraete, Petra, Wurth, Bettina, Franckx, Hilde, Ieven, Greet, Van Simaey, Leen, Van Daele, Sabine, Verhulst, Stijn, De Baets, Frans, & Vaneechoutte, Mario (2016). Epidemic Achromobacter xylosoxidans strain among Belgian cystic fibrosis patients and review of literature. BMC Microbiology, 16, 122. DOI link.
  • De Vos, D., Pirnay, J. P., Bilocq, F., Jennes, S., Verbeken, G., Rose, T., Keersebilck, E., Bosmans, P., Pieters, T., Hing, M., Heuninckx, W., De Pauw, F., Soentjens, P., Merabishvili, M., Deschaght, P., Vaneechoutte, M., Bogaerts, P., Glupczynski, Y., Pot, B., van der Reijden, T. J., & Dijkshoorn, L. (2016). Molecular epidemiology and clinical impact of Acinetobacter calcoaceticus-baumannii complex in a Belgian burn wound center. PLoS ONE, 11, e0156237. DOI link.
  • Jackson, Brendan R, Tarr, Cheryl, Strain, Errol, Jackson, Kelly A, Conrad, Amanda, Carleton, Heather, Katz, Lee S, Stroika, Steven, Gould, L Hannah, Mody, Rajal K, & others (2016). Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clinical Infectious Diseases, 63, 380-386. DOI link.
  • Jerome, M., Mace, S., Dousset, X., Pot, B., & Joffraud, J. J. (2016). Genetic diversity analysis of isolates belonging to the Photobacterium phosphoreum species group collected from salmon products using AFLP fingerprinting. Int. J. Food Microbiol., 217, 101-109. DOI link.
  • Kluytmans-van den Bergh, M. F., Huizinga, P., Bonten, M. J., Bos, M., De Bruyne, K., Friedrich, A. W., Rossen, J. W., Savelkoul, P. H., & Kluytmans, J. A. (2016). Presence of mcr-1-positive Enterobacteriaceae in retail chicken meat but not in humans in the Netherlands since 2009. Eurosurveillance, 21, 12-18. DOI link.
  • Lindsey, Rebecca L, Pouseele, Hannes, Chen, Jessica C, Strockbine, Nancy A, & Carleton, Heather A (2016). Implementation of whole genome sequencing (WGS) for identification and characterization of shiga toxin-producing Escherichia coli (STEC) in the United States. Frontiers in Microbiology, 7, . DOI link.
  • Moura, Alexandra, Criscuolo, Alexis, Pouseele, Hannes, Maury, Mylène M, Leclercq, Alexandre, Tarr, Cheryl, Björkman, Jonas T, Dallman, Timothy, Reimer, Aleisha, Enouf, Vincent, & others (2016). Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nature Microbiology, 2, 16185. DOI link.
  • Oberle, M., Wohlwend, N., Jonas, D., Maurer, F. P., Jost, G., Tschudin-Sutter, S., Vranckx, K., & Egli, A. (2016). The technical and biological reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) based typing: Employment of bioinformatics in a multicenter study. PLoS ONE, 11, e0164260. DOI link.
  • Roisin, S, Gaudin, C, De Mendonça, R, Bellon, J, Van Vaerenbergh, K, De Bruyne, K, Byl, B, Pouseele, H, Denis, O, & Supply, P (2016). Pan-genome multilocus sequence typing and outbreak-specific reference-based single nucleotide polymorphism analysis to resolve two concurrent Staphylococcus aureus outbreaks in neonatal services. Clinical Microbiology and Infection, 22, 520-526. DOI link.

2015

  • Barfod, K. K., Vranckx, K., Mirsepasi-Lauridsen, H. C., Hansen, J. S., Hougaard, K. S., Larsen, S. T., Ouwenhand, A. C., & Krogfelt, K. A. (2015). The murine lung microbiome changes during lung inflammation and intranasal vancomycin treatment. Open Microbiol. J., 9, 167-179. DOI link.
  • Dhieb, C., Normand, A. C., L'Ollivier, C., Gautier, M., Vranckx, K., El Euch, D., Chaker, E., Hendrickx, M., Dalle, F., Sadfi, N., Piarroux, R., & Ranque, S. (2015). Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans. Journal of Mass Spectrometry, 50, 371-377. DOI link.
  • Pouseele, Hannes & Supply, Philip (2015). Chapter 10: Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis. In: Current and Emerging Technologies for the Diagnosis of Microbial Infections. (Vol. 42, p. 359-394). Academic Press. DOI link.
  • Zhang, L., Vranckx, K., Janssens, K., & Sandrin, T. R. (2015). Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA). J. Vis. Exp., e52064. DOI link.

2014

  • Pot, Bruno, Felis, Giovanna E., Bruyne, Katrien De, Tsakalidou, Effie, Papadimitriou, Konstantinos, Leisner, Jørgen, & Vandamme, Peter (2014). The genus Lactobacillus. In: Lactic Acid Bacteria. p. 249-353John Wiley & Sons, Ltd. DOI link.
  • Vandamme, Peter, De Bruyne, Katrien, & Pot, Bruno (2014). Phylogenetics and systematics. In: Lactic Acid Bacteria. p. 31-44John Wiley & Sons, Ltd. DOI link.
  • Vaz, Cátia, Francisco, Alexandre P., Silva, Mickael, Jolley, Keith A., Bray, James E., Pouseele, Hannes, Rothganger, Joerg, Ramirez, Mário, & Carriço, João A. (2014). TypOn: the microbial typing ontology. Journal of Biomedical Semantics, 5, 43. DOI link.
  • Wieme, Anneleen D., Spitaels, Freek, Aerts, Maarten, De Bruyne, Katrien, Van Landschoot, Anita, & Vandamme, Peter (2014). Effects of Growth Medium on Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectra: a Case Study of Acetic Acid Bacteria. Applied and Environmental Microbiology, 80, 1528-1538. DOI link.
  • Wieme, Anneleen D., Spitaels, Freek, Aerts, Maarten, De Bruyne, Katrien, Van Landschoot, Anita, & Vandamme, Peter (2014). Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. International Journal of Food Microbiology, 185, 41-50. DOI link.

2013

  • Bosch, Thijs, Verkade, Erwin, van Luit, Martijn, Pot, Bruno, Vauterin, Paul, Burggrave, Ronald, Savelkoul, Paul, Kluytmans, Jan, & Schouls, Leo (2013). High Resolution Typing by Whole Genome Mapping Enables Discrimination of LA-MRSA (CC398) Strains and Identification of Transmission Events. PLOS ONE, 8, e66493. DOI link.
  • Snauwaert, Isabel, Hoste, Bart, De Bruyne, Katrien, Peeters, Karolien, De Vuyst, Luc, Willems, Anne, & Vandamme, Peter (2013). Carnobacterium iners sp nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond. International Journal of Systematic and Evolutionary Microbiology, 63, 1370-1375. DOI link.

2011

  • Arias, Covadonga R, Oliveras-Fuster, Oscar, & Goris, Johan (2011). High intragenomic heterogeneity of 16S rRNA genes in a subset of Vibrio vulnificus strains from the western Mediterranean coast. International Microbiology, 13, 179. DOI link.
  • De Bruyne, Katrien, Slabbinck, Bram, Waegeman, Willem, Vauterin, Paul, De Baets, Bernard, & Vandamme, Peter (2011). Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning. Systematic and Applied Microbiology, 34, 20-29. DOI link.
  • Pouseele, Hannes, Vauterin, Paul, & Vauterin, Luc (2011). A resampling strategy for reliable network construction. Molecular Phylogenetics and Evolution, 60, 273-286. DOI link.

2010

  • Asteri, Ioanna-Areti, Papadimitriou, Konstantinos, Boutou, Effrossyni, Anastasiou, Rania, Pot, Bruno, Vorgias, Constantinos E., & Tsakalidou, Effie (2010). Characterization of pLAC1, a cryptic plasmid isolated from Lactobacillus acidipiscis and comparative analysis with its related plasmids. International Journal of Food Microbiology, 141, 222-228. DOI link.
  • Hyytia-Trees, Eija, Lafon, Patricia, Vauterin, Paul, & Ribot, Efrain M. (2010). Multilaboratory Validation Study of Standardized Multiple-Locus Variable-Number Tandem Repeat Analysis Protocol for Shiga Toxin-Producing Escherichia coli O157: A Novel Approach to Normalize Fragment Size Data Between Capillary Electrophoresis Platforms. Foodborne Pathogens and Disease, 7, 129-136. DOI link.

2009

  • Zaiß, N Henning, Rupnik, Maja, Kuijper, Ed J, Harmanus, Celine, Michielsen, Dolf, Janssens, Koen, & Nübel, Ulrich (2009). Typing Clostridium difficile strains based on tandem repeat sequences. BMC Microbiology, 9, 6. DOI link.

2007

  • De Bruyne, V., Al-Mulla, F., & Pot, B. (2007). Methods for microarray data analysis. Methods Mol. Biol., 382, 373-391. DOI link.

2005

  • Hunter, SB, Vauterin, P, Lambert-Fair, MA, Van Duyne, MS, Kubota, K, Graves, L, Wrigley, D, Barrett, T, & Ribot, E (2005). Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: Converting the national databases to the new size standard. Journal of Clinical Microbiology, 43, 1045-1050. DOI link.
  • Schouls, LM, van der Ende, A, van de Pol, I, Schot, C, Spanjaard, L, Vauterin, P, Wilderbeek, D, & Witteveen, S (2005). Increase in genetic diversity of Haemophilus influenzae serotype b (Hib) strains after introduction of hib vaccination in the Netherlands. Journal of Clinical Microbiology, 43, 2741-2749. DOI link.

2004

  • Schouls, LM, van der Heide, HGJ, Vauterin, L, Vauterin, P, & Mooi, FR (2004). Multiple-locus variable-number tandem repeat analysis of dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990s. Journal of Bacteriology, 186, 5496-5505. DOI link.

2003

  • Ritter, Kerry J, Carruthers, Ethan, Carson, C Andrew, Ellender, RD, Harwood, Valerie J, Kingsley, Kyle, Nakatsu, Cindy, Sadowsky, Michael, Shear, Brian, West, Brian, & others (2003). Assessment of statistical methods used in library-based approaches to microbial source tracking. Journal of water and health, 1, 209-223. DOI link.