Bernd W Brandt

Summary

Affiliation: Academic Centre for Dentistry Amsterdam
Country: The Netherlands

Publications

  1. pmc NatalieQ: a web server for protein-protein interaction network querying
    Mohammed El-Kebir
    Life Sciences, Centrum Wiskunde and Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands
    BMC Syst Biol 8:40. 2014
  2. pmc TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage
    Bernd W Brandt
    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
    Nucleic Acids Res 40:W82-7. 2012
  3. ncbi request reprint Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
    Ali May
    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU and AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands and NBIC Netherlands Bioinformatics Centre, Nijmegen, The NetherlandsDepartment of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU and AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands and NBIC Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
    Bioinformatics 30:1530-8. 2014
  4. pmc A protein prioritization approach tailored for the FA/BRCA pathway
    Anneke Haitjema
    Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
    PLoS ONE 8:e62017. 2013
  5. ncbi request reprint Comparing clustering and pre-processing in taxonomy analysis
    Marc J Bonder
    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, VU University Amsterdam, The Netherlands
    Bioinformatics 28:2891-7. 2012
  6. ncbi request reprint Protein analysis tools and services at IBIVU
    Bernd W Brandt
    Centre for Integrative Bioinformatics, IBIVU, VU University Amsterdam, De Boelelaan 1081a, Amsterdam, The Netherlands
    J Integr Bioinform 8:168. 2011

Collaborators

Detail Information

Publications6

  1. pmc NatalieQ: a web server for protein-protein interaction network querying
    Mohammed El-Kebir
    Life Sciences, Centrum Wiskunde and Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands
    BMC Syst Biol 8:40. 2014
    ..We recently developed Natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization...
  2. pmc TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage
    Bernd W Brandt
    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
    Nucleic Acids Res 40:W82-7. 2012
    ..TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/...
  3. ncbi request reprint Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
    Ali May
    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU and AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands and NBIC Netherlands Bioinformatics Centre, Nijmegen, The NetherlandsDepartment of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU and AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands and NBIC Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
    Bioinformatics 30:1530-8. 2014
    ..Here, we use in silico microbial datasets to better understand how the experimental data are transformed into taxonomic clusters by computational methods...
  4. pmc A protein prioritization approach tailored for the FA/BRCA pathway
    Anneke Haitjema
    Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
    PLoS ONE 8:e62017. 2013
    ..This approach may be useful for prioritization of putative novel FA or breast cancer genes from next generation sequencing efforts...
  5. ncbi request reprint Comparing clustering and pre-processing in taxonomy analysis
    Marc J Bonder
    Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam ACTA, University of Amsterdam and VU University Amsterdam, VU University Amsterdam, The Netherlands
    Bioinformatics 28:2891-7. 2012
    ..Recent reports suggest that data pre-processing should be performed before clustering. We assessed combinations of data pre-processing steps and clustering algorithms on cluster accuracy for oral microbial sequence data...
  6. ncbi request reprint Protein analysis tools and services at IBIVU
    Bernd W Brandt
    Centre for Integrative Bioinformatics, IBIVU, VU University Amsterdam, De Boelelaan 1081a, Amsterdam, The Netherlands
    J Integr Bioinform 8:168. 2011
    ..We provide an overview of these tools and their application...