1. *Jensen, P., *Zhu Z. and van Opijnen T. 2017. Antibiotics disrupt coordination between transcriptional and phenotypic stress responses in pathogenic bacteria. Cell Reports, volume 20, Issue 7, 1705-1716 (* equal 1st author contribution)
  2. *McCoy K.M., *Antonio M.L. and van Opijnen T. 2017. MAGenTA; a Galaxy implemented tool for complete Tn-Seq analysis and data visualization. Bioinformatics May 11. doi: 10.1093/bioinformatics/btx320(* equal 1st author contribution - scripts and manual available at https://vanopijnenlab.github.io/MAGenTA/)
  3. *Jensen, P., *Zhu Z. and van Opijnen T. 2016. Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome. (available at bioRxiv http://dx/doi.org/10/1101/071704; * equal 1st author contribution)
  4. van Opijnen T., Dedrick S. and Bento J. 2016. Strain dependent genetic networks for antibiotic-sensitivity in a bacterial pathogen with a large pan-genome. PLoS Pathogens. September 8, 2016, http://dx.doi.org/10.1371/journal.ppat.1005869
  5. van Opijnen T., Lazinski, D and Camilli A. 2015. Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms. Current protocols in Molecular Biology Feb 2; 36: 1E.3.1-1E.3.24. PMID: 25641100.
  6. *Carter R., *Wolf J., *Van Opijnen T., Muller M., Obert C., Burnham C., Mann B., Li Y., Hayden R.T., Pestina T., Persons D., Camilli A., Flynn P.M.,Tuomanen E.I., Rosch J.W. 2014. Genomic analysis of pneumococci from children with sickle cell disease reveals disease-specific bacterial adaptations and deficits in current clinical interventions. Cell Host and Microbe, 15(5):587-99. PMID: 248432453 (* equal 1st author contribution).
  7. Van Opijnen T., Lazinski D.W., and Camilli A. 2014. Genome-wide fitness and genetic interactions determined by Tn-seq, a high throughput massively parallel sequencing method for microorganisms. Current protocols in Molecular Biology, 106:7.16.1-7.16.24.
  8. Van Opijnen T., and Camilli A. 2013. Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature Reviews Microbiology July 11: 435-442.
  9. Van Opijnen T., and Camilli A. 2012. A fine scale phenotype-genotype virulence map of a bacterial pathogen. Genome Research, 22 : 2541-2551.
  10. *Mann B., *Van Opijnen T., Wang J., Obert C., Wang Y.D., Carter R., McGoldrick D.J., Ridout G., Camilli A., Tuomanen E.I., Rosch J.W. 2012. Control of virulence by small RNAs in Streptococcus pneumoniae. Plos Pathogens Jul;8(7):e1002788. (* equal 1st author contribution).
  11. Van Opijnen T., and Camilli A. 2010. Genome-wide fitness and genetic interactions determined by Tn-seq, a high throughput massively parallel sequencing method for microorganisms. Current protocols in Microbiology, Chapter 1: Unit1E.3. PMID: 21053251.
  12. Van Opijnen T., Bodi K.L., and Camili A. 2009. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nature Methods 6(10): 767-772.  PMID: 19767758.
  13. Van Opijnen T., de Ronde, A., Boerlijst, M.C., and Berkhout B. 2007. Adaptation of HIV-1 depends on the host-cell environment. PLoS ONE 2(3): e271. PMID: 17342205.
  14. Van Opijnen T., Boerlijst, M.C., and Berkhout B. 2006. Effects of random mutations in the Human Immunodeficiency Virus Type 1 transcriptional promoter on viral fitness in different Host Cell environments. J. Virology 80:6678-6685. PMID: 16775355.
  15. Van Opijnen T. and Berkhout B. 2005. The host environment drives HIV-1 fitness. Rev. Med. Virol. 15: 219-233. PMID: 15942979.
  16. Van Opijnen T., Baudry E., Bartos J., Baldo L. and Werren J.H. 2005. Genetic variability in the three genomes of Nasionia: Nuclear, mitochondrial and Wolbachia. Insect Molecular Biology 14:653-663. PMID: 16313565.
  17. Velthuis, B., Yang, W., Van Opijnen, T. and Werren, J.H. 2005. Genetics of female mate discrimination to heterospecific males in Nasonia (Hym., Pteromalidae). Animal Behaviour 69: 1107-1120.
  18. Lemieux AM, Pare ME, Audet B, Legault E, Lefort S, Boucher N, Landry S, van Opijnen T., Berkhout B, Naghavi MH, Tremblay MJ, Barbeau B. 2004. T-cell activation leads to poor activation of the HIV-1 clade E long terminal repeat and weak association of nuclear factor-kappaB and NFAT with its enhancer region. J Biol Chem. 17:52949-52960. PMID: 15466412.
  19. Van Opijnen, T., Kamoschinski J., Jeeninga, R., and Berkhout, B. 2004. The Human Immunodeficiency Virus Type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication. J. Virology 78 (13) 6883-6890. PMID: 15194764.
  20. Van Opijnen, T., Jeeninga, R.E., Boerlijst, M.C. and Berkhout, B. 2004. Human Immunodeficiency Virus Type 1 subtypes have a distinct long terminal repeat that determines the replication rate in a host-cell-specific manner. J. Virology 78 (7) 3675-3683. PMID: 15016888.
  21. Vala, F., Van Opijnen, T., Breeuwer, J.A.J. and Sabelis M.W. 2003. Genetic conflicts over Sex Ratio: Mite-Endosymbiont Interactions. The American Naturalist 161: 254-266. PMID: 12675371.
  22. Weeks, A.R., Van Opijnen, T. and Breeuwer, J.A.J. 2000. AFLP fingerprinting for assessing intraspecific variation and genome mapping in mites. Exp. Appl. Acarol 24:775-793. PMID: 11345315.
  23. Van Opijnen, T. and Breeuwer, J.A.J. 1999. High temperatures eliminate Wolbachia, a cytoplasmic incompatibility inducing endosymbiont, from the two-spotted spider mite. Exp. Appl. Acarol. 23: (11) 871-881. PMID: 10668862.