1. Julien Dénéréaz, Elise Eray, Bimal Jana, Vincent de Bakker, Horia Todor, Tim van Opijnen, Xue Liu, Jan-Willem Veening. 2024. Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle. Under review and available at bioRxiv 2024.08.14.607739. doi.org/10.1101/2024.08.14.607739.

  2. Jana B, Liu X, Dénéréaz J, Park H, Leshchiner D, Liu B, Gallay C, Veening JW, van Opijnen T. 2024. CRISPRi-TnSeq: A genome-wide high-throughput tool for bacterial essential-nonessential genetic interaction mapping. Nature Microbiology doi.org/10.1038/s41564-024-01759-x.

  3. Yuhan Lyu, Fan Yang, Bharathi Sundaresh, Federico Rosconi, Tim van Opijnen, Jianmin Gao. 2024. Covalent Inhibition of a HostPathogen ProteinProtein Interaction Reduces the Infectivity of Streptococcus pneumoniae. JACS Au au-2024-00195c doi: 10.1021/jacsau.4c00195

  4. Pardue EJ, Sartorio MG, Jana B, Scott NE, Beatty W, Ortiz-Marquez JC, van Opijnen T, Hsu FF, Potter R, Feldman MF. 2024. Dual Membrane-spanning Anti-Sigma Factors Regulate Vesiculation in Gut Bacteroidota. PNAS 121 (10)e2321910121 doi: 10.1073/pnas.2321910121

  5. Rachel L. Huang, Delilah Jewel, Rachel E. Kelemen, Quan Pham, Tarah J. Yared, Shu Wang, Soumya Jyoti Singha Roy, Zeyi Huang, Samantha D. Levinson, Bharathi Sundaresh, Suyen Espinoza Miranda, Tim van Opijnen, and Abhishek Chatterjee. 2024. Directed Evolution of a Bacterial LeucyltRNA in Mammalian Cells for Enhanced Noncanonical Amino Acid Mutagenesis. ACS Synthetic Biology doi: 10.1021/acssynbio.4c00196

  6. Fabiana Bisaro, Clay D. Jackson-Litteken, Jenna C. McGuffey, Anna J. Hooppaw, Sophie Bodrog, Leila Jebeli, Juan C. Ortiz-Marquez, Tim van Opijnen, Nichollas E. Scott, Gisela Di Venanzio, Mario F. Feldman. 2024. Diclofenac sensitizes multi-drug resistant Acinetobacter baumannii to colistin. under review and available at bioRxiv 2024.05.17.594771; doi: 10.1101/2024.05.17.594771

  7. Indu Warrier, Ariana Perry, Sara M. Hubbell, Matthew Eichelman, Tim van Opijnen, Michelle M. Meyer. 2024. Evaluation of the fitness benefit conferred by RNA cis-regulators to Streptococcus pneumoniae during infection. PLoS Genetics doi.org/10.1371/journal.pgen.1011188

  8. Delilah Jewel; Rachel E. Kelemen; Rachel L. Huang; Zeyu Zhu; Bharathi Sundaresh; Kaitlin Malley; Quan Pham; Conor Loynd; Zeyi Huang; Tim van Opijnen, Abhishek Chatterjee. 2024 Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis. Angewandte Chemie Int. Ed. e202316428. https://doi.org/10.1002/anie.202316428

  9. Dao T., Nishimoto A., van Opijnen T. and Rosch J.W. 2024. Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones. mBio Feb 14;15(2):e0282823. https://doi.org/10.1128/mbio.02828-23

  10. Michael Geiwitz, Owen Page, Tio Marello, Narendra Kumar, Stephen Hummel, Vsevolod Belosevich, Qiong Ma, Tim van Opijnen, Bruce Batten, Michelle Meyer, Kenneth S. Burch. 2024. Graphene Multiplexed Sensor for Point-of-Need Viral Wastewater-Based Epidemiology. ACS Applied Bio Materials in press.

  11. Price SL, Thibault D, Garrison TM, Brady A, Guo H, Kehl-Fie TE, Garneau-Tsodikova S, Perry RD, van Opijnen T, Lawrenz MB. 2023. Droplet Tn-Seq identifies the primary secretion mechanism for yersiniabactin in Yersinia pestis. EMBO Reports. Oct 9;24(10):e57369. doi: 10.15252/embr.202357369

  12. Frisinger FS, Jana B, Ortiz-Marquez JC, van Opijnen T, Donadio S, Guardabassi L. 2023. LptD depletion disrupts morphological homeostasis and upregulates carbohydrate metabolism in Escherichia coli. FEMS Microbes. ;4:xtad013. doi: 10.1093/femsmc/xtad013.

  13. Bai J, Raustad N, Denoncourt J, van Opijnen T, Geisinger E. 2023. Genome-wide phage susceptibility analysis in Acinetobacter baumannii reveals capsule modulation strategies that determine phage infectivity. PLoS Pathogens. Jun;19(6):e1010928. doi: 10.1371/journal.ppat.1010928.

  14. Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Cao X, Malley K, Huang Z, Pasha M, Anthony J, van Opijnen T, Chatterjee A. 2023. Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells. Nature Methods. Jan;20(1):95-103. doi: 10.1038/s41592-022-01706-w

  15. Nishimoto AT, Dao TH, Jia Q, Ortiz-Marquez JC, Echlin H, Vogel P, van Opijnen T, Rosch JW. 2022. Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae. Cell Reports. Dec 13;41(11):111835. doi: 10.1016/j.celrep.2022.111835

  16. Federico Rosconi, Emily Rudmann, Jien Li, Defne Surujon, Jon Anthony, Matthew Frank, Dakota S. Jones, Charles Rock, Jason W. Rosch, Christopher D. Johnston, Tim van Opijnen. 2022. A bacterial pan-genome makes gene essentiality strain-dependent and evolvable. Nature Microbiology 10.1038/s41564-022-01208-7 (Accompanying News & Views: https://doi.org/10.1038/s41564-022-01231-8)

  17. Leshchiner D., Rosconi F., Sundaresh B., Rudmann E., Nieto L., Nishimoto A.T., Wood S.J., Jana B., Bujan N., Li K., Gao J., Frank M., Reeve S.M., Lee R.E., Rock C.O., Rosch J.W. and van Opijnen T. 2022. A genome-wide atlas of antibiotic susceptibility-targets, and pathways to tolerance in S. pneumoniae. Nature Communications 13, 3165 | 10.1038/s41467-022-30967-4

  18. Huo W. Busch L.M., Hamami E., Hernandez-Bird J., Marshall C.W., Geisinger E., Cooper., V.S., van Opijnen T., Rosch J.W., and Isberg R.R. 2022. Immunosuppression broadens evolutionary pathways to treatment failure during Acinetobacter baumannii pneumonia. Nature Microbiology 7, 796-809

  19. Kumar N., Muhit R.. Geiwitz M., KhanN.I., Catalano M., Ortiz-Marquez J.C., Weber, A., Dweik B., Xi L., van Opijnen T., Argun A., Burch K. 2022. Rapid, multianalyte detection of opioid metabolites in wastewater. ACS Nano 16, 3, 3704-3714 | doi.org/10.1021/acsnano.1c07094

  20. Rachel E. Kelemen, Delilah Jewel, Rachel L. Huang, Zeyu Zhu, Xiaofu Cao, Muhammad Pasha, Jon Anthony, Tim van Opijnen, Abhishek Chatterjee. 2022. Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells. In press at Nature Methods | bioRxiv doi.org/10.1101/2022.01.21.477302

  21. Alvarez-Manzo H.S., Davidson R.K., Van Cauwelaert de Wyels J., Cotten K.L., Nguyen B., Zhu Z., Anthony J.S., van Opijnen T., Davis K.M. 2022. Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications. PLoS Pathogens https://doi.org/10.1371/journal.ppat.1010556

  22. Anna Hooppaw, Jenna McGuffey, Gisela Di Venanzio, Juan Ortiz-Marquez, Brent Weber, Tasia Joy Lightly, Tim van Opijnen, Nichollas Scott, Silvia Cardona, and Mario Feldman. 2022. The phenylacetic acid catabolic pathway regulates antibiotic and oxidative stress responses in Acinetobacter. mBio doi.org/10.1128/mbio.01863-21

  23. Stevens E., Morse D., Duggan S., Brignoli T., Recker M., Lees J., Bentley S., Croucher N., Wilson D., Earles S., Nobbs A., Jenkinson H., van Opijnen T., Thibault D., Wilkinson O., Dillingham M., and Massey R.C. 2022. Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae. Microbial Genomics Vol. 8 Issue 4. | https://doi.org/10.1099/mgen.0.000784

  24. Bharathi Sundaresh, Shuying Xu, Michael K. Mansour, Brian Noonen, John M. Leong, Tim van Opijnen. 2021. Host-informed therapies for the treatment of pneumococcal pneumonia. Trends in Molecular Medicine Volume 27, ISSUE 10, P971-989, | doi.org/10.1016/j.molmed.2021.07.008

  25. Smith A.P., Lane L.C., van Opijnen T., Woolard S., Carter R., Iverson A., Burnham C., Vogel P., Roeber D., Hochu G., McCullers J., Johnson M., Rosch J., Smith A.M. 2021. Dynamic pneumococcal genetic adaptations support bacterial growth and inflammation during coinfection with influenza. Infection and Immunity Vol. 89, No. 7 | doi.org/10.1128/IAI.00023-21.

  26. Bai J., Dai Y., Farinha A., Tang A.Y., Syal S., Vargas-Cuebas G., van Opijnen T., Isberg R.R. and Geisinger E. 2021. Essential gene analysis in Acinetobacter baumannii by high-density transposon mutagenesis and CRISPR interference. J. Bac. 203 (12) e00565-20; DOI: 10.1128/JB.00565-20.

  27. * Zhu, Z.,* Surujon, D., Ortiz-Marquez, J.C., Huo, W., Isberg, R.R. and van Opijnen T. 2020. Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity. Nature Communications 11, 4365. https://doi.org/10.1038/s41467-020-18134-z

  28. Cain A.K., Barquist L., Goodman A.L., Paulsen I.T., Parkhill J. and van Opijnen T. 2020. Reflecting on a Decade of Transposon-Insertion Sequencing. Nature Reviews Genetics 21, 526–540, doi.org/10.1038/s41576-020-0244-x.

  29. Stacie A. Clark, Derek Thibault, Lauren M. Shull, Kimberly M. Davis, Emily Aunins, Tim van Opijnen* and Ralph R Isberg*. 2020. Topologically correct synthetic reconstruction of pathogen social behavior found in deep tissue sites. eLife 2020;9:e58106 doi: 10.7554/eLife.58106 (*corresponding authors).

  30. Kelly, M., Cambray, S., McCarthy, K., Wang, W.,  Geisinger, E., Ortiz-Marquez, J., van Opijnen, T., Gao, J. 2020. Peptide Probes of Colistin Resistance Discovered via Chemically Enhanced Phage Display. ACS Infectious Diseases 6 (9), 2410-2418 doi: 10.1021/acsinfecdis.0c00206

  31. Tim van Opijnen and Henry L. Levin. 2020. Transposon Insertion Sequencing, a Global Measure of Gene Function. Annual Review of Genetics 54:1 doi.org/10.1146/annurev-genet-112618-043838.

  32.  Narendra Kumar, Mason Gray, Juan C. Ortiz-Marquez, Andrew Weber, Cameron R. Desmond, Avni Argun, Tim van Opijnen, Kenneth S. Burch. 2020. Detection of a multi-disease biomarker in Saliva with Graphene Field Effect Transistors. Medical Devices & Sensors doi:10.1002/mds3.10121.

  33. Ortiz-Marquez J.C., Zhu Z., Surujon D., Wood S., Rosconi F., and van Opijnen T. 2020. A pan-genomic perspective on the emergence, maintenance and predictability of antibiotic resistance. Chapter in: The Pangenome | Editors: Hervé Tettelin and Duccio Medini | freely available https://link.springer.com/chapter/10.1007/978-3-030-38281-0_8

  34. Surujon D., Bento J., and van Opijnen T. 2020. Boundary-Forest Clustering: Large-Scale Consensus Clustering of Biological Sequences. under review and availabe at bioRxiv https://doi.org/10.1101/2020.04.28.065870 and on GitHub.

  35. Edward Geisinger, Nadav J. Mortman, Yunfei Dai, Murat Cokol, Sapna Syal, Andrew Farinha, Delaney Fisher, Amy Tang, David Lazinski, Stephen Wood, Jon Anthony, Tim van Opijnen, Ralph R. Isberg. 2020. Antibiotic hypersensitivity signatures identify targets for attack in the Acinetobacter baumannii cell envelope. Nature Communications 11, 4522 https://doi.org/10.1038/s41467-020-18301-2.

  36. *Kumar N., *Wenjian W., *Ortiz-Marquez J.C., Catalano M., Gray M., Biglari N., Kitadai H., Ling X., **Gao J., **van Opijnen T., **Burch K. 2020. Rapid, selective and single cell electrical detection of antibiotic resistant bacteria. Biosensors and Bioelectronics 156, 112123; https://doi.org/10.1016/j.bios.2020.112123; *Shared 1st; **Corresponding authors.

  37. Surujon D. and van Opijnen T. 2020. ShinyOmics: Collaborative Exploration of Omics-Data. BMC Bioinformatics 21, 22 doi:10.1186/s12859-020-3360-x | also available at GitHub.

  38. Thibault D., Jensen P.A., Wood S., Qabar C., Clark S., Shainheit M.G., Isberg R.R. and van Opijnen T. 2019. Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes. Nature Communications 10, 5729 doi:10.1038/s41467-019-13719-9

  39. Hannah M Rowe, Erik Karlsson, Haley Echlin, Ti-Cheng Chang, Lei Wang, Tim van Opijnen, Stanley B. Pounds, Stacey Schultz-Cherry, Jason W. Rosch. 2019. Bacterial Factors Required for Transmission of Streptococcus pneumoniae in Mammalian Hosts. Cell Host & Microbe, Volume 25 (6) p884-891.

  40. Geisinger E., Vargas-Cuebas G., Mortman N.J., Syal S., Wainwright W., Lazinski D.W., Wood S., Zhu Z., Anthony J.S., van Opijnen T., Isberg R.R. 2019. The landscape of intrinsic and evolved fluoroquinolone resistance in Acinetobacter baumannii includes suppression of drug-induced prophage replication. mBio 10:e01127-19

  41. McCarthy K.A., Kelly M.A., Li K., Cambray S., Hosseini A.S., van Opijnen T., Gao J. 2018. Phage Display of Dynamic Covalent Binding Motifs Enables Facile Development of Targeted Antibiotics. JACS 140 (19), pp 6137–6145, doi: 10.1021/jacs.8b02461.

  42. Warrier I., Ram-Mohan N., Zhu Z., Hazery A., Meyer M.M., van Opijnen T. 2018. The Transcriptional landscape of Streptococcus pneumoniae reveals a complex operon architecture and abundant riboregulation critical for growth and virulence. bioRxiv 286344; doi: https://doi.org/10.1101/286344 | PLOS Pathogens https://doi.org/10.1371/journal.ppat.1007461.

  43. 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

  44. 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 - scripts and manual available at https://vanopijnenlab.github.io/MAGenTA/

  45. 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).

  46. 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

  47. 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.

  48. *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).

  49. 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.

  50. 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.

  51. van Opijnen T., and Camilli A. 2012. A fine scale phenotype-genotype virulence map of a bacterial pathogen. Genome Research, 22 : 2541-2551.

  52. *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).

  53. 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.

  54. 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.

  55. 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.

  56. 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.

  57. van Opijnen T. and Berkhout B. 2005. The host environment drives HIV-1 fitness. Rev. Med. Virol. 15: 219-233. PMID: 15942979.

  58. 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.

  59. 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.

  60. 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.

  61. 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.

  62. 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.

  63. 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.

  64. 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.

  65. 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. -