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Bosch, B., DeJesus, M.A.,*, Poulton, N.C., Zhang, W., Engelhart, C.A., Zaveri, A., Lavalette, S., Ruecker, N., Trujillo, C., Wallach, J.B., Li, S., Ehrt, S., Chait, B.T, Schnappinger, S., Rock, J.M. (2021). Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell. doi: 10.1016/j.cell.2021.06.033
Jinich, A., Zaveri, A., DeJesus, M.A., Flores-Bautista, E., Smith, C.M., Sassetti, C.M., Rock, J.M., Ehrt, S., Schnappinger, D., Ioerger, T.R., Rhee, K. (2021). Mycobacterium tuberculosis transposon sequencing database (MtbTnDB): a large-scale guide to genetic conditional essentiality. biorxiv.
Subramaniyam, S., DeJesus, M.A., Zaveri, A., Smith, C.M., Baker, R.E., Ehrt, S., Schnappinger, D., Sassetti, C.M., Ioerger, T.R. Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. BMC bioinformatics. 10.1186/s12859-019-3156-z
Xu, W., DeJesus, M.A., Rucker, N., Engelhart, C., Wright, M.G., Healy, C., Lin, K., Wang, R., Park, S.W., Ioerger, T.R., Schnappinger, D., and Ehrt, S. (2017). Chemical genomic interaction profiling reveals determinants of antibiotic susceptibility in Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy. doi: 10.1128/AAC.01334-17
Maxwell, S.A. and Wallis, D. and Zhou, N. and Baker, D. and Mousavi-Fard, S. and Loesch, K. and Galaviz, S. and Sun, Q. and Threadgill, D.M. and Rojas, C.M. and O'Brien, M. and Clubb, F.J. and Ioerger, T. and DeJesus, M. and Dong, W. and Seemann, G. and Fossum, T. and Sacchettini, J.C. (2017). Development of novel, non-toxic Rifamycins that reverse drug resistance in diffuse large b-cell lymphoma (DLBCL). Hematological Oncology, vol 35. doi: 10.1002/hon.2438_118
DeJesus, M.A., Nambi, S., Smith, C.M., Baker, R.E., Sassetti, C.M., and Ioerger, T.R. (2017). Statistical Analysis of Genetic Interactions in TnSeq Data. Nucleic Acids Research, 45(11):e93.
DeJesus, M.A., Gerrick, E.R., Xu, W., Park, S.W., Long, J.E., Boutte, C.C., Rubin, E.J., Schnappinger, D., Ehrt, S., Fortune, S.M., Sassetti, C.M., and Ioerger, T.R. (2017). Comprehensive essentiality analysis of the Mycobacterium tuberculosis genome via saturating transposon mutagenesis. mBio, 8(1):e02133-16.
Korte, J., Alber, M., Trujillo, C.M., Syson, K., Koliwer-Brandl, H., Deenen, R., Köhrer, K., DeJesus, M.A., Hartman, T., Jacobs Jr. W.R., Bornemann, S., Ioerger, T.R., Ehrt, S., Kalscheuer, R. (2016) Trehalose-6-Phosphate-Mediated Toxicity Determines Essentiality of OtsB2 in Mycobacterium tuberculosis In Vitro and in Mice. PLOS Pathogens 12(12): e1006043. doi: 10.1371/journal.ppat.1006043
Orsini, C., Setlow, B., DeJesus, M., Galaviz, S., Loesch, K., Ioerger, T.R., and Wallis, D. (2016). Behavioral and transcriptomic profiling of mice null for Lphn3, a gene implicated in ADHD and addiction. Molecular Genetics & Genomic Medicine 4(3):322-43.
DeJesus, M.A. and Ioerger, T.R. (2016). Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. Journal of Bioinformatics and Computational Biology, 14(3):1642004.
DeJesus, M.A., Ambadipudi, C., Baker, R., Sassetti, C., and Ioerger, T.R. (2015). TRANSIT - a Software Tool for Himar1 TnSeq Analysis.PLOS Computational Biology. 11(10):e1004401
Loesch, K., Galaviz, S., Sun, Q., DeJesus, M.A., Ioerger, T.R., Sacchettini, J.C. and Wallis, D. (2015). High throughput differentiation and screening of a library of mutant stem cell clones defines new host-based genes involved in rabies virus infection. Stem Cells, 33(8):2509-22.
Loesch, K., Clanton, R., Akabani, G., Deveau, M., DeJesus, M., Ioerger, T.R., Galaviz, S., Sacchettini, J.C., and Wallis, D. (2015). Functional genomics screening utilizing mutant mouse embryonic stem cells identifies novel radiation-response genes. PLOS ONE. 10(4): e0120534. doi:10.1371/journal.pone.0120534
DeJesus M.A. and Ioerger, T.R. (2015). Reducing type I errors in Tn-Seq experiments by correcting the skew in read count distributions. 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015).
Long J.E., DeJesus M., Ward D., Baker R.E., Ioerger T., Sassetti C.M. (2015). Identifying Essential Genes in Mycobacterium tuberculosis by Global Phenotypic Profiling. Methods Mol Biol. 2015;1279:79-95. doi: 10.1007/978-1-4939-2398-4_6.
DeJesus M.A. and Ioerger, T.R. (2014). Capturing uncertainty by modeling local transposon insertion frequencies improves discrimination of essential genes. IEEE Transactions on Computational Biology and Bioinformatics. vol.PP, no.99, pp.1,1 doi: 10.1109/TCBB.2014.2326857
DeJesus M.A. and Ioerger, T.R. (2013). A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. BMC Bioinformatics.
DeJesus M.A. and Ioerger, T.R. (2013). Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. ACM Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM-BCB), Washington, DC, Sept 22-25, 2013. Best Paper Award.
DeJesus M.A., Zhang, Y.J., Sassetti, C.M., Rubin, E.J., Sacchettini, J.C., and Ioerger, T.R. (2013). Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. Bioinformatics, 29(6):695-703.
DeJesus M.A., Sacchettini, J.C., and Ioerger, T.R. (2013). Reannoation of translational start sites in the genome of Mycobacterium tuberculosis. Tuberculosis, 93:18-25.
Griffin JE, Gawronski JD, DeJesus MA, Ioerger TR, Akerley BJ, et al. (2011) High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism. PLoS Pathogens, 7(9): e1002251. doi:10.1371/journal.ppat.1002251
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