% Publications of Michael A. DeJesus -- the single source of truth. % % Used by: the CV (this repo), the research statement, and mad-lab.org. % Keep entries in the order the CV lists them: newest first within each % category (journal articles, preprints, proceedings, chapter, posters); % the CV and website preserve file order among papers from the same year. % % Standard fields are what BibTeX styles print. Extra fields, ignored by % BibTeX, carry what the CV and website need: % author+an biblatex-style author annotations: cofirst / cosenior % (e.g. {1=cofirst; 2=cofirst; 22=cosenior}) % keywords preprint | poster (otherwise the entry type decides the section) % pubstate e.g. {Accepted in principle}; CV shows it instead of a year, % the website leaves the entry out % award e.g. {Best Paper Award} % Theses (@mastersthesis, @phdthesis) appear on the CV only, not the website. % `note` is printed by BibTeX styles (research statement), not by the CV/website. @article{theriault2026crispri, author = {Theriault, Monique E. and Wong, Andrew I. and DeJesus, Michael A. and Pisu, Davide and Lee, B. N. R. and Kirukubar, Greana and Li, Shuqi and Wallach, Joshua B. and Schnappinger, Dirk and L{\^e}-Bury, Gabrielle and Russell, David G. and Rock, Jeremy M.}, title = {Utilization of a {CRISPRi-based} ex vivo challenge model to reveal temporally dependent gene essentiality in intracellular {Mycobacterium} tuberculosis}, journal = {mBio}, year = {2026}, volume = {17}, number = {5}, pages = {e0061026}, doi = {10.1128/mbio.00610-26} } @article{eckartt2026attenuation, author = {Eckartt, Kathryn A. and Munsamy-Govender, Vanisha and Qui{\~n}ones-Garcia, Stefany and DeJesus, Michael A. and Ju, Xiangwu and Liu, Shixin and Rock, Jeremy M.}, title = {Transcription attenuation amplifies collateral vulnerabilities in rifampicin-resistant {Mycobacterium} tuberculosis}, journal = {Nature Microbiology}, year = {2026}, volume = {11}, pages = {1696--1710}, doi = {10.1038/s41564-026-02357-9} } @article{jinich2025mtbtndb, author = {Jinich, Adrian and Zaveri, Anisha and DeJesus, Michael A. and Spencer, Amanda and Almada-Monter, Ricardo and Flores-Bautista, Emanuel and Smith, Clare M. and Sassetti, Christopher M. and Rock, Jeremy M. and Ehrt, Sabine and Schnappinger, Dirk and Ioerger, Thomas R. and Rhee, Kyu Y.}, title = {The {Mycobacterium} tuberculosis {Transposon} {Sequencing} {Database} ({MtbTnDB}): {A} large-scale guide to genetic conditional essentiality}, journal = {Molecular Microbiology}, year = {2025}, volume = {124}, number = {1}, pages = {91--101}, doi = {10.1111/mmi.15370} } @article{mishra2025transmission, author = {Mishra, S. and Singh, P. R. and Hu, X. and Lopez-Quezada, L. and Jinich, A. and Jahn, R. and Geurts, L. and Shen, N. and DeJesus, M. A. and Hartman, T. and Rhee, K. and Zimmerman, M. and Dartois, V. and Jones, R. M. and Jiang, X. and Almada-Monter, R. and Bourouiba, L. and Nathan, C.}, title = {Candidate transmission survival genome of {Mycobacterium tuberculosis}}, journal = {Proceedings of the National Academy of Sciences}, year = {2025}, volume = {122}, number = {10}, pages = {e2425981122}, doi = {10.1073/pnas.2425981122} } @article{eckartt2024nusg, author = {Eckartt, Kathryn A. and Delbeau, Madeleine and Munsamy-Govender, Vanisha and DeJesus, Michael A. and Azadian, Zachary A. and Reddy, Abhijna K. and Chandanani, Joshua and Poulton, Nicholas C. and Qui{\~n}ones-Garcia, Stefany and Bosch, Barbara and Landick, Robert and Campbell, Elizabeth A. and Rock, Jeremy M.}, title = {Compensatory evolution in {NusG} improves fitness of drug-resistant {M}. tuberculosis}, journal = {Nature}, year = {2024}, volume = {628}, number = {8006}, pages = {186--194}, doi = {10.1038/s41586-024-07206-5} } @article{poulton2024whib7, author = {Poulton, Nicholas C. and DeJesus, Michael A. and Munsamy-Govender, Vanisha and Kanai, Mariko and Roberts, Cameron G. and Azadian, Zachary A. and Bosch, Barbara and Lin, Karl Matthew and Li, Shuqi and Rock, Jeremy M.}, title = {Beyond antibiotic resistance: {The} {whiB7} transcription factor coordinates an adaptive response to alanine starvation in mycobacteria}, journal = {Cell Chemical Biology}, year = {2024}, volume = {31}, number = {4}, pages = {669--682.e7}, doi = {10.1016/j.chembiol.2023.12.020} } @article{choudhery2024dose, author = {Choudhery, Sanjeevani and DeJesus, Michael A. and Srinivasan, Aarthi and Rock, Jeremy M. and Schnappinger, Dirk and Ioerger, Thomas R.}, title = {A dose-response model for statistical analysis of chemical genetic interactions in {CRISPRi} screens}, journal = {PLOS Computational Biology}, year = {2024}, volume = {20}, number = {5}, pages = {e1011408}, doi = {10.1371/journal.pcbi.1011408} } @article{bosch2024weak, author = {Bosch, Barbara and DeJesus, Michael A. and Schnappinger, Dirk and Rock, Jeremy M.}, title = {Weak links: {Advancing} target-based drug discovery by identifying the most vulnerable targets}, journal = {Annals of the New York Academy of Sciences}, year = {2024}, volume = {1535}, number = {1}, pages = {10--19}, doi = {10.1111/nyas.15139} } @article{babunovic2022retinoic, author = {Babunovic, Gregory H. and DeJesus, Michael A. and Bosch, Barbara and Chase, Michael R. and Barbier, Thibault and Dickey, Amy K. and Bryson, Bryan D. and Rock, Jeremy M. and Fortune, Sarah M.}, title = {{CRISPR} interference reveals that all-trans-retinoic acid promotes macrophage control of {Mycobacterium} tuberculosis by limiting bacterial access to cholesterol and propionyl coenzyme {A}}, journal = {mBio}, year = {2022}, volume = {13}, pages = {e03683-21}, doi = {10.1128/mbio.03683-21} } @article{li2022chemical, author = {Li, S. and Poulton, N. C. and Chang, J. S. and Azadian, Z. A. and DeJesus, M. A. and Ruecker, N. and Zimmerman, M. D. and Eckartt, K. A. and Bosch, B. and Engelhart, C. A. and Sullivan, D. F. and Gengenbacher, M. and Dartois, V. A. and Schnappinger, D. and Rock, J. M.}, title = {{CRISPRi} chemical genetics and comparative genomics identify genes mediating drug potency in {Mycobacterium tuberculosis}}, journal = {Nature Microbiology}, year = {2022}, volume = {7}, number = {6}, pages = {766--779}, doi = {10.1038/s41564-022-01130-y} } @article{poulton2022rv0678, author = {Poulton, Nicholas C. and Azadian, Zachary A. and DeJesus, Michael A. and Rock, Jeremy M.}, title = {Mutations in rv0678 confer low-level resistance to benzothiazinone {DprE1} inhibitors in {Mycobacterium} tuberculosis}, journal = {Antimicrobial Agents and Chemotherapy}, year = {2022}, volume = {66}, pages = {e00904-22}, doi = {10.1128/aac.00904-22} } @article{dutta2021chemical, author = {Dutta, Esha and DeJesus, Michael A. and Ruecker, Nadine and Zaveri, Anisha and Koh, Eun-Ik and Sassetti, Christopher M. and Schnappinger, Dirk and Ioerger, Thomas R.}, title = {An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence}, journal = {PLOS ONE}, year = {2021}, volume = {16}, pages = {e0257911}, doi = {10.1371/journal.pone.0257911} } @article{bosch2021vulnerability, author = {Bosch, Barbara and DeJesus, Michael A. and Poulton, Nicholas C. and Zhang, Wenzhu and Engelhart, Curtis A. and Zaveri, Anisha and Lavalette, Sophie and Ruecker, Nadine and Trujillo, Carolina and Wallach, Joshua B. and Li, Shuqi and Ehrt, Sabine and Chait, Brian T. and Schnappinger, Dirk and Rock, Jeremy M.}, title = {Genome-wide gene expression tuning reveals diverse vulnerabilities of {M. tuberculosis}}, journal = {Cell}, year = {2021}, volume = {184}, number = {17}, pages = {4579--4592.e24}, doi = {10.1016/j.cell.2021.06.033}, note = {Co-first authors: Barbara Bosch and Michael A. DeJesus}, author+an = {1=cofirst; 2=cofirst} } @article{subramaniyam2019zinb, author = {Subramaniyam, Siddharth and DeJesus, Michael A. and Zaveri, Anisha and Smith, Clare M. and Baker, Richard E. and Ehrt, Sabine and Schnappinger, Dirk and Sassetti, Christopher M. and Ioerger, Thomas R.}, title = {Statistical analysis of variability in {TnSeq} data across conditions using zero-inflated negative binomial regression}, journal = {BMC Bioinformatics}, year = {2019}, volume = {20}, pages = {603}, doi = {10.1186/s12859-019-3156-z} } @article{dejesus2017genetic, author = {DeJesus, Michael A. and Nambi, Subhalaxmi and Smith, Clare M. and Baker, Richard E. and Sassetti, Christopher M. and Ioerger, Thomas R.}, title = {Statistical analysis of genetic interactions in {Tn-Seq} data}, journal = {Nucleic Acids Research}, year = {2017}, volume = {45}, number = {11}, pages = {e93}, doi = {10.1093/nar/gkx128} } @article{xu2017chemical, author = {Xu, Weizhen and DeJesus, Michael A. and Ruecker, Nadine and Engelhart, Curtis A. and Wright, Meredith G. and Healy, Claire and Lin, Kan and Wang, Ruojun and Park, Sae Woong and Ioerger, Thomas R. and Schnappinger, Dirk and Ehrt, Sabine}, title = {Chemical genetic interaction profiling reveals determinants of intrinsic antibiotic resistance in {Mycobacterium} tuberculosis}, journal = {Antimicrobial Agents and Chemotherapy}, year = {2017}, volume = {61}, pages = {e01334-17}, doi = {10.1128/AAC.01334-17} } @article{dejesus2017essentiality, author = {DeJesus, Michael A. and Gerrick, Elias R. and Xu, Weizhen and Park, Sae Woong and Long, Jarukit E. and Boutte, Cara C. and Rubin, Eric J. and Schnappinger, Dirk and Ehrt, Sabine and Fortune, Sarah M. and Sassetti, Christopher M. and Ioerger, Thomas R.}, title = {Comprehensive essentiality analysis of the {Mycobacterium tuberculosis} genome via saturating transposon mutagenesis}, journal = {mBio}, year = {2017}, volume = {8}, number = {1}, pages = {e02133-16}, doi = {10.1128/mBio.02133-16} } @article{korte2016trehalose, author = {Korte, Jan and Alber, Marina and Trujillo, Carolina M. and Syson, Karl and Koliwer-Brandl, Hendrik and Deenen, Ren{\'e} and K{\"o}hrer, Karl and DeJesus, Michael A. and Hartman, Travis and Jacobs, Jr., William R. and Bornemann, Stephen and Ioerger, Thomas R. and Ehrt, Sabine and Kalscheuer, Rainer}, title = {Trehalose-6-phosphate-mediated toxicity determines essentiality of {OtsB2} in {Mycobacterium} tuberculosis in vitro and in mice}, journal = {PLOS Pathogens}, year = {2016}, volume = {12}, number = {12}, pages = {e1006043}, doi = {10.1371/journal.ppat.1006043} } @article{orsini2016lphn3, author = {Orsini, C. and Setlow, Barry and DeJesus, Michael A. and Galaviz, Stacy and Loesch, Kimberly and Ioerger, Thomas R. and Wallis, Deeann}, title = {Behavioral and transcriptomic profiling of mice null for {Lphn3}, a gene implicated in {ADHD} and addiction}, journal = {Molecular Genetics \& Genomic Medicine}, year = {2016}, volume = {4}, number = {3}, pages = {322--343}, doi = {10.1002/mgg3.207} } @article{dejesus2016normalization, author = {DeJesus, Michael A. and Ioerger, Thomas R.}, title = {Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes}, journal = {Journal of Bioinformatics and Computational Biology}, year = {2016}, volume = {14}, number = {3}, pages = {1642004}, doi = {10.1142/S021972001642004X} } @article{dejesus2015transit, author = {DeJesus, Michael A. and Ambadipudi, Chaitra and Baker, Richard and Sassetti, Christopher and Ioerger, Thomas R.}, title = {{TRANSIT} - {A} software tool for {Himar1} {TnSeq} analysis}, journal = {PLOS Computational Biology}, year = {2015}, volume = {11}, number = {10}, pages = {e1004401}, doi = {10.1371/journal.pcbi.1004401} } @article{wallis2015rabies, author = {Wallis, Deeann and Loesch, Kimberly and Galaviz, Stacy and Sun, Qingan and DeJesus, Michael A. and Ioerger, Thomas R. and Sacchettini, James C.}, title = {High-throughput differentiation and screening of a library of mutant stem cell clones defines new host-based genes involved in rabies virus infection}, journal = {Stem Cells}, year = {2015}, volume = {33}, number = {8}, pages = {2509--2522}, doi = {10.1002/stem.1983} } @article{loesch2015radiation, author = {Loesch, Kimberly and Galaviz, Stacy and Hamoui, Zaher and Clanton, Ryan and Akabani, Gamal and Deveau, Michael and DeJesus, Michael A. and Ioerger, Thomas R. and Sacchettini, James C. and Wallis, Deeann}, title = {Functional genomics screening utilizing mutant mouse embryonic stem cells identifies novel radiation-response genes}, journal = {PLOS ONE}, year = {2015}, volume = {10}, number = {4}, pages = {e0120534}, doi = {10.1371/journal.pone.0120534} } @article{dejesus2015uncertainty, author = {DeJesus, Michael A. and Ioerger, Thomas R.}, title = {Capturing uncertainty by modeling local transposon insertion frequencies improves discrimination of essential genes}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, year = {2015}, volume = {12}, number = {1}, pages = {92--102}, doi = {10.1109/TCBB.2014.2326857} } @article{dejesus2013hmm, author = {DeJesus, Michael A. and Ioerger, Thomas R.}, title = {A hidden Markov model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data}, journal = {BMC Bioinformatics}, year = {2013}, volume = {14}, pages = {303}, doi = {10.1186/1471-2105-14-303} } @article{dejesus2013gumbel, author = {DeJesus, Michael A. and Zhang, Yanjia J. and Sassetti, Christopher M. and Rubin, Eric J. and Sacchettini, James C. and Ioerger, Thomas R.}, title = {Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries}, journal = {Bioinformatics}, volume = {29}, number = {6}, pages = {695-703}, year = {2013}, month = {03}, abstract = {Motivation: Next-generation sequencing affords an efficient analysis of transposon insertion libraries, which can be used to identify essential genes in bacteria. To analyse this high-resolution data, we present a formal Bayesian framework for estimating the posterior probability of essentiality for each gene, using the extreme-value distribution to characterize the statistical significance of the longest region lacking insertions within a gene. We describe a sampling procedure based on the Metropolis–Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters.Results: Using a sequence dataset from a transposon library for Mycobacterium tuberculosis, we show that this Bayesian approach predicts essential genes that correspond well with genes shown to be essential in previous studies. Furthermore, we show that by using the extreme-value distribution to characterize genomic regions lacking transposon insertions, this method is capable of identifying essential domains within genes. This approach can be used for analysing transposon libraries in other organisms and augmenting essentiality predictions with statistical confidence scores.Availability: A python script implementing the method described is available for download from http://saclab.tamu.edu/essentiality/.Contact: michael.dejesus@tamu.edu or ioerger@cs.tamu.eduSupplementary information: Supplementary data are available at Bioinformatics online.}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btt043}, url = {https://doi.org/10.1093/bioinformatics/btt043}, eprint = {https://academic.oup.com/bioinformatics/article-pdf/29/6/695/48902504/bioinformatics_29_6_695.pdf} } @article{dejesus2013reannotation, author = {DeJesus, Michael A. and Sacchettini, James C. and Ioerger, Thomas R.}, title = {Reannotation of translational start sites in the genome of {Mycobacterium} tuberculosis}, journal = {Tuberculosis}, year = {2013}, volume = {93}, pages = {18--25}, doi = {10.1016/j.tube.2012.11.012} } @article{griffin2011phenotypic, author = {Griffin, Jennifer E. and Gawronski, Jeffrey D. and DeJesus, Michael A. and Ioerger, Thomas R. and Akerley, Brian J. and Sassetti, Christopher M.}, title = {High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism}, journal = {PLOS Pathogens}, year = {2011}, volume = {7}, pages = {e1002251}, doi = {10.1371/journal.ppat.1002251} } @article{todor2026interaction, author = {Todor, Horia and Kim, Lili M. and Billings, Evan and Grzegorzewicz, Anna E. and Burkhart, Hannah N. and DeJesus, Michael A. and Na, Allen and Nitz, Samuel and Shell, Scarlet S. and Campbell, Elizabeth A. and Jackson, Mary and Mancia, Filippo and Rock, Jeremy M. and Gross, Carol A. and Chen, James}, title = {Predicting the protein interaction landscape of a mycobacterial pathogen}, journal = {bioRxiv}, year = {2026}, doi = {10.64898/2026.07.15.738315}, keywords = {preprint} } @article{singh2026resuscitation, author = {Singh, Prabhat Ranjan and Gengenbacher, Martin and Mishra, Saurabh and Jinich, Adrian and Jiang, Xiuju and Tsang, Felipe and Cristaldo, Melissa and DeJesus, Michael A. and Rhee, K. and Kaner, R. and Leopold, P. and Crystal, Ronald G. and Kathayat, Dipak and VanderVen, Brian C. and Nathan, Carl F.}, title = {{\emph{Mycobacterium tuberculosis}} genes needed for intra-alveolar resuscitation after airborne transmission}, journal = {bioRxiv}, year = {2026}, doi = {10.1101/2025.09.15.676370}, keywords = {preprint} } @article{gouzy2026metabolic, author = {Gouzy, Alexandre and Li, Shuqi and Chen, James and Na, Allen and Saleh, Anas and Azadian, Zachary A. and Tam, Kayan and Munsamy-Govender, Vanisha and Poulton, Nicholas C. and DeJesus, Michael A. and Schnappinger, Dirk and Rhee, Kyu Y. and Ehrt, Sabine and Rock, Jeremy M.}, title = {Metabolic control of drug resistance by a mycobacterial ion channel}, journal = {bioRxiv}, year = {2026}, doi = {10.64898/2026.03.10.710584}, keywords = {preprint} } @article{deschner2025chlorotonils, author = {Deschner, Felix and Chengalroyen, Melissa D. and Ames, Lauren and Quach, Diana and Aguilera Olvera, Rodrigo and Bosch, Barbara and Castro, Anthony and Kim, Heather and Raman, Kaushik and Thornton, Natalie and Wallach, Joshua and da Costa, Fernanda Rodrigues and Allen, Renee and Lupien, Andr{\'e}anne and Zuma, Mandisa and Lynch, Sasha and Pogliano, Joe and Sugie, Joseph and Rock, Jeremy M. and Schnappinger, Dirk and Parish, Tanya and Mizrahi, Valerie and DeJesus, Michael A. and M{\"u}ller, Rolf and Herrmann, Jennifer}, title = {Chlorotonils exhibit potent activity against {\emph{Mycobacterium tuberculosis}}, while resistance is mediated by {MmpR5-MmpL5}}, journal = {bioRxiv}, year = {2025}, doi = {10.64898/2025.12.09.693342}, keywords = {preprint} } @inproceedings{dejesus2015skew, author = {DeJesus, Michael A. and Ioerger, Thomas R.}, title = {Reducing type {I} errors in {Tn-Seq} experiments by correcting the skew in read count distributions}, booktitle = {Proceedings of the 7th International Conference on Bioinformatics and Computational Biology (BICoB)}, year = {2015}, note = {Best Paper Award}, award = {Best Paper Award} } @inproceedings{dejesus2013insertion, author = {DeJesus, Michael A. and Ioerger, Thomas R.}, title = {Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data}, booktitle = {Proceedings of the ACM Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM-BCB)}, year = {2013}, pages = {144--151}, doi = {10.1145/2506583.2506610}, note = {Best Paper Award}, award = {Best Paper Award} } @incollection{long2015essential, author = {Long, Jarukit E. and DeJesus, Michael A. and Ward, Doyle and Baker, Richard E. and Ioerger, Thomas R. and Sassetti, Christopher M.}, title = {Identifying essential genes in {Mycobacterium} tuberculosis by global phenotypic profiling}, booktitle = {Gene Essentiality: Methods and Protocols}, series = {Methods in Molecular Biology}, volume = {1279}, pages = {79--95}, publisher = {Springer New York}, year = {2015}, doi = {10.1007/978-1-4939-2398-4_6} } @article{maxwell2017rifamycins, author = {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. R. and DeJesus, M. A. and Dong, W. and Seemann, G. and Fossum, T. and Sacchettini, J. C.}, title = {Development of novel, non-toxic rifamycins that reverse drug resistance in diffuse large {B-cell} lymphoma ({DLBCL})}, journal = {Hematological Oncology}, year = {2017}, volume = {35}, number = {S2}, pages = {253--254}, doi = {10.1002/hon.2438_118}, keywords = {poster} }