Publications Associated with NIH (P01) PAT and (U19) FLUTE Projects

Healy C, Ehrt S, Gouzy A. An exacerbated phosphate starvation response triggers Mycobacterium tuberculosis glycerol utilization at acidic pH. mBio. 2025 Jan 8;16(1):e0282524. doi: 10.1128/mbio.02825-24. Epub 2024 Nov 29. PMID: 39611843; PMCID: PMC11708021.
Luna MJ, Oluoch PO, Miao J, Culviner P, Papavinasasundaram K, Jaecklein E, Shell SS, Ioerger TR, Fortune SM, Farhat MR, Sassetti CM. Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures. mBio. 2025 Mar 12;16(3):e0376224. doi: 10.1128/mbio.03762-24. Epub 2025 Jan 28. PMID: 39873486; PMCID: PMC11898584.
Peters RG, Kelly JM, Bibeau S, Zhou Y, Shell SS. Functional Analysis of Promoters, mRNA Cleavage, and mRNA Secondary Structure on esxB-esxA in Mycolicibacterium smegmatis. Pathogens. 2024 Nov 27;13(12):1041. doi: 10.3390/pathogens13121041. PMID: 39770301; PMCID: PMC11728522.
Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. PLoS Pathog. 2024 Feb 29;20(2):e1012050. doi: 10.1371/journal.ppat.1012050. PMID: 38422159; PMCID: PMC10931510.
Sun H, Vargas-Blanco DA, Zhou Y, Masiello CS, Kelly JM, Moy JK, Korkin D, Shell SS. Diverse intrinsic properties shape transcript stability and stabilization in Mycolicibacterium smegmatis. NAR Genom Bioinform. 2024 Nov 4;6(4):lqae147. doi: 10.1093/nargab/lqae147. PMID: 39498432; PMCID: PMC11532794.
Kahne SC, Yoo JH, Chen J, Nakedi K, Iyer LM, Putzel G, Samhadaneh NM, Pironti A, Aravind L, Ekiert DC, Bhabha G, Rhee KY, Darwin KH. Identification of a depupylation regulator for an essential enzyme in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2024 Dec 3;121(49):e2407239121. doi: 10.1073/pnas.2407239121. Epub 2024 Nov 25. PMID: 39585979; PMCID: PMC11626117.
Stanley S, Spaulding CN, Liu Q, Chase MR, Ha DTM, Thai PVK, Lan NH, Thu DDA, Quang NL, Brown J, Hicks ND, Wang X, Marin M, Howard NC, Vickers AJ, Karpinski WM, Chao MC, Farhat MR, Caws M, Dunstan SJ, Thuong NTT, Fortune SM. Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains. Lancet Microbe. 2024 Jun;5(6):e570-e580. doi: 10.1016/S2666-5247(24)00022-3. Epub 2024 May 8. PMID: 38734030; PMCID: PMC11229950.
Qu D, Ge P, Botella L, Park SW, Lee HN, Thornton N, Bean JM, Krieger IV, Sacchettini JC, Ehrt S, Aldrich CC, Schnappinger D. Mycobacterial biotin synthases require an auxiliary protein to convert dethiobiotin into biotin. Nat Commun. 2024 May 16;15(1):4161. doi: 10.1038/s41467-024-48448-1. PMID: 38755122; PMCID: PMC11099021.
Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. PLoS Comput Biol. 2024 May 20;20(5):e1011408. doi: 10.1371/journal.pcbi.1011408. PMID: 38768228; PMCID: PMC11104602.
Martini MC, Alonso MN, Cafiero JH, Xiao J, Shell SS. Loss of glycerol catabolism confers carbon-source-dependent artemisinin resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2024 Oct 8;68(10):e0064524. doi: 10.1128/aac.00645-24. Epub 2024 Aug 28. PMID: 39194262; PMCID: PMC11459938.
Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. PLoS Pathog. 2024 Feb 29;20(2):e1012050. doi: 10.1371/journal.ppat.1012050. PMID: 38422159; PMCID: PMC10931510.
Grigsby SJ, Prasad GVRK, Wallach JB, Mittal E, Hsu FF, Schnappinger D, Philips JA. CpsA mediates infection of recruited lung myeloid cells by Mycobacterium tuberculosis. Cell Rep. 2024 Jan 23;43(1):113607. doi: 10.1016/j.celrep.2023.113607. Epub 2023 Dec 20. Erratum in: Cell Rep. 2024 May 28;43(5):114201. doi: 10.1016/j.celrep.2024.114201. PMID: 38127624; PMCID: PMC10900767.
Wong AI, Beites T, Planck KA, Fieweger RA, Eckartt KA, Li S, Poulton NC, VanderVen BC, Rhee KY, Schnappinger D, Ehrt S, Rock J. Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis. Elife. 2023 Feb 22;12:e81177. doi: 10.7554/eLife.81177. PMID: 36810158; PMCID: PMC9995111.
Zhou Y, Sun H, Rapiejko AR, Vargas-Blanco DA, Martini MC, Chase MR, Joubran SR, Davis AB, Dainis JP, Kelly JM, Ioerger TR, Roberts LA, Fortune SM, Shell SS. Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs. J Biol Chem. 2023 Nov;299(11):105312. doi: 10.1016/j.jbc.2023.105312. Epub 2023 Oct 5. PMID: 37802316; PMCID: PMC10641625.
Freeman AH, Tembiwa K, Brenner JR, Chase MR, Fortune SM, Morita YS, Boutte CC. Arginine methylation sites on SepIVA help balance elongation and septation in Mycobacterium smegmatis. Mol Microbiol. 2023 Feb;119(2):208-223. doi: 10.1111/mmi.15006. Epub 2022 Dec 4. PMID: 36416406; PMCID: PMC10023300.
Zhu J, Liu YJ, Fortune SM. Spatiotemporal perspectives on tuberculosis chemotherapy. Curr Opin Microbiol. 2023 Apr;72:102266. doi: 10.1016/j.mib.2023.102266. Epub 2023 Feb 4. PMID: 36745965; PMCID: PMC10023397.
Bar-Oz M, Martini MC, Alonso MN, Meir M, Lore NI, Miotto P, Riva C, Angala SK, Xiao J, Masiello CS, Misiakou MA, Sun H, Moy JK, Jackson M, Johansen HK, Cirillo DM, Shell SS, Barkan D. The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence. PLoS Pathog. 2023 Aug 21;19(8):e1011575. doi: 10.1371/journal.ppat.1011575. PMID: 37603560; PMCID: PMC10470900.
Choudhery S, Ioerger TR. Dual ICA to extract interacting sets of genes and conditions from transcriptomic data. ACM BCB. 2023 Sep;2023:8. doi: 10.1145/3584371.3612968. Epub 2023 Oct 4. PMID: 38162633; PMCID: PMC10757798.
Xu Y, Ehrt S, Schnappinger D, Beites T. Synthetic lethality of Mycobacterium tuberculosis NADH dehydrogenases is due to impaired NADH oxidation. mBio. 2023 Dec 19;14(6):e0104523. doi: 10.1128/mbio.01045-23. Epub 2023 Nov 30. PMID: 38032200; PMCID: PMC10746327.
Liu Q, Zhu J, Dulberger CL, Stanley S, Wilson S, Chung ES, Wang X, Culviner P, Liu YJ, Hicks ND, Babunovic GH, Giffen SR, Aldridge BB, Garner EC, Rubin EJ, Chao MC, Fortune SM. Tuberculosis treatment failure associated with evolution of antibiotic resilience. Science. 2022 Dec 9;378(6624):1111-1118. doi: 10.1126/science.abq2787. Epub 2022 Dec 8. PMID: 36480634; PMCID: PMC9968493.
Martini MC, Hicks ND, Xiao J, Alonso MN, Barbier T, Sixsmith J, Fortune SM, Shell SS. Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis. PLoS Pathog. 2022 Jul 13;18(7):e1010705. doi: 10.1371/journal.ppat.1010705. PMID: 35830479; PMCID: PMC9312406.
Arginine methylation sites on SepIVA help balance elongation and septation in Mycobacterium smegmatis. Freeman AH, Tembiwa K, Brenner JR, Chase MR, Fortune SM, Morita YS, Boutte CC. Arginine methylation sites on SepIVA help balance elongation and septation in Mycobacterium smegmatis. Mol Microbiol. 2022 Nov 23. doi: 10.1111/mmi.15006. Epub ahead of print. PMID: 36416406.
Activity-based annotation: the emergence of systems biochemistry. Rhee KY, Jansen RS, Grundner C. Activity-based annotation: the emergence of systems biochemistry. Trends Biochem Sci. 2022 Sep;47(9):785-794. doi: 10.1016/j.tibs.2022.03.017. Epub 2022 Apr 13. PMID: 35430135; PMCID: PMC9378515.
Analysis of Gene Essentiality from TnSeq Data Using Transit. Ioerger TR. Analysis of Gene Essentiality from TnSeq Data Using Transit. Methods Mol Biol. 2022;2377:391-421. doi: 10.1007/978-1-0716-1720-5_22. PMID: 34709629; PMCID: PMC8941984.">
Rv0954 Is a Member of the Mycobacterial Cell Division Complex. Wang R, Ehrt S. Rv0954 Is a Member of the Mycobacterial Cell Division Complex. Front Microbiol. 2021 Apr 20;12:626461. doi: 10.3389/fmicb.2021.626461. PMID: 33959103; PMCID: PMC8093794.
Growth of Mycobacterium tuberculosis at acidic pH depends on lipid assimilation and is accompanied by reduced GAPDH activity. Gouzy A, Healy C, Black KA, Rhee KY, Ehrt S. Growth of Mycobacterium tuberculosis at acidic pH depends on lipid assimilation and is accompanied by reduced GAPDH activity. Proc Natl Acad Sci U S A. 2021 Aug 10;118(32):e2024571118. doi: 10.1073/pnas.2024571118. PMID: 34341117; PMCID: PMC8364206.
Global Analysis of the Specificities and Targets of Endoribonucleases from Escherichia coli Toxin-Antitoxin Systems. Culviner PH, Nocedal I, Fortune SM, Laub MT. Global Analysis of the Specificities and Targets of Endoribonucleases from Escherichia coli Toxin-Antitoxin Systems. mBio. 2021 Oct 26;12(5):e0201221. doi: 10.1128/mBio.02012-21. Epub 2021 Sep 21. PMID: 34544284; PMCID: PMC8546651.
Spatiotemporal localization of proteins in mycobacteria. Zhu J, Wolf ID, Dulberger CL, Won HI, Kester JC, Judd JA, Wirth SE, Clark RR, Li Y, Luo Y, Gray TA, Wade JT, Derbyshire KM, Fortune SM, Rubin EJ. Spatiotemporal localization of proteins in mycobacteria. Cell Rep. 2021 Dec 28;37(13):110154. doi: 10.1016/j.celrep.2021.110154. PMID: 34965429; PMCID: PMC8861988.
Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets. Choudhery S, Brown AJ, Akusobi C, Rubin EJ, Sassetti CM, Ioerger TR. Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets. mSystems. 2021 Oct 26;6(5):e0087621. doi: 10.1128/mSystems.00876-21. Epub 2021 Oct 19. PMID: 34665010; PMCID: PMC8525568.
ClpX Is Essential and Activated by Single-Strand DNA Binding Protein in Mycobacteria. Kester JC, Kandror O, Akopian T, Chase MR, Zhu J, Rubin EJ, Goldberg AL, Fortune SM. ClpX Is Essential and Activated by Single-Strand DNA Binding Protein in Mycobacteria. J Bacteriol. 2021 Jan 25;203(4):e00608-20. doi: 10.1128/JB.00608-20. PMID: 33229461; PMCID: PMC7847540.
Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria. Bandekar AC, Subedi S, Ioerger TR, Sassetti CM. Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria. Curr Biol. 2020 Oct 19;30(20):3961-3971.e6. doi: 10.1016/j.cub.2020.07.070. Epub 2020 Sep 10. PMID: 32916109; PMCID: PMC7578119.
Mycobacterium smegmatis HtrA Blocks the Toxic Activity of a Putative Cell Wall Amidase. Wu KJ, Boutte CC, Ioerger TR, Rubin EJ. Mycobacterium smegmatis HtrA Blocks the Toxic Activity of a Putative Cell Wall Amidase. Cell Rep. 2019 May 21;27(8):2468-2479.e3. doi: 10.1016/j.celrep.2018.12.063. PMID: 31116989; PMCID: PMC6538288.
Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape.Baranowski C, Welsh MA, Sham LT, Eskandarian HA, Lim HC, Kieser KJ, Wagner JC, McKinney JD, Fantner GE, Ioerger TR, Walker S, Bernhardt TG, Rubin EJ, Rego EH. Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape. Elife. 2018 Oct 16;7. pii: e37516. doi: 10.7554/eLife.37516. PMID: 30324906. PMCID: PMC6231781.
Tuberculosis: Just the FAQs.Guinn KM and Rubin EJ. Tuberculosis: Just the FAQs. MBio. 2017 Dec 19;8(6). pii: e01910-17. doi: 10.1128/mBio.01910-17. PMID: 29259086. PMCID: PMC5736911.
Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response.Gerrick ER, Barbier T, Chase MR, Xu R, François J, Lin VH, Szucs MJ, Rock JM, Ahmad R, Tjaden B, Livny J, Fortune SM. Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6464-6469. doi: 10.1073/pnas.1718003115. Epub 2018 Jun 5. PMID: 29871950. PMCID: PMC6016810.
The Capacity of Mycobacterium tuberculosis To Survive Iron Starvation Might Enable It To Persist in Iron-Deprived Microenvironments of Human GranulomasKurthkoti K, Amin H, Marakalala MJ, Ghanny S, Subbian S, Sakatos A, Livny J, Fortune SM, Berney M, Rodriguez GM. The Capacity of Mycobacterium tuberculosis To Survive Iron Starvation Might Enable It To Persist in Iron-Deprived Microenvironments of Human Granulomas. MBio. 2017 Aug 15;8(4). pii: e01092-17. doi: 10.1128/mBio.01092-17. PMID: 28811344. PMCID: PMC5559634.
Chemical Genetic Interaction Profiling Reveals Determinants of Intrinsic Antibiotic Resistance in Mycobacterium tuberculosis.Weizhen Xu, Michael A. DeJesus, Nadine Rucker, Curtis A. Engelhart, Meredith G. Wright, Claire Healy, Kan Lin, Ruojun Wang, Sae Woong Park, Thomas R. Ioerger, Dirk Schnappinger, Sabine Ehrt. Chemical Genetic Interaction Profiling Reveals Determinants of Intrinsic Antibiotic Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2017 Nov 22;61(12). PMID: 28893793. PMCID: PMC5700314.
Mycobacterium tuberculosis is protected from NADPH oxidase and LC3-associated phagocytosis by the LCP protein CpsA.Köster S, Upadhyay S, Chandra P, Papavinasasundaram K, Yang G, Hassan A, Grigsby SJ, Mittal E, Park HS, Jones V, Hsu FF, Jackson M, Sassetti CM, Philips JA. Mycobacterium tuberculosis is protected from NADPH oxidase and LC3-associated phagocytosis by the LCP protein CpsA. Proc Natl Acad Sci U S A. 2017 Sep 27. pii: 201707792. doi: 10.1073/pnas.1707792114. [Epub ahead of print]. PMID: 28973896. PMCID: PMC5642705.
Emerging approaches in TB drug development: At home in the metabolome.Kyu Rhee and Robert Jansen. Emerging approaches in TB drug development: At home in the metabolome. Trends Pharmacol Sci. 2017 Feb 3. pii: S0165-6147(17)30021-4. Review. PMID: 28169001. PMCID: PMC5367985.
Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Jeremy M. Rock, Forrest F. Hopkins, Alejandro Chavez, Marieme Diallo, Michael R. Chase, Elias R. Gerrick, Justin R. Pritchard, George M. Church, Eric J. Rubin, Christopher M. Sassetti, Dirk Schnappinger, Sarah M. Fortune. Nat Microbiol. 2017 Feb 6;2:16274. PMID: 28165460.
Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis. Michael A. DeJesus, Elias R. Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E. Long, Cara C. Boutte, Eric J. Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M. Fortune, Christopher M. Sassetti, Thomas R. Ioerger. MBio. 2017 Jan 17;8(1). pii: e02133-16. PMID: 28096490.
Statistical Analysis of Genetic Interactions inTnSeq data.Michael A. DeJesus, Subhalaxmi Nambi, Clare M. Smith, Richard E. Baker, Christopher M. Sassetti, and Thomas R. Ioerger. Statistical Analysis of Genetic Interactions inTnSeq data. Nucleic Acids Res. 2017 Feb 22. doi: 10.1093/nar/gkx128. PMID: 28334803. PMCID: PMC5499643.
Mycobacterium tuberculosis protease MarP activates a peptidoglycan hydrolase during acid stress.Helene Botella, Julien Vaubourgeix, Myung Hee Lee, Naomi Song, Weizhen Xu, Hideki Makinoshima, Michael S. Glickman and Sabine Ehrt. EMBO J. 2017 Jan 5. pii: e201695028. PMID: 28057704.
Deletion of a mycobacterial divisome factor collapses single-cell phenotypic heterogeneity.E. Hesper Rego, Rebecca E. Audette, and Eric J. Rubin. Deletion of a mycobacterial divisome factor collapses single-cell phenotypic heterogeneity. Nature. 2017 Jun 1;546(7656):153-157. Epub 2017 May 31. PMID: 28569798 PMCID: PMC5567998
A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall synthesis. Boutte CC, Baer CE, Papavinasasundaram K, Liu W, Chase MR, Meniche X, Fortune SM, Sassetti CM, Ioerger TR, Rubin EJ. Elife. 2016 Jun 15;5. pii: e14590. PMID: 27304077.
Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis.Mishra BB, Lovewell RR, Olive AJ, Zhang G, Wang W, Eugenin E, Smith CM, Phuah JY, Long JE, Dubuke ML, Palace SG, Goguen JD, Baker RE, Nambi S, Mishra R, Booty MG, Baer CE, Shaffer SA, Dartois V, McCormick BA, Chen X, Sassetti CM. Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis. Nat Microbiol. 2017 May 15;2:17072. PMID: 28504669. PMCID: PMC5461879.
Structural insights into Mycobacterium tuberculosis Rv2671 protein as a dihydrofolate reductase functional analogue contributing to para-aminosalicylic acid resistance. Yu-Shan Cheng, James C. Sacchettini. Structural insights into Mycobacterium tuberculosis Rv2671 protein as a dihydrofolate reductase functional analogue contributing to para-aminosalicylic acid resistance. Biochemistry. 2016 Feb 23;55(7):1107-19. Epub 2016 Feb 5. PMID: 26848874
Normalization of transposon-mutant library sequencing datasets to improve identifcation of conditionally essential genes. Michael A. DeJesus, Thomas R. Ioerger. Normalization of transposon-mutant library sequencing datasets to improve identifcation of conditionally essential genes. Journal of Bioinformatics and Computational Biology. 2016 Jan 14:1642004. PMID: 26932272
TRANSIT - a Software Tool for Himar1 TnSeq Analysis. Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher Sassetti, Thomas R. Ioerger. TRANSIT - a Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol. 2015 Oct 8;11(10):e1004401. PMID: 26447887
Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility. Kieser, K.J., Baranowski, C., Chao, M.C., Long, J.E., Sassetti, C.M., Waldor, M.K., Sacchettini, J.C., Ioerger, T.R, and Rubin, E.J. (2015). Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility. PNAS, 112(42):13087-92.
Two enzymes with redundant fructose bisphosphatase activity sustain gluconeogenesis and virulence in Mycobacterium tuberculosis. Uday Ganapathy, Joeli Marrero, Susannah Calhoun, Hyungjin Eoh, Luiz Pedro Sorio de Carvalho, Kyu Rhee, Sabine Ehrt. Two enzymes with redundant fructose bisphosphatase activity sustain gluconeogenesis and virulence in Mycobacterium tuberculosis. Nature Communications. 2015 Aug 10;6:7912. doi: 10.1038/ncomms8912. PMID: 26258286 PMCID: PMC4535450
Identifying Essential Genes in Mtb by Global Phenotypic Profiling. Jarukit E. Long, Michael DeJesus, Doyle Ward, Richard E. Baker, Thomas R. Ioerger, Christopher M. Sassetti. Identifying Essential Genes in Mtb by Global Phenotypic Profiling. Methods Mol Biol. 2015;1279:79-95. PMID: 25636614
Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape. Shell SS, Wang J, Lapierre P, Mir M, Chase MR, Pyle MM, Gawande R, Ahmad R, Sarracino DA, Ioerger TR, Fortune SM, Derbyshire KM, Wade JT, Gray TA. Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape. PLoS Genetics. 2015 Nov 4;11(11):e1005641. doi:10.1371/journal.pgen.1005641. eCollection 2015 Nov. PMID: 26536359
Reducing type I errors in Tn-Seq experiments by correcting the skew in read count distributions. 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).
The oxidative stress network of Mycobacterium tuberculosis reveals a virulence-associated oxido-reductase complex Subhalaxmi Nambi, Jarukit E. Long, Bibhuti B. Mishra, Richard Baker, Kenan C. Murphy and Christopher M. Sassetti. The oxidative stress network of Mycobacterium tuberculosis reveals a virulence-associated oxido-reductase complex. Cell Host Microbe. 2015 Jun 10;17(6):829-37.
Mycobacterial Recombineering Kenan C. Murphy, Kadamba Papavinasasundaram, Christopher M. Sassetti. Mycobacterial Recombineering. Methods Mol Biol. 2015;1285:177-99. doi: 10.1007/978-1-4939-2450-9_10. PMID: 25779316
Disruption of an M. tuberculosis membrane protein causes a magnesium-dependent cell division defect and failure to persist in mice. N. Goodsmith, X.V. Guo, O.H. Vandal, J. Vaubourgeix, R. Wang, H. Botella, S. Song, K. Bhatt, A. Liba, P. Salgame, D. Schnappinger, S. Ehrt. Disruption of an M. tuberculosis Membrane Protein Causes a Magnesium-dependent Cell Division Defect and Failure to Persist in Mice" PLoS Pathog. 2015 Feb 6;11(2):e1004645. PMID: 25658098
Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. DeJesus, MA and Ioerger, TR. 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.
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data.DeJesus, MA and Ioerger, TR. A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. BMC Bioinformatics, 2013 Oct 8;14:303. PubMed PMID: 24103077; PubMed Central PMCID: PMC3854130.
TargetRNA2: identifying targets of small regulatory RNAs in bacteria.Kery MB, Feldman M, Livny J, and Tjaden B. TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res. 2014 Apr 21. PubMed PMID: 24753424.