Functional Analysis of Promoters, mRNA Cleavage, and mRNA Secondary Structure on esxB-esxA in Mycolicibacterium smegmatis
Peters, R. G.*, Kelly, J. M.*, Bibeau, S., Zhou, Y., and Shell, S. S .
MDPI Pathogens. doi.org/10.3390/pathogens13121041
*Contributed equally to this work.

Diverse intrinsic properties shape transcript stability and stabilization in Mycolicibacterium smegmatis
Sun, H., Vargas-Blanco, D. A., Zhou, Y., Masiello, C. S., Kelly, J. M., Moy, J. K., and Shell, S. S .
NAR Genomics and Bioinformatics. doi.org/10.1093/nargab/lqae147

Loss of glycerol catabolism confers carbon-source-dependent artemisinin resistance in Mycobacterium tuberculosis
Martini, M.C.*, Alonso, M. N.*, Cafiero, J. H., Xiao, J., and Shell, S. S.
Antimicrobial Chemotherapy. doi.org/10.1128/aac.00645-24
*Contributed equally to this work.

An O-methylflavone from Artemisia afra kills non-replicating hypoxic Mycobacterium tuberculosis
Kellogg, J. J., Alonso, M. N., Jordan, R. T., Xiao, J., Cafiero, J. H., Bush, T., Chen, X., Towler, M., Weathers, P., and Shell, S. S.
Journal of Ethnopharmacology. doi:10.1016/j.jep.2024.118500

Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs
Zhou,Y.*, Sun,H.*, Rapiejko, A.R., Vargas-Blanco, D.A., Martini, M.C., Chase, M.R., Joubran, S.R., Davis, A.B., Dainis, J.P., Kelly, J.M., Ioerger, T.R., Roberts, L.A., Fortune, S.M., and Shell, S.S.
J Biol Chem. 2023;299(11):105312. doi:10.1016/j.jbc.2023.105312
*Contributed equally to this work.

The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence
Bar-Oz, M.*, Martini, M.C.*, Alonso, M.N.*, Meir, M., Lore, N.I., Miotto, P., Riva, C., Angala, S.K., Xiao, J., Masiello, C.S., Misiakou, M.A., Sun, H., Moy, J.K., Jackson, M., Johansen, H.K., Cirillo, D.M., Shell, S.S., & Barkan, D.
PLoS Pathog. 2023;19(8):e1011575. doi:10.1371/journal.ppat.1011575
*Contributed equally to this work.

Artemisia afra and Artemisia annua Extracts Have Bactericidal Activity against Mycobacterium tuberculosis in Physiologically Relevant Carbon Sources and Hypoxia
Kiani, BH.* Alonso, MN.* Weathers, PJ. Shell, S.S. Pathogens. 2023;12(2):227. Published 2023 Feb 1. doi:10.3390/pathogens12020227
*Contributed equally to this work.

A research program-linked, course-based undergraduate research experience that allows undergraduates to participate in current research on mycobacterial gene regulation
Roberts, L.A. and Shell, S.S. Front Microbiol. 2022;13:1025250. doi.org/10.3389/fmicb.2022.1025250

Loss of RNase J leads to multi-drug tolerance and accumulation of highly structured mRNA fragments in Mycobacterium tuberculosis
Martini, M.C., Hicks, N.D., Xiao, J., Alonso, M.N., Barbier, T., Sixsmith, J., Fortune, S.M., and Shell, S.S.
PLoS Pathog. 2022;18(7):e1010705. doi:10.1371/journal.ppat.1010705

RNA Sequencing for Transcript 5′-End Mapping in Mycobacteria
Martini, M.C.; Sun, H.; and Shell, S.S. Methods Mol Biol. 2021;2314:513-531. doi:10.1007/978-1-0716-1460-0_22

MamA essentiality in Mycobacterium smegmatis is explained by the presence of an apparent cognate restriction endonuclease
Randall, S.E.*; Martini, M.C.*; Zhou, Y; Joubran, S.R.; and Shell, S.S. BMC Res Notes. 2020;13(1):462. doi:10.1186/s13104-020-05302-z
*Contributed equally to this work.

Regulation of mRNA Stability During Bacterial Stress Responses
Vargas-Blanco, D.A. and Shell, S.S. Front Microbiol. 2020;11:2111. doi:10.3389/fmicb.2020.02111

Artemisia annua and Artemisia afra extracts exhibit strong bactericidal activity against Mycobacterium tuberculosis
Martini, C.M.; Zhang, T.; Williams, J.T.; Abramovitch, R.B.; Weathers, P.J.; and Shell, S.S. J Ethnopharmacol. 2020;262:113191. doi:10.1016/j.jep.2020.113191

The Impact of Leadered and Leaderless Gene Structures on Translation Efficiency, Transcript Stability, and Predicted Transcription Rates in Mycobacterium smegmatis
Nguyen, T.A.*; Vargas-Blanco, D.A.*; Roberts, L.A.; and Shell, S.S. J Bacteriol. 2020;202(9):e00746-19. doi:10.1128/JB.00746-19
*Joint first authors.

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacterium smegmatis
Vargas-Blanco, D.A., Zhou, Y., Zamalloa, L.G., Antonelli, T., and Shell, S.S. mBio. 2019;10(4):e00957-19. doi:10.1128/mBio.00957-19

Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia
Martini, C.M., Zhou, Y., Sun, H., and Shell, S.S. Front Microbiol. 2019;10:591. doi:10.3389/fmicb.2019.00591

Mycobacterium tuberculosis Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network. Journal of Immunology
Keegan, C., Krutzik, S., Schenk, M., Scumpia, P.O., Lu, J., Pang, Y.L.J., Russell, B.S., Lim, K.S., Shell, S.S., Prestwich, E.G., Su, D., Elashoff, D., Hershberg, R.M., Bloom, B.R., Belisle, J.T., Fortune, S.M., Dedon, P.C., Pellegrini, M., Modlin, R.L. J Immunol. 2018;200(9):3244-3258. doi:10.4049/jimmunol.1701733

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape
Shell, S.S.*, Wang, J.*, Lapierre, P., Mir, M., Chase, M.R., Pyle, M.M., Gawande, R., Ahmad, R., Sarracino, D.A., Ioerger, T.R., Fortune, S.M., Derbyshire, K.M., Wade, J.T. and Gray, T.A. PLoS Genet. 2015;11(11):e1005641. doi:10.1371/journal.pgen.1005641
*Joint first authors.

The Psp system of Mycobacterium tuberculosis integrates envelope stress sensing and envelope preserving functions
Datta, P., Ravi, J., Guerrini, V., Chauhan, R., Neiditch, M.B., Shell, S.S., Fortune, S.M., Hancioglu, B., Igoshin, O., Gennaro, M.L. Mol Microbiol. 2015;97(3):408-422. doi:10.1111/mmi.13037

RNA sequencing for transcript 5′-end mapping in mycobacteria
Shell, S.S., Chase, M.R., Ioerger, T.R., & Fortune, S.M. Methods Mol Biol. 2015;1285:31-45. doi:10.1007/978-1-4939-2450-9_3

DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium tuberculosis
Shell, S.S., Prestwich, E.G., Baek, S.H., Shah, R.R., Sassetti, C.M., Dedon, P.C., and Fortune, S.M. PLoS Pathog. 2013;9(7):e1003419. doi:10.1371/journal.ppat.1003419

Interaction between the MSH2 and MSH6 nucleotide-binding sites in the S. cerevisiae MSH2-MSH6 complex
Hargreaves, V.V., Shell, S.S., Mazur, D.J., Hess, M.T., and Kolodner, R.D. J Biol Chem. 2010;285(12):9301-9310. doi:10.1074/jbc.M109.096388

Chimeric Saccharomyces cerevisiae Msh6 protein with an Msh3 mispair-binding domain combines properties of both proteins
Shell, S.S., Putnam, C.D., and Kolodner, R.D. Proc Natl Acad Sci U S A. 2007;104(26):10956-10961. doi:10.1073/pnas.0704148104

The N-terminal region of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA
Shell, S.S.*, Putnam, C.D.*, and Kolodner, R.D. Mol Cell. 2007;26(4):565-578. doi:10.1016/j.molcel.2007.04.024
*Joint first authors.

Dominant effects of an Msh6 missense mutation on DNA repair and cancer susceptibility
Yang, G., Scherer, S.J., Shell, S.S., Yang., K., Kim, L., Lipkin, M., Kucherlapati, R., Kolodner, R.D., and Edelmann, W. Cancer Cell. 2004;6(2):139-150. doi:10.1016/j.ccr.2004.06.024