Choudhery, S., Brown, A.J., Akusobi, C., Rubin, E.J., Sassetti, C.M.,
and Ioerger, T.R (2021). Modeling site-specific nucleotide biases
affecting Himar1 transposon insertion frequencies in TnSeq datasets.
mSystems, 6(5):e0087621.
pubmed
Subramaniyam, S., DeJesus, M.A., Zaveri, A., Smith, C.M., Baker, R.E.,
Ehrt, S., Schnappinger, D., Sassetti, C.M., and Ioerger, T.R. (2019).
Statistical analysis of variability in TnSeq data across conditions
using Zero-Inflated Negative Binomial Regression.
BMC Bioinformatics, 20(1):603.
pubmed
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.
pubmed
PDF
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.
pubmed
PDF
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.
pubmed
PDF
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.
pubmed
PDF
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).
Best Paper Award!
PDF
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,
12(1):92-102.
pubmed
PDF
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, 14:303.
pubmed
PDF
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!
PDF
DeJesus, M.A., Zhang, Y.J., Sassettti, 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. pubmed
PDF
Zhang, Y.J., Ioerger, T.R., Huttenhower, C., Chen, X., Mohaideen, N.,
Long, J., Sassetti, C.M., Sacchettini, J.C. and Rubin, E.J. (2012).
Global assessment of genomic regions required for growth in Mycobacterium
tuberculosis. PLoS Pathogens, 8(9):e1002946.
pubmed
PDF
Griffin, J.E., Gawronski, J.D., DeJesus, M.A., Ioerger, T.R., Akerley, B.J.,
Sassetti, C.M. (2011). High-resolution phenotypic profiling defines genes
essential for mycobacterial survival and cholesterol catabolism. PLoS
Pathogens, 7(9):e1002251. pubmed
PDF
Ioerger, T.R. (2022). Analysis of Gene Essentiality from TnSeq Data
Using Transit. in: Zhang R. (eds) Essential Genes and
Genomes. Methods in Molecular Biology, vol 2377. Humana, New York,
NY, 2377:391-421.
pubmed
Long, J.E., DeJesus, M., Ward, D., Baker, R.E., Ioerger, T.R. and
Sassetti, C.M. (2015).
Identifying essential genes in Mycobacterium tuberculosis by global
phenotypic profiling. in:
Methods in Molecular Biology: Gene Essentiality,
(Long Jason Lu, ed.), vol. 1279.
Drug Discovery
Yadav, V., Boshoff, H., Trifonov, L., Roma, J., Ioerger, T., Barry, C., Oh, S. (2023).
Synthesis and structure-activity relationships of a new class of
oxadiazoles targeting DprE1 as antitubercular agents.
ACS Medicinal Chemistry Letters, 14(9):1275-1283.
pubmed
Koller, T., Scheid, U,. Koesel, T,. Herrmann, J,. Krug, D,. Boshoff,
H., Beckert, B., Evans, J., Schlemmer, J., Sloan, B., Weiner, D., Via,
L., Moosa, A., Ioerger, T., Graf, M., Zinshteyn, B., Abdelshahid, M.,
Nguyen, F., Arenz, S., Gille, F., Siebke, M., Seedorf, T.,
Plettenburg, O., Green, R., Warnke, A.-L., Ullrich, J., Warrass, R.,
Barry, C., Warner, D., Mizrahi, V., Kirschning, A., Wilson, D.,
Mueller, R. (2022). The Myxobacterial Antibiotic Myxovalargin:
Biosynthesis, Structural Revision, Total Synthesis and Molecular
Characterization of Ribosomal Inhibition.
Journal of the American Chemical Society, 145(2):851-863.
pubmed
Singh, V., Grzegorzewicz, A., Fienberg, S., Mueller, R., Khonde, L.P.,
Sanz, O., Alfonso, S., Urones, B., Drewes, G., Bantscheff, M.,
Ghidelli-Disse, S., Ioerger, T.R., Angala, B., Liu, J.,
Lee, R., Sacchettini, J.C., Krieger, I., Jackson, M., Chibale, K.,
Ghorpade, S. (2022).
1,3-Diarylpyrazolyl-acylsulfonamides target HadAB/BC complex in
Mycobacterium tuberculosis.
ACS Infectious Diseases, 8(11):2315-2326.
pubmed
Pepi MJ, Chacko S, Marqus GM, Singh V, Wang Z, Planck K, Cullinane RT,
Meka PN, Gollapalli DR, Ioerger TR, Rhee KY, Cuny GD, Boshoff HIM,
Hedstrom L. (2022). A D-phenylalanine-benzoxazole derivative reveals
the role of the essential enzyme Rv3603c in the pantothenate
biosynthetic pathway of Mycobacterium tuberculosis.
ACS Infectious Diseases, 8(2):330-342.
pubmed
Consalvi, S., Venditti, G., Zhu, J., Boshoff, H.I., Arora, K., De Logu, A.,
Ioerger, T.R., Rubin, E.J., Biava, M., and Poce, G. (2021).
6-Fluorophenylbenzohydrazides inhibit Mycobacterium tuberculosis
growth through alteration of tryptophan biosynthesis. European Journal
of Medicinal Chemistry, 226:113843.
pubmed
Oh S, Libardo MDJ, Azeeza S, Pauly GT, Roma JSO, Sajid A, Tateishi
Y, Duncombe C, Goodwin M, Ioerger TR, Wyatt PG, Ray PC, Gray DW,
Boshoff HIM, Barry CE 3rd. (2021). Structure-Activity Relationships of
Pyrazolo[1,5-a]pyrimidin-7(4H)-ones as Antitubercular Agents. ACS
Infectious Diseases, 7(2):479-492.
pubmed
Libardo MDJ, Duncombe CJ, Green SR, Wyatt PG, Thompson S, Ray PC,
Ioerger TR, Oh S, Goodwin MB, Boshoff HIM, Barry CE 3rd. (2021). Resistance
of Mycobacterium tuberculosis to indole 4-carboxamides occurs through
alterations in drug metabolism and tryptophan biosynthesis. Cell Chem Biol, 28(8):1180-1191.e20.
pubmed
Shelton, C., McNeil, M., Early, J., Ioerger, T.R., and Parish, T. (2021).
Deletion of Rv2571c confers resistance to arylamide compounds in
Mycobacterium tuberculosis.
Antimicrobial Agents and Chemotherapy, 65(5):e02334-20.
pubmed
Chengalroyen, M.D., Jordaan, A., Seldon, R., Ioerger, T.R., Franzblau,
S.G., Nasr, M., Warner, D.F., and Mizrahi, V. (2020). Biological
profiling enables rapid mechanistic classification of phenotypic
screening hits and identification of KatG activation-dependent
pyridine carboxamide prodrugs with activity against Mycobacterium
tuberculosis.
Frontiers in Cellular and Infection Microbiology, 10:582416.
pubmed
Rehberg, N., Sommer, G., Driessen, D., Kruppa, M., Adeniyi, E., Chen, S., Wang, L.,
Wolf, K., Tasch, B, Ioerger, T.R., Zhu, K, Mueller, T.J.J. and Kalscheuer, R.K.
(2020).
Nature-inspired
(di)azine-bridged bisindole alkaloids with potent antibacterial in
vitro and in vivo efficacy against
Methicillin-resistant Staphylococcus aureus.
Journal of Medicinal Chemistry, 63(21):12623-12641.
pubmed
van Geelen, L., Kaschani, F., Sazzadeh, S.S., Adeniyi, E.T., Meier, D., Proksch, P., Pfeffer, K., Kaiser, M., Ioerger, T.R., and Kalscheuer, R. (2020).
Natural brominated phenoxyphenols kill persistent and biofilm-incorporated cells of MRSA and other pathogenic bacteria.
Applied Microbiology and Biotechnology, 104(13):5985-5998.
pubmed
Akester, J., Njaria, P., Nchinda, A., Le Manach, C., Myrick, A., Singh, V., Lawrence, N., Njoroge, M., Taylor, D., Moosa, A., Smith, A., Brooks, E., Lenaerts, A., Robertson, G., Ioerger, T.R., Mueller, R., and Chibale, K. (2020).
Synthesis, structure activity relationship and mechanistic studies of aminoquinazolinones displaying antimycobacterial activity.
ACS Infectious Diseases, 6(7):1951-1964.
pubmed
Poce, G., Consalvi, S., Venditti, G., Alfonso, S., Desideri, N.,
Fernandez-Menendez, R., Bates, R., Ballell, L., Barros Aguirre, D.,
Rullas, J., De Logu, A., Gardner, M., Ioerger, T.R., Rubin, E. and Biava, M. (2019).
Novel pyrazole containing compounds active against Mycobacterium tuberculosis.
ACS Medicinal Chemistry Letters, 10(10):1423-1429.
pubmed
Park, Y. Ahn, Y.-M., Jonnala, S., Oh, S., Fisher, J., Goodwin,
M. Ioerger, T.R., Via, L., Bayliss, T., Green, S., Ray, P., Wyatt, P.,
Barry, C., and Boshoff, H. (2019). Inhibition of CorA-dependent
magnesium homeostasis is cidal in Mycobacterium tuberculosis.
Antimicrobial Agents & Chemotherapy, 63(10):e01006-19.
pubmed
Rehberg, N., Omeje, E., Ebada, S., van Geelen, L., Liu, Z,
Sureechatchayan, P., Kassack, M., Ioerger, T.R., Proksch, P. and
Kalscheuer, R. (2019). 3-O-Methyl-alkylgallates inhibit fatty acid
desaturation in Mycobacterium tuberculosis. Antimicrobial
Agents and Chemotherapy, 63(9):e00136-19.
pubmed
Johnson, E.O., LaVerriere, E., Stanley, M., Office, E., Meyer, E.,
Kawate, T., Gomez, J., Audette, R.E., Bandyopadhyay, N., Betancourt,
N., Delano, K., Da Silva, I., Davis, J., Gallo, C., Gardner, M.,
Golas, A., Guinn, K.M., Korn, R., McConnell, J.A., Moss, C.E., Murphy,
K.C., Neitupski, R., Papavinasasundaram, K.G., Pinkham, J.T., Pine,
P.A., Proulx, M.K., Ruecker, N., Song, N., Thompson, M., Trujillo, C.,
Wakabayashi, S., Wallack, J.B., Watson, C., Ioerger, T.R,. Lander,
E.S., Hubbard, B.K., Serrano-Wu, M.H., Ehrt, S., Fitzgerald, M.,
Rubin, E.J., Sassetti, C.M., Schnappinger, D., and Hung, D.T. (2019).
Large-scale chemical-genetics yields new M. tuberculosis
inhibitor classes.
Nature, s41586-019-1315-z.
pubmed
PDF
Ballinger, E, Mosior, J., Harman, T., Burns-Huang, K. Gold, B., Morris, R.,
Goullieux, L., Blanc, I., Lagrange, Sl., Fraisee, L., Sans, S., Couturier, C.,
Bacque, E., Rhee, K., Scarry, S.M., Aube, J., Yang, G., Ouerfelli, O.,
Schnappinger, D., Ioerger, T.R., Engelhart, C.A., McConnell, J.A.,
McAulay, K., Roubert, C., Sacchettini, J.C., and Nathan, C. (2019).
Opposing reactions in coenzyme A metabolism make Mycobacterium tuberculosis
vulnerable to inhibition of a new target. Science, 363(6426):eaau8959.
pubmed
PDF
Singh, S.B., Odingo, J., Bailey, M.A., Sunde, B., Korkegian, A.,
O'Malley, T., Ovechkina, Y., Ioerger, T.R., Sacchettini, J.C., Young,
K., Olsen, D.B., and Parish, T. (2018). Identification of cyclic
hexapeptides natural products with inhibitory potency
against Mycobacterium tuberculosis. BMC Research Notes, 11(1):416.
pubmed
PDF
Xia, Y., Zhou, Y., Carter, D., McNeil, M., Choi, W., Halladay, J., Berry, P.,
Mao, W., Hernandez, V., O'Malley, T., Korkegian, A., Sunde, B., Flint, L.,
Woolhiser, L., Scherman, M., Gruppo, V., Hastings, C., Robertson, G.,
Ioerger, T.R., Sacchettini, J.C., Tonge, P., Lenaerts, A., Parish, T.,
and M.R.K. Alley (2018).
Discovery of a cofactor-independent inhibitor of Mycobacterium tuberculosis InhA.
Life Science Alliance, 113(49):E7880-E7889.
pubmed
PDF
Ganley, J.G. Carr, G., Ioerger, T.R., Sacchettini, J.C., Clardy,
J. and Derbyshire, E.R. (2018). Discovery of antimicrobial
lipodepsipeptides produced by a Serratia sp. within
mosquito microbiomes.
ChemBioChem, 19(15):1590-1594.
pubmed
PDF
Murugesan, D., Ray, P.C., Bayliss, T., Prosser, G.A., Harrison, J.R., Green, K.,
Soares de Melo, C., Feng, T.-S., Street, L.J., Chibale, K.,
Warner, D.F., Mizrahi, V., Epemolu, O., Scullion, P., Ellis, L.,
Riley, J., Shishikura, Y., Ferguson, L., Osuna-Cabello, M., Read, K.D., Green, S.R.,
Lamprecht, D.A., Finin, P.M., Steyn, A.J.C., Ioerger, T.R., Sacchettini, J.C.,
Rhee, K.Y., Arora, K., Barry, III, C.E., Wyatt, P.G., Boshoff, H.I.M. (2018).
2-Mercapto-quinazolinones as inhibitors of NDH-2 and Mycobacterium tuberculosis:
Structure-activity relationships, mechanism of action and ADME characterization.
ACS Infectious Diseases, 4(6):954-969.
pubmed
PDF
Negri, A., Javidnia, P., Mu, R., Zhang, X., Vendome, A., Gold, B., Roberts, J.,
Barman, D., Ioerger, T.R., Sacchettini, J.C., Jiang, X., Burns-Huang, K., Warrier, T.,
Ling, Y., Warren, D., Oren, D., Beuming, T., Wang, H., Wu, J., Li, H., Rhee, K.,
Nathan, C., Liu, G., Somersan-Karakaya, S. (2018). Identification of a
mycothiol-dependent nitroreductase from Mycobacterium tuberculosis.
ACS Infectious Disease, 4(5):771-787.
pubmed
PDF
Tiwari, D., Park, S.W., Essawy, M.M., Dawadi, S., Mason, A., Nandakumar, M.,
Zimmerman, M., Mina, M., Ho, H.P., Engelhart, C., Ioerger, T.R., Sacchettini,
J.C., Rhee, K., Ehrt, S., Aldrich, C.C., Dartois, V. and Schnappinger, D. (2018). Targeting protein biotinylation enhances tuberculosis chemotherapy.
Science Translational Medicine, 10:eeal1803.
pubmed
PDF
Korkegian, A., O'Malley, T., Xia, Y., Zhou, Y., Carter, D.S., Sunde,
B., Flint, L., Thompson, D., Ioerger, T.R., Sacchettini, J.C., Alley,
M.R.K,., Parish, T. (2018). The 7-phenyl benzoxaborole series is
active against Mycobacterium tuberculosis. Tuberculosis,
108:96-98.
pubmed
PDF
Rehberg, N., Akone, H., Ioerger, T.R., Erlenkamp, G., Daletos, G.,
Gohlke, H., Proksch, P., and Kalscheuer, R. (2017).
Chlorflavonin targets acetohydroxyacid synthase catalytic
subunit IlvB1 for synergistic killing of Mycobacterium
tuberculosis. ACS Infectious Disease, 4(2):123-134.
pubmed
PDF
Chandrasekara, N., Berube, B., Shetye, G., O'Malley, T., Chettiar, S.,
Manning, A., Flint, L., Awasthi, D., Ioerger, T.R., Sacchettini, J.C.,
Masquelin, T., Hipskind, P., Odingo, J. and Parish, T. (2017).
Improved phenoxyalkylbenzimidazoles with activity against
Mycobacterium tuberculosis appear to target QcrB.
ACS Infectious Diseases, 3(12):898-916.
pubmed
PDF
Moosa, A., Lamprecht, D., Arora, K., Barry C.E., Boshoff, H.I.M.,
Ioerger, T.R., Steyn, A., Mizrahi, V. and Warner, D. (2017).
Susceptibility of Mycobacterium tuberculosis cytochrome bd oxidase mutants to compounds targeting the terminal respiratory oxidase, cytochrome c.
Antimicrobial Agents and Chemotherapy, 61(10):e01338-17.
pubmed
PDF
Patel, N., O'Malley, T., Zhang, Y.-K., Xia, Y., Sunde, B., Flint, L.,
Korkegian, A., Ioerger, T.R., Sacchettini, J.C., Alley, M.R.K, and
Parish, T. (2017). A novel 6-benzyl ether benzoxaborole is active
against Mycobacterium tuberculosis in vitro. Antimicrobial
Agents and Chemotherapy, 61(9):e01205-17.
pubmed
PDF
Aggarwal, A., Parai, M.K., Shetty, N., Wallis, D., Woolhiser, L.,
Hastings, C., Dutta, N.K., Galaviz, S., Dhakal, R.C., Shrestha, R.,
Wakabayashi, S., Walpole, C., Matthews, D., Floyd, D., Scullion, P.,
Riley, J., Epemolu, O., Norval, S., Snavely, T., Robertson, G.T.,
Rubin, E.J., Ioerger, T.R., Sirgel, E.A., van der Merwe, R., van
Helden, P.D., Keller, P., Böttger, E.C., Karakousis, P.C.,
Lenaerts, A.J., Sacchettini, J.C. (2017). Development of a novel
lead that targets M. tuberculosis polyketide synthase
13. Cell, 170(2):249-259.
pubmed
PDF
Park, Y.,
Pacitto, A.,
Bayliss, T.,
Cleghorn, L.A.T,
Wang, Z.,
Hartman, T.,
Arora, K.,
Ioerger, T.R.,
Saccettini, J.C.,
Rizzi, M.,
Zhou, N.,
Dartois, V.,
Jonnala, S.,
Via, L.E.,
Mizrahi, V.,
et al,
Barry, C.E. and
Boshoff, H.I.M. (2017).
Essential but not vulnerable: indazole sulfonamides targeting IMPDH as
potential leads against Mycobacterium tuberculosis.
ACS Infectious Diseases, 3(1):18-33.
pubmed
PDF
Palencia, A. Li, X., Bu., W., Choi, W., Ding, C., Easom, E., Feng, L.,
Hernandez, V., Houston, P., Liu, L., Meewan, M., Mohan, M., Rock, F., Sexton,
H., Zhang, S., Zhou, Y., Wan, B., Wang, Y., Franzblau, S., Woolhiser, L.,
Gruppo, V., Lenaerts, A., O'Malley, T., Parish, T., Cooper, C., Waters, M.G.,
Ma, Z., Ioerger, T.R., Sacchettini, J.C., Rullas, J., Angulo-Barturen, I.,
Perez-Herran, E., Mendoza-Losana, A., Barros-Aquirre, D., Cusack, S.,
Plattner, J., and Alley, M.R.K. (2016). Discovery of novel oral protein
synthesis inhibitors of Mycobacterium tuberculosis that target
leucyl-tRNA synthetase. Antimicrobial Agents and Chemotherapy,
60(10):6271-80.
pubmed
PDF
Warrier, T., Kapilashrami, K., Argyou, A., Ioerger, T.R., Little, D., Murphy,
K., Nandakumar, M., Park, S., Gold, B., Mi, J., Zhang, T., Meiler, E., Rees,
M., Somersan-Karakaya, S., Porras-De Francisco, E., Martinez-Hoyos, M.,
Burns-Huang, K., Roberts, J., Ling, Y., Rhee, K., Mendoza-Losana, A., Luo,
M. and Nathan, C. (2016). N-methylation of a bactericidal compound as a
resistance mechanism in Mycobacterium tuberculosis. PNAS,
113(31):E4523-E4530.
pubmed
PDF
Dragset, M., Poce, G., Alfonso, S., Padilla-Benavides, T., Ioerger,
T.R., Kaneko, T., Sacchettini, J.C., Biava, M., Parish, T., Arguello,
J., Steigedal, M., and Rubin, E.J. (2015). A novel antimycobacterial
compound acts as an intracellular iron chelator. Antimicrobial
Agents and Chemotherapy, 59(4):2256-64.
pubmed
PDF
Odingo J, O'Malley T, Kesicki EA, Alling T, Bailey MA, Early J, Ollinger J,
Dalai S, Kumar N, Singh RV, Hipskind PA, Cramer JW, Ioerger T, Sacchettini J,
Vickers R, Parish T. (2014).
Synthesis and evaluation of the 2,4-diaminoquinazoline series as
anti-tubercular agents.
Bioorg Med Chem., 22(24):6965-79.
pubmed
PDF
Ioerger, T.R., O'Malley, T., Liao, R., Guinn, K.M., Hickey, M.J., Mohaideen,
N., Murphy, K.C., Boshoff, H.I.M., Mizrahi, V., Rubin, E.J., Sassetti, C.M.,
Barry, C.E., Sherman, D.R., Parish, T., and Sacchettini, J.C.
(2013). Identification of new drug targets and resistance mechanisms in
Mycobacterium tuberculosis. PLOS ONE, 8(9):e75245.
pubmed
PDF
Stanley, S.A., Kawate, T., Iwase, N., Shimizu, M., Clatworthy, A.,
Kazyanskaya, E., Sacchettini, J.C., Ioerger, T.R., Siddiqi, N., Minami, S.,
Aquadro, J.A., Grant, S.S., Rubin, E.J. and Hung, D.T. (2013).
Diarylcoumarins inhibit mycolic acid biosynthesis and
kill M. tuberculosis by targeting FadD32. Proceedings of the National Academy of Sciences (PNAS), 110(28):11565-70.
pubmed
PDF
Krieger, I., Freundlich, J., Gawandi, Vijay, Roberts, J., Gawandi, Vidya, Sun,
Q., Owen, J., Fraile, M., Huss, S., Duncan, K., Lavandera, J.-L., Ioerger,
T.R., and Sacchettini, J.C. (2012). Structure-guided discovery of phenyl
diketo-acids as potent inhibitors of M. tuberculosis malate synthase.
Chemistry & Biology, 19(12):1556-1567.
pubmed
PDF
La Rosa, V., Poce, G., Canseco, J.O., Buroni, S.,
Pasca, M.R., Biava, M., Raju, R.M., Porretta, C. Alfonso, S.
Battilocchio, C., Javid, B., Sorrentino, F., Ioerger, T., Sacchettini,
J., Manetti, F., Botta, M., De Logu, A., Rubin, E., and De Rossi, E.
(2012). MmpL3 is the
cellular target of the antitubercular pyrrole derivative BM212.
Antimicrobial Agents and Chemotherapy, 56(1):324-31.
pubmed
PDF
Cho, Y., Ioerger, T.R. and Sacchettini, J.C. (2008).
Discovery of novel nitrobenzothiazole inhibitors for M. tuberculosis
ATP phosphoribosyl transferase (HisG) through virtual screening.
Journal of Medicinal Chemistry, 51(19):5984-5992.
pubmed
Antibiotic Resistance
Omollo, C., Singh, V., Kigondu, E., Wasuna, A.,
Agarwal, P., Moosa, A., Ioerger, T.R., Mizrahi, V., Chibale, K.
and Warner, D. (2021).
Developing synergistic drug combinations to restore antibiotic
sensitivity in drug-resistant Mycobacterium tuberculosis.
Antimicrobial Agents and Chemotherapy, 5(5):e02554-20.
pubmed
Rifat, D., Li, S-Y, Ioerger, T.R., Shah, K. Lanoix, J-P, Lee,
J. Bashiri, G., Sacchettini, J.C., and Nuermberger, E. (2020).
Mutations in fbiD (Rv2983) as a novel determinant of resistance to
pretomanid and delamanid in Mycobacterium
tuberculosis. Antimicrobial Agents and Chemotherapy, AAC.01948-20.
pubmed
Morbidoni, H.R., de loa Iglesia, A.I., Figueroa, V., di Capua, C.,
Ioerger, T.R., and Parish, T. (2019).
Mutations in the anti-sigma H factor RshA confer resistance to econazole and clotrimazole in Mycobacterium smegmatis.
Access Microbiology,
1(10):acmi.0.0000070.
Farhat, M.R., Freschi, L., Calderon, R., Ioerger, T.R., Snyder, M.,
Meehan, C.J., de Jong, B., Rigouts, L., Sloutsky, A., Kaur, D.,
Sunyaev, S., van Soolingen, D., Shendure, J., Sacchettini, J.C.,
and Murray, M. (2019).
Genome wide association with quantitative resistance phenotypes in
Mycobacterium tuberculosis reveals novel resistance genes and
regulatory regions. Nature Communications, 10(1):2128.
pubmed
PDF
Blanc, L., Sarathy, J., Cabrera, N.A., O'Brien, P., Dias-Freedman, I.,
Mina, M., Sacchettini, J.C., Savic, R., Gengenbacher, M., Podell, B.,
Prideaux, B., Ioerger, T.R., Dick, T., and Dartois, V. (2018).
Impact of immunopathology on the antituberculous activity of
pyrazinamide. Journal of Experimental Medicine, 215(8):1975-1986.
pubmed
PDF
Campodonico, V.L., Rifat, D., Chuang, Y.-M., Ioerger, T.R, and Karakousis, P.C. (2018).
Altered Mycobacterium tuberculosis cell wall metabolism and physiology associated with
RpoB mutation H526D. Frontiers in Microbiology, 9:494.
pubmed
PDF
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,
61(12):e01334-17.
pubmed
PDF
Yadon, A.N., Maharaj, K., Adamson, J.H., Lai, Y.-P., Sacchettini, J.C.,
Ioerger, T.R., Rubin, E.J., and Pym, A.S. (2017).
Comprehensive characterization of pncA polymorphisms conferring
resistance to pyrazinamide. Nature Communications, 8(1):588.
pubmed
PDF
Gomez, J.,
Kaufmann-Malaga, B., Wivagg, C., Kim, P.,
Silvis, M., Renedo, N., Ahmad, R., Livny, J.,
Ioerger, T.R., Sacchettini, J.C., Carr, S., and Hung, D. (2017).
Ribosomal mutations promote the evolution of antibiotic resistance in
a multidrug environment. eLife, 6:e20420.
pubmed
PDF
Lanzas, F., Ioerger, T.R., Shah, H., Acosta, W., and Karakousis, P.C. (2016).
First evaluation of GenoType MTBDRPlus 2.0 performed directly on respiratory
specimens in Central America. Journal of Clinical Microbiology,
54(10):2498-502.
pubmed
PDF
Almeida, D., Ioerger, T.R., Tyagi, S. Li, S.-Y., Mdluli, K., Andries, K.,
Grosset, J., Sacchettini, J.C., and Nuermberger, E. (2016) Mutations in pepQ
confer low-level resistance to bedaquiline and clofazimine in Mycobacterium
tuberculosis. Antimicrobial Agents and Chemotherapy, 60(8):4590-9.
pubmed
PDF
Lanoix, J.P, Ioerger, T.R., Ormond, A., Kaya, F., Sacchettini, J., Dartois,
V., and Nuermberger, E. (2015). Selective inactivity of pyrazinamide against
tuberculosis in C3HeB/FeJ mice is best explained by neutral pH of caseum.
Antimicrobial Agents and Chemotherapy, 60(2):735-43.
pubmed
PDF
Chia, B.-S., Lanzas, F., Rifat, D., Herrera, A., Kim, E.Y., Sailer, C.,
Torres-Chavolla, E., Narayanaswamy, P., Einarsson, V., Bravo, J., Pascale,
J.M., Ioerger, T.R., Sacchttini, J.C. and Karakousis, P.C. (2012). Use of
multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect
multidrug-resistant Tuberculosis in Panama. PLoS ONE, 7(7):e40456.
pubmed
PDF
Wang, F., Jain, P., Gulten, G., Liu, Z., Feng, Y., Ganesula, K., Motiwala,
A.S., Ioerger, T.R., Alland, D., Vilcheze, C., Jacobs, W.R. and Sacchettini1,
J.C. (2010). Mycobacterium tuberculosis dihydrofolate reductase is not
a target relevant to the anti-tubercular activity of
isoniazid. Antimicrobial Agents and Chemotherapy, 54(9):3776-3782.
pubmed
PDF
Tuberculosis Biology
Zhou, Y., Sun, H., Vargas-Blanco, D.A., Martini, M.C., Raplejkl, A.R., Chase, M.R.,
Jourban, S.R., Davis, A.B., Dainis, J.P., Kelly, J.M., Ioerger, T.R.,
Roberts, L.A., Fortune, S.M., and Shell, S.S. (2023).
Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs.
Journal of Biological Chemistry, 299(11):105312.
pubmed
Matern, W.M., Harris, H.T., Danchik, C., McDonald, M, Patel, G., Srivastava, A. Ioerger, T.R., Bader, J.S., and Karakousis, P.C. (2023).
Functional whole genome screen of nutrient-starved Mycobacterium
tuberculosis identifies genes involved in antibiotic tolerance.
Microorganisms, 11(9):2269.
pubmed
Nelson SJ, Williams JT, Buglino JA, Nambi S, Lojek LJ, Glickman MS,
Ioerger TR, Sassetti CM. (2023).
The Rip1 intramembrane protease contributes
to iron and zinc homeostasis in Mycobacterium
tuberculosis. mSphere, e0038922.
pubmed
Vargas, R., Luna, M.J., Freschi, L., Marin, M., Froom, R., Murphy,
K.C., Campbell, E.A., Ioerger, T.R., Sassetti, C.M., and Farhat
M.R. (2023). Phase variation as a major mechanism of adaptation in
Mycobacterium tuberculosis complex.
PNAS, 120(28):e2301394120.
pubmed
Akusobi, C., Benghomari, B.S., Zhu, J., Wolf, I.D.,
Singhvi, S., Dulberger, C.L., Ioerger, T.R., and Rubin, E.J. (2022).
High-density transposon mutagenesis in Mycobacterium abscessus
identifies an essential penicillin-binding lipo-protein (PBP-lipo)
involved in septal peptidoglycan
synthesis and antibiotic sensitivity.
eLife, 10.7554/eLife.71947.
pubmed
Koh EI, Oluoch PO, Ruecker N, Proulx MK, Soni V, Murphy KC,
Papavinasasundaram K, Reames CJ, Trujillo C, Zaveri A, Zimmerman MD,
Aslebagh R, Baker RE, Shaffer SA, Guinn KM, Fitzgerald M, Dartois V,
Ehrt S, Hung DT, Ioerger TR, Rubin EJ, Rhee KY, Schnappinger D,
Sassetti CM. (2022).
Chemical-genetic interaction mapping links carbon metabolism and cell
wall structure to tuberculosis drug efficacy.
PNAS, 119(15):e2201632119.
pubmed
Carey, A., Wang, X., Cicchetti, N., Spaulding, C., Liu, Q., Hopkins,
F., Brown, J., Sixsmith, J., Sutiwisesak, R., Behar, S., Ioerger,
T.R., and Fortune, S. (2022). Multiplexed strain phenotyping defines
consequences of genetic diversity in Mycobacterium tuberculosis for
infection and vaccination outcomes. mSystems, 7(3):e0011022.
pubmed
Smith, C.M., Baker, R.E., Proulx, M.K., Mishra, B.B., Long, J.E.,
Park, S.W., Lee, H.-N., Kiritsy, M.C., Bellerose, M.M., Olive, A.J.,
Murphy, K.C., Papavinasasundaram, K. Boehm, F.J., Reames, C.J., Meade,
R.K., Hampton, B.K., Linnertz, C.L., Shaw, G.D., Hock, P., Bell, T.A.,
Ehrt, S., Schnappinger, D., Pardo-Manuel de Villena, F., Ferris, M.T.,
Ioerger, T.R., and Sassetti, C.M. (2022). Host-pathogen genetic
interactions underlie tuberculosis susceptibility in genetically
diverse mice. eLife, 11:e74419.
pubmed
Babu Sait, M.R., Koliwer-Brandl, H., Stewart, J.A., Swarts, B.M.,
Jacobsen, M., Ioerger, T.R., and Kalscheuer R. (2022). PPE51 mediates
uptake of trehalose across the mycomembrane of Mycobacterium
tuberculosis. Scientific Reports, 12(1):2097.
pubmed
Mesman, A., Baek, S.-H., Huang, C.-C., Kim, Y.M.,
Cho, S.-R., Ioerger, T.R, Barreda, N.N., Calderon, R.,
Sassetti, C.M., and Murray, M. (2021).
Characterization of drug-resistant lipid-dependent differentially
detectable Mycobacterium tuberculosis.
Journal of Clinical Medicine, 10(15):3249.
pubmed
Su, H., Lin, K., Tiwari, D., Healy, C., Trujillo, C., Liu, Y.,
Ioerger, T.R., Schnappinger, D., and Ehrt, S. (2021). Genetic models
of latent tuberculosis in mice reveal differential control by adaptive
immunity. Journal of Experimental Medicine, 218(9):e20210332.
pubmed
Fishbein, S., Tomasi, F., Wolf, I., Dulberger, C., Wang, A., Keshishian, H., Wallace, L., Carr, S., Ioerger, T.R., Rego, E.H. and Rubin, E.J. (2020).
The conserved translation factor LepA is required for optimal synthesis of a porin family in Mycobacterium smegmatis.
Journal of Bacteriology, 203(6):e00604-20.
pubmed
Bandekar, A.C., Subedi, S., Ioerger, T.R., and Sassetti, C.M. (2020).
Cell cycle-associated expression patterns predict gene function
in mycobacteria. Current Biology, 30(20):3961-3971.
pubmed
Bellerose, M.M., Proulx, M.K., Smith, C.M., Baker, R.E., Ioerger, T.R.,
and Sassetti, C.M. (2020).
Distinct bacterial pathways influence the efficacy of antibiotics against
Mycobacterium tuberculosis. mSystems, 5(4):e00396-20.
pubmed
Zhang, L., Hendrickson, R.C., Meikle, V., Lefkowitz, E.J.,
Ioerger, T.R., and Niederweis, M. (2020).
Comprehensive analysis of iron utilization by Mycobacterium tuberculosis.
PLoS Pathogens, 16(2):e1008337.
pubmed
Dragset, M., Ioerger, T.R., Loevenich, M., Haug, M., Sivakumar, N.,
Marstad, A., Cardona, P., Klinkenberg, G., Rubin, E.J., Steigedal, M.,
and Flo, T. (2019). Global assessment of Mycobacterium avium
subspecies hominissuis genetic requirement for growth and
virulence. mSystems,
4(6):e00402-19.
pubmed
Dragset, M.S., Ioerger, T.R., Zhang, Y.J., Zekarias, Maerk, M., Ginbot, Z.,
Sacchettini, J.C., Flo, T.H., Rubin, E.J., Steigedal, M. (2019).
Genome-wide phenotypic profiling identifies and categorizes genes
required for mycobacterial low iron fitness.
Scientific Reports, 9(1):11394.
pubmed
Kannan, N., Lai, Y.-P., Haug, M., Lilleness, K.,
Bakke, S., Marstad, A., Hov, H., Nausdal, T., Afset, J.E., Ioerger, T.R.,
Flo, T., and Steigedal, M. (2019).
Genetic variation/evolution and differential host responses resulting
from in-patient adaptation of Mycobacterium avium.
Infection and Immunity, IAI.00323-18.
pubmed
PDF
Wu, K.J., Boutte, C.C., Ioerger, T.R., and Rubin, E.J. (2018).
Mycobacterium smegmatis HtrA blocks the toxic activity of a
putative cell wall amidase. Cell Reports, 27(8):2468-2479.e3.
pubmed
PDF
Steindor, M., Nkwouano, V. Stefanski, A., Stuehler, K., Ioerger, T.R.,
Bogumil, D., Jacobsen, M., Mackenzie, C.R., Kalscheuer, R. (2018). A
proteomics approach for the identification of species-specific
immunogenic proteins in the Mycobacterium abscessus complex.
Microbes and Infection, pii: S1286-4579(18)30168-0.
pubmed
PDF
Rego, H., Baranowski, C., Welch, M., Sham, L.-T., Eskandarian, H., Lim, H.,
Kieser, K., Wagner, J., McKinney, J., Fantner, G., Ioerger, T.R.,
Walker, S., Berhardt, T., and Rubin, E.J. (2018).
Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical
crosslinks to maintain shape. eLife, e37516.
pubmed
PDF
Carey, A.F., Rock, J.M., Krieger, I.V., Chase, M.R., Fernandez-Suarez,
M., Gagneux, S., Sacchettini, J.C., Ioerger, T.R, and Fortune,
S.M. (2018). TnSeq of Mycobacterium tuberculosis clinical isolates
reveals strain-specific antibiotic liabilities.
PLOS Pathogens, 14(3):e1006939.
pubmed
PDF
Perkowski, E.F., Zulauf, K.E., Weerakoon, D., Hayden, J.D., Ioerger, T.R.,
Oreper, D., Gomez, S., Sacchettini, J.C., and Braunstein, M. (2017).
The EXIT Strategy: An approach for identifying bacterial proteins exported during host infection. mBio, 8(2):e00333-17.
pubmed
PDF
Puckett, S., Trujillo, C., Wang, Z., Eoh, H., Ioerger, T.R., Krieger, I., Sacchettini, J.C.,
Schnappinger, D., Rhee, K.Y., and Ehrt, S. (2017).
Glyoxylate detoxification is an essential function of malate synthase
required for carbon assimilation in Mycobacterium tuberculosis.
PNAS, 114(11):E2225-E2232.
pubmed
PDF
Korte, J., Alber, M., Trujullo, C.M., Syson, K. Koliwer-Brandl, H., Deenen, R.,
Köhrer, K., DeJesus, M.A., Hartman, T., Jacobs, W.R. Jr.,
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.
pubmed
PDF
Koliwer-Brandl, H., Syson, K., van de Weerd, R., Chandra, G., Appelmelk, B.,
Alber, M., Ioerger, T.R., Jacobs, W.R., Geurtsen, J., Bornemann, S.,
Kalscheuer, R. (2016). Metabolic network for the biosynthesis of intra- and
extracellular alpha-glucans required for virulence of Mycobacterium
tuberculosis. PLOS Pathogens, 12(8):e1005768.
pubmed
PDF
Boutte, C.C., Baer, C.E., Papavinasasundaram, K., Liu, W., Chase, M.R.,
Meniche, X., Fortune, S.M., Sassetti, C.M., Ioerger, T.R, and Rubin
E.J. (2016). A cytoplasmic peptidoglycan amidase homologue controls
mycobacterial cell wall synthesis. eLife, 5:e14590.
pubmed
PDF
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.
pubmed
PDF
Maksymiuk, C., Ioerger, T.R., Balakrishnan, A., Bryk, R., Rhee, K.,
Sacchettini, J.C., and Nathan C. (2015).
Comparison of transposon and deletion mutants in Mycobacterium
tuberculosis: The case of Rv1248c, encoding 2-hydroxy-3-oxoadipate
synthase. Tuberculosis, 95(6):689-94.
pubmed
PDF
Shi, X., Festa, R.A., Ioerger, T.R., Butler-Wu, S., Sacchettini, J.C.
Darwin, K.H. and Samanovic, M.I. (2014).
The copper-responsive RicR regulon contributes to
Mycobacterium tuberculosis virulence. mBio, e00876-13.
pubmed
PDF
Lin, P.L., Ford, C.B, Coleman, M.T., Myers, A., Gawande, R., Ioerger, T.R.,
Sacchettini, J.C., Fortune, S.M. and Flynn, J.L. (2014).
Sterilization of granulomas is common in both active and latent tuberculosis
despite extensive within-host variability in bacterial killing.
Nature Medicine, 20(1):75-9. pubmed
PDF
Zhang, Y.J., Reddy, M.C., Ioerger, T.R., Rothchild, A.C., Dartois, V.,
Schuster, B.M., Trauner, A., Wallis, D.E., Galaviz, S., Huttenhower, C.,
Saccettini, J.C., Behar, S.M., and Rubin, E.J. (2013).
Tryptophan biosynthesis protects mycobacteria from CD4 T cell-mediated killing.
Cell, 155(6):1296-308. pubmed
PDF
Ngubane, N.Q.C, Gresh, L., Ioerger, T.R., Sacchettini, J.C., Zhang, Y.J.,
Rubin, E.J., Pym, A. and Khati, M. (2013). High-throughput sequencing enhanced
phage display identifies peptides that bind mycobacteria. PLOS ONE,
e77844. pubmed
PDF
Small, J.L., Park, S.W., Kana, B., Ioerger, T.R., Sacchettini, J.C. and Ehrt,
S. (2013). Perturbation of cytochrome C maturation reveals adaptability of
the respiratory chain in Mycobacterium tuberculosis. mBio,
4(5):e00475-13. pubmed
PDF
Gopinath, K., Venclovas, C., Ioerger, T.R., Sacchettini, J.C.,
McKinney, J.D., Mizrahi, V. and Warner, D.F. (2013).
A vitamin B12 transporter in Mycobacterium tuberculosis.
Open Biology, 3(2):120175.
pubmed
PDF
James, J.N., Hasan, Z., Ioerger, T.R., Brown, A.C., Personne, Y., Carroll, P.,
Ikeh, M., Tilston-Lunel, N.L., Palavecino, C., Sacchettini, J.C., and Parish,
T. (2012). Deletion of SenX3-RegX3, a key two component regulatory system of
Mycobacterium smegmatis, results in growth defects under
phosphate-limiting conditions. Microbiology,
158(Pt 11):2724-31.
pubmed
PDF
Tuberculosis Genomics
Shell, S.S., Wang, J., Lapierre, P., Mir, M., Chase, M.R., Hunter, M.,
Gawande, R., Ahmad, R., Sarracino, D., Ioerger, T.R., Fortune, S.M.,
Derbyshire, K.M., Wade, J.T. and Gray, T.A. (2015).
Leaderless transcripts and small proteins are common features of the
mycobacterial translational landscape. PLOS Genetics, 11(11): e1005641.
pubmed
PDF
Lanzas, F., Karakousis, P.K, Sacchettini, J.C. and Ioerger, T.R. (2013).
Multidrug-resistant tuberculosis in Panama is
driven by clonal expansion of an MDR-TB strain related to the KZN
XDR-TB strain from South Africa. Journal of Clinical Microbiology,
51(10):3277-3285.
pubmed
PDF
DeJesus, M.A., Sacchettini, J.C., and Ioerger, T.R. (2013).
Reannotation of translational start sites in the genome of Mycobacterium
tuberculosis. Tuberculosis,
93:18-25.
pubmed
PDF
Ford, C., Yusim, K., Ioerger, T.R., Feng, S., Chase, M., Greene, M., Korber,
B., and Fortune, S. (2012). Mycobacterium tuberculosis: Heterogeneity
revealed through whole genome sequencing. Tuberculosis, 92(3):194-201.
pubmed
PDF
Ford, C.B., Lin, P.L., Chase, M., Shah, R.R., Iartchouk, O., Galagan, J.,
Mohaideen, N., Ioerger, T.R., Sacchettini, J.C., Lipsitch, M., Flynn, J.L.,
and Fortune, S.M. (2011). Use of whole genome sequencing to estimate the
mutation rate of Mycobacterium tuberculosis during latent
infection. Nature Genetics, 43:482.486.
pubmed
PDF
Ioerger, T.R., Feng, Y., Chen, X., Dobos, K.M., Victor, T.C.,
Streicher, E.M., Warren, R.M., Gey van Pittius, N.C., Van Helden P.D.
and Sacchettini, J.C. (2010).
The non-clonality of drug resistance in Beijing-genotype isolates
of Mycobacterium tuberculosis from
the Western Cape of South Africa.
BMC Genomics, 11(1):670. pubmed
PDF
Ioerger, T.R., Feng, Y., Ganseula, K., Chen, X., Dobos, K.M., Fortune, S.,
Jacobs, W.R., Mizrahi, V., Parish, T., Rubin, E., Sassetti, C. and
Sacchettini, J.C. (2010).
Variation among genome sequences of H37Rv strains of M. tuberculosis
from multiple laboratories. Journal of Bacteriology, 192(14):3645-3653.
pubmed
PDF
Ioerger, T.R., Koo, S., No, E.-G., Chen, X., Larsen, M.H., Jacobs,
W.R., Pillay, M., Sturm, A.W., and Sacchettini, J.C. (2009). Genome
analysis of multi- and extensively-drug-resistant Tuberculosis from
KwaZulu-Natal, South Africa. PLoS ONE, 4(11):e7778.
pubmed
PDF
Shell SS, Chase MR, Ioerger TR, Fortune SM. (2015).
RNA sequencing for transcript 5'-end mapping in mycobacteria.
in Methods in Molecular Biology, vol. 1285, pp. 31-45.
pubmed
Protein Structures and Structural Genomics
Swanson, S., Ioerger, T.R., Rigel, N.W., Miller, B.K., Braunstein, M., and
Sacchettini, J.C. (2016).
Structural similarities and differences between two functionally distinct SecA
proteins: the Mycobacterium tuberculosis SecA1 and SecA2. Journal of
Bacteriology, 198(4):720-30.
pubmed
PDF
Liu Z, Ioerger TR, Wang F, Sacchettini JC. (2013).
Structures of Mtb FadD10 reveal a new type of adenylate-forming enzyme.
Journal of Biological Chemistry, 288(25):18473-83.
pubmed
PDF
Gokulan, K., O'Leary, S.E., Russell, W.K., Russell, D.H., Lalgondar, M.,
Begley, T.P., Ioerger, T.R., and Sacchettini, J.C. (2013).
Crystal structure of Mycobacterium tuberculosis PKS11 reveals intermediates in
the synthesis of methyl-branched alkylpyrones.
Journal of Biological Chemistry, 288(23):16484-94.
pubmed
PDF
Ioerger, T.R. and Sacchettini, J.C. (2009).
Structural genomics approach to drug discovery for Mycobacterium tuberculosis.
Current Opinion in Microbiology, 12:318-325. pubmed
PDF
Reddy, C.M.C., Kuppan, G., Shetty, N.D., Owen, J.L., Ioerger, T.R.,
Sacchettini, J.C. (2008). Crystal structures of Mycobacterium
tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex
with substrate and inhibitors.
Protein Science, 17(12):2134-2144.
pubmed
Javid-Majd, F., Yang, D., Ioerger, T.R., and Sacchettini, J.C. (2008).
The 1.25 A resolution structure of phosphoribosyl-ATP
pyrophosphohydrolase from Mycobacterium tuberculosis. Acta
Crystallographica, D:64(6):627-635.
pubmed
Reddy C.M., Gokulan, K., Jacobs, W.R., Ioerger, T.R., and Sacchettini,
J.C. (2008). Crystal structure of Mycobacterium tuberculosis LrpA, a
leucine-responsive global regulator associated with starvation
response. Protein Science, 17(1):159-170.
pubmed
Murillo, A.C., Alber, T.C., Baker, E.N., Berger, J.M., Cherney, L.T.,
Cherney, M.M., Eisenberg, D., Garen, C.R., Hung, L.W., Ioerger, T.R.,
Jacobs, W.R., James, M.N.G., Kim, C., Kriger, I., Li, H., Lott, J.S.,
Sankaranarayanan, R., Segelke, B.R., Terwilliger, T.C., Wang, F.,
and Sacchettini, J.C. (2007). High Throughput Crystallography of
TB Drug Targets. Infectious Disorders - Drug Targets, 7(2):127-139.
pubmed
Ye S, Vakonakis I, Ioerger TR, LiWang AC, Sacchettini JC. (2004).
Crystal structure of circadian clock protein KaiA from Synechococcus
elongatus.
Journal of Biological Chemistry, 279(19):20511-20518.
pubmed
Musa, T.L., Ioerger, T.R., and Sacchettini, J.C. (2009).
The Tuberculosis Structural Genomics Consortium: A Structural
Genomics Approach to Drug Discovery.
Advances in Protein Chemistry and Structural Biology,
Volume 77, pp. 41-76.
Protein Crystallography
Gopal, K., McKee, E., Romo, T., Pai, R., Smith, J., Sacchettini, J.C.
and Ioerger, T.R. (2007). Crystallographic Protein Model-Building on
the Web. Bioinformatics, 23:375-377.
Romo, T.D., Sacchettini, J.C., and Ioerger, T.R. (2006).
Improving amino acid identification, fit, and C-alpha prediction using
the Simplex method in automated model building.
Acta Crystallographica, D62(11):1401-1406.
pubmed
PDF
Gopal, K., Romo, T.D., McKee, E.W., Pai, R., Smith, J.N., Sacchettini, J.C.
and Ioerger, T.R. (2006). TEXTAL: Crystallographic Model Building Using
AI and Pattern Recognition. AI Magazine, 27(3):15-24.
AI Mag
PDF
Pai, R., Sacchettini, J.C. and Ioerger, T.R. (2006). Identifying
non-crystallographic symmetry in protein electron-density maps: a
feature-based approach. Acta Crystallographica, D62(9):1012-1021.
PDF
Romo, T.D., Gopal, K., McKee, E., Kanbi, L., Pai, R., Smith, J.,
Sacchettini, J.C., and Ioerger, T.R. (2005). TEXTAL: AI-based
Structural Determination for X-ray Protein Crystallography.
IEEE Intelligent Systems, 20(6):59-63.
PDF
McKee, E.W., Kanbi, L.D., Childs, K.L., Grosse-Kunstleve, R.W.,
Adams, P.D., Sacchettini J.C. and Ioerger, T.R. (2005). FINDMOL:
Automated Identification of Macromolecules in Electron Density Maps.
Acta Crystallographica, D61(11):1514-1520.
pubmed
Gopal, K., Romo, T., Sacchettini, J.C., and Ioerger, T.R. (2005).
Determining Relevant Features to Recognize Electron Density
Patterns in X-ray Protein Crystallography.