• 19 Innovation walk, 76

    3800 Monash University

    Australia

  • Room 252, 19 Innovation Walk, 76

    3800 Melbourne

Accepting PhD Students

1988 …2020
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Research Output 1988 2019

2019

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Davies, M. R., McIntyre, L., Mutreja, A., Lacey, J. A., Lees, J. A., Towers, R. J., Duchêne, S., Smeesters, P. R., Frost, H. R., Price, D. J., Holden, M. T. G., David, S., Giffard, P. M., Worthing, K. A., Seale, A. C., Berkley, J. A., Harris, S. R., Rivera-Hernandez, T., Berking, O., Cork, A. J. & 18 others, Torres, R. S. L. A., Lithgow, T., Strugnell, R. A., Bergmann, R., Nitsche-Schmitz, P., Chhatwal, G. S., Bentley, S. D., Fraser, J. D., Moreland, N. J., Carapetis, J. R., Steer, A. C., Parkhill, J., Saul, A., Williamson, D. A., Currie, B. J., Tong, S. Y. C., Dougan, G. & Walker, M. J., 1 Jun 2019, In : Nature Genetics. 51, 6, p. 1035-1043 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Bastion3: A two-layer ensemble predictor of type III secreted effectors

Wang, J., Li, J., Yang, B., Xie, R., Marquez-Lago, T. T., Leier, A., Hayashida, M., Akutsu, T., Zhang, Y., Chou, K-C., Selkrig, J., Zhou, T., Song, J. & Lithgow, T., 1 Jun 2019, In : Bioinformatics. 35, 12, p. 2017-2028 12 p., bty914.

Research output: Contribution to journalArticleResearchpeer-review

cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria

Belousoff, M. J., Venugopal, H., Wright, A., Seoner, S., Stuart, I., Stubenrauch, C., Bamert, R. S., Lupton, D. W. & Lithgow, T., 5 Mar 2019, In : ChemMedChem. 14, 5, p. 527-231 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Determination of the molecular basis for coprogen import by Gram-negative bacteria

Grinter, R. & Lithgow, T., May 2019, In : IUCrJ. 6, 3, p. 401-411 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Filamentous phages: masters of a microbial sharing economy

Hay, I. D. & Lithgow, T., 1 Jun 2019, In : EMBO Reports. 20, 6, 24 p., e47427.

Research output: Contribution to journalReview ArticleResearchpeer-review

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins

Zhang, Y., Yu, S., Xie, R., Li, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Smith, A. I., Ge, Z., Wang, J., Lithgow, T. & Song, J., 8 Aug 2019, (Accepted/In press) In : Bioinformatics. 8 p., btz629.

Research output: Contribution to journalArticleResearchpeer-review

Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly

Sakaue, H., Shiota, T., Ishizaka, N., Kawano, S., Tamura, Y., Tan, K. S., Imai, K., Motono, C., Hirokawa, T., Taki, K., Miyata, N., Kuge, O., Lithgow, T. & Endo, T., 7 Mar 2019, In : Molecular Cell. 73, 5, p. 1044-1055 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Positive-unlabelled learning of glycosylation sites in the human proteome

Li, F., Zhang, Y., Purcell, A. W., Webb, G. I., Chou, K-C., Lithgow, T., Li, C. & Song, J., 6 Mar 2019, In : BMC Bioinformatics. 20, 1, 17 p., 112.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches

Wang, J., Yang, B., An, Y., Marquez-Lago, T., Leier, A., Wilksch, J., Hong, Q., Zhang, Y., Hayashida, M., Akutsu, T., Webb, G. I., Strugnell, R. A., Song, J. & Lithgow, T., 21 May 2019, In : Briefings in Bioinformatics. 20, 3, p. 931-951 21 p.

Research output: Contribution to journalArticleResearchpeer-review

The TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes

Stubenrauch, C. J. & Lithgow, T., 27 Feb 2019, In : EcoSal Plus. 8, 2, 7 p.

Research output: Contribution to journalArticleResearchpeer-review

2018

An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis

Torres, V. V. L., Heinz, E., Stubenrauch, C. J., Wilksch, J. J., Cao, H., Yang, J., Clements, A., Dunstan, R. A., Alcock, F., Webb, C. T., Dougan, G., Strugnell, R. A., Hay, I. D. & Lithgow, T., Sep 2018, In : Molecular Microbiology. 109, 5, p. 584-599 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors

Wang, J., Yang, B., Leier, A., Marquez-Lago, T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K-C., Strugnell, R. A., Song, J. & Lithgow, T., 1 Jan 2018, In : Bioinformatics. 34, 15, p. 2546-2555 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI

An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G. I., Song, J. & Lithgow, T., 1 Jan 2018, In : Briefings in Bioinformatics. 19, 1, p. 148-161 14 p., bbw100.

Research output: Contribution to journalArticleResearchpeer-review

Erratum: Correction for Nguyen et al., "Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers" (mBio (2017) 8 6 PII: e02207-17)

Nguyen, S., Baker, K., Padman, B. S., Patwa, R., Dunstan, R. A., Weston, T. A., Schlosser, K., Bailey, B., Lithgow, T., Luque, A., Rohwer, F., Blumberg, R. S. & Barr, J. J., 2 Jan 2018, In : mBio. 9, 1

Research output: Contribution to journalComment / DebateOtherpeer-review

FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants

Grinter, R., Hay, I. D., Song, J., Wang, J., Teng, D., Dhanesakaran, V., Wilksch, J. J., Davies, M. R., Littler, D., Beckham, S. A., Henderson, I. R., Strugnell, R. A., Dougan, G. & Lithgow, T., 2 Aug 2018, In : PLoS Biology. 16, 8, 21 p., e2006026.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa

Zhu, Y., Czauderna, T., Zhao, J., Klapperstueck, M., Mahamad Maifiah, M. H. B., Han, M-L., Lu, J., Sommer, B., Velkov, T., Lithgow, T., Song, J., Schreiber, F. & Li, J., 1 Apr 2018, In : GigaScience. 7, 4, 18 p., giy021.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium

Husna, A. U., Wang, N., Cobbold, S. A., Newton, H. J., Hocking, D. M., Wilksch, J. J., Scott, T. A., Davies, M. R., Hinton, J. C., Tree, J. J., Lithgow, T., McConville, M. J. & Strugnell, R. A., 15 Dec 2018, In : Journal of Biological Chemistry. 293, 24, p. 9506-9519 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis

Deo, P., Chow, S. H., Hay, I. D., Kleifeld, O., Costin, A., Elgass, K. D., Jiang, J-H., Ramm, G., Gabriel, K., Dougan, G., Lithgow, T., Heinz, E. & Naderer, T., 30 Mar 2018, In : PLoS Pathogens. 14, 3, 30 p., e1006945.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

Li, F., Li, C., Marquez-Lago, T. T., Leier, A., Akutsu, T., Purcell, A. W., Smith, A. I., Lithgow, T., Daly, R. J., Song, J. & Chou, K-C., 15 Dec 2018, In : Bioinformatics. 34, 24, p. 4223-4231 9 p., bty522.

Research output: Contribution to journalArticleResearchpeer-review

Structure and membrane topography of the vibrio-type secretin complex from the type 2 secretion system of enteropathogenic Escherichia coli

Hay, I. D., Belousoff, M. J., Dunstan, R. A., Bamert, R. S. & Lithgow, T., 1 Mar 2018, In : Journal of Bacteriology. 200, 5, 15 p., e00521-17.

Research output: Contribution to journalArticleResearchpeer-review

The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane

Gunasinghe, S. D., Shiota, T., Stubenrauch, C. J., Schulze, K. E., Webb, C. T., Fulcher, A. J., Dunstan, R. A., Hay, I. D., Naderer, T., Whelan, D. R., Bell, T. D. M., Elgass, K. D., Strugnell, R. A. & Lithgow, T., 29 May 2018, In : Cell Reports. 23, 9, p. 2782-2794 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., Haffari, G., Revote, J., Akutsu, T., Chou, K-C., Purcell, A. W., Pike, R. N., Webb, G. I., Smith, A. I., Lithgow, T., Daly, R. J., Whisstock, J. C. & Song, J., 2018, (Accepted/In press) In : Briefings in Bioinformatics. 17 p., bby077.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017

Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers

Nguyen, S., Baker, K., Padman, B. S., Patwa, R., Dunstan, R. A., Weston, T. A., Schlosser, K., Bailey, B., Lithgow, T., Lazarou, M., Luque, A., Rohwer, F., Blumberg, R. S. & Barr, J. J., 21 Nov 2017, In : mBio. 8, 6, 14 p., e01874-17.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function

Stubenrauch, C. J., Dougan, G., Lithgow, T. & Heinz, E., 15 Nov 2017, In : Open Biology. 7, 11, 10 p., 170144.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Defining membrane protein localization by isopycnic density gradients

Dunstan, R. A., Hay, I. D. & Lithgow, T., 2017, Bacterial Protein Secretion Systems: Methods and Protocols. Journet, L. & Cascales, E. (eds.). Humana Press, Vol. 1615. p. 81-86 6 p. (Methods in Molecular Biology; vol. 1615).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

Extensively drug-resistant klebsiella pneumoniae causing nosocomial bloodstream infections in China: Molecular investigation of antibiotic resistance determinants, Informing therapy, and clinical outcomes

Bi, W., Liu, H., Dunstan, R. A., Li, B., Torres, V. V. L., Cao, J., Chen, L., Wilksch, J. J., Strugnell, R. A., Lithgow, T. & Zhou, T., 30 Jun 2017, In : Frontiers in Microbiology. 8, 12 p., 1230.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Wang, Y., Song, J., Marquez-Lago, T., Leier, A., Li, C., Lithgow, T., Webb, G. I. & Shen, H-B., 1 Dec 2017, In : Scientific Reports. 7, 1, 5755.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Phylogenetic analysis of Klebsiella pneumoniae from hospitalized children, Pakistan

Ejaz, H., Wang, N., Wilksch, J. J., Page, A. J., Cao, H., Gujaran, S., Keane, J. A., Lithgow, T., Ul-Haq, I., Dougan, G., Strugnell, R. A. & Heinz, E., 1 Nov 2017, In : Emerging infectious diseases. 23, 11, p. 1872-1875 4 p.

Research output: Contribution to journalArticleResearchpeer-review

POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles

Wang, J., Yang, B., Revote, J., Leier, A., Marquez-Lago, T. T., Webb, G., Song, J., Chou, K-C. & Lithgow, T., 1 Jan 2017, In : Bioinformatics. 33, 17, p. 2756-2758 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori

Webb, C. T., Chandrapala, D., Oslan, S. N., Bamert, R. S., Grinter, R. D., Dunstan, R. A., Gorrell, R. J., Song, J., Strugnell, R. A., Lithgow, T. & Kwok, T., 1 Dec 2017, In : MicrobiologyOpen. 6, 6, 17 p., e00513.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G. I., Lithgow, T. & Song, J., 23 Jan 2017, In : Scientific Reports. 7, 10 p., 41031.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Structural basis for linezolid binding site rearrangement in the Staphylococcus aureus ribosome

Belousoff, M. J., Eyal, Z., Radjainia, M., Ahmed, T., Bamert, R. S., Matzov, D., Bashan, A., Zimmerman, E., Mishra, S., Cameron, D., Elmlund, H., Peleg, A. Y., Bhushan, S., Lithgow, T. & Yonath, A., 9 May 2017, In : mBio. 8, 3, 7 p., e00395-17.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery

Bamert, R. S., Lundquist, K., Hwang, H., Webb, C. T., Shiota, T., Stubenrauch, C. J., Belousoff, M. J., Goode, R. J. A., Schittenhelm, R. B., Zimmerman, R., Jung, M., Gumbart, J. C. & Lithgow, T., 1 Oct 2017, In : Molecular Microbiology. 106, 1, p. 142-156 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Structural basis of type 2 secretion system engagement between the inner and outer bacterial membranes

Hay, I. D., Belousoff, M. J. & Lithgow, T., 17 Oct 2017, In : mBio. 8, 5, 6 p., e01344-17.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Super-resolution imaging of protein secretion systems and the cell surface of gram-negative bacteria

Gunasinghe, S. D., Webb, C. T., Elgass, K. D., Hay, I. D. & Lithgow, T., 29 May 2017, In : Frontiers in Cellular and Infection Microbiology. 7, 10 p., 220.

Research output: Contribution to journalReview ArticleOtherpeer-review

Open Access
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The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold

Josts, I., Stubenrauch, C. J., Vadlamani, G., Mosbahi, K., Walker, D., Lithgow, T. & Grinter, R., 5 Dec 2017, In : Structure. 25, 12, p. 1898-1906 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex

Daimon, Y., Iwama-Masui, C., Tanaka, Y., Shiota, T., Suzuki, T., Miyazaki, R., Sakurada, H., Lithgow, T., Dohmae, N., Mori, H., Tsukazaki, T., Narita, S. I. & Akiyama, Y., 1 Dec 2017, In : Molecular Microbiology. 106, 5, p. 760-776 17 p.

Research output: Contribution to journalArticleResearchpeer-review

2016

Antibacterial poly(ethylene glycol) hydrogels from combined epoxy-amine and thiol-ene click reaction

Zhou, C., Truong, V. X., Qu, Y., Lithgow, T., Fu, G. & Forsythe, J. S., 2016, In : Journal of Polymer Science, Part A: Polymer Chemistry. 54, 5, p. 656 - 667 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family

Heinz, E., Stubenrauch, C. J., Grinter, R., Croft, N. P., Purcell, A. W., Strugnell, R. A., Dougan, G. & Lithgow, T., 13 Jun 2016, In : Genome Biology and Evolution. 8, 6, p. 1690-1705 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Effective assembly of fimbriae in Escherichia coli depends on the translocation assembly module nanomachine

Stubenrauch, C., Belousoff, M. J., Hay, I. D., Shen, H-H., Lillington, J., Tuck, K. L., Peters, K. M., Phan, M-D., Lo, A. W., Schembri, M. A., Strugnell, R. A., Waksman, G. & Lithgow, T., 2016, In : Nature Microbiology. 1, p. 1-8 8 p., 16064 .

Research output: Contribution to journalArticleResearchpeer-review

Open Access

Eliminating Legionella by inhibiting BCL-XL to induce macrophage apoptosis

Speir, M., Lawlor, K. E., Glaser, S. P., Abraham, G., Chow, S., Vogrin, A., Schulze, K. E., Schuelein, R., O'Reilly, L. A., Mason, K., Hartland, E. L., Lithgow, T., Strasser, A., Lessene, G., Huang, D. C. S., Vince, J. E. & Naderer, T., 24 Feb 2016, In : Nature Microbiology. 1, 3, 9 p., 15034.

Research output: Contribution to journalArticleResearchpeer-review

GlycoMinestruct: A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

Li, F., Li, C., Revote, J., Zhang, Y., Webb, G. I., Li, J., Song, J. & Lithgow, T., 6 Oct 2016, In : Scientific Reports. 6, 16 p., 34595.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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The modular nature of the β-barrel assembly machinery, illustrated in Borrelia burgdorferi

Stubenrauch, C. J., Grinter, R. & Lithgow, T. J., 24 Nov 2016, In : Molecular Microbiology. 102, 5, p. 753-756 4 p.

Research output: Contribution to journalArticleOtherpeer-review

2015

Antibiotic regimen based on population analysis of residing persister cells eradicates Staphylococcus epidermidis biofilms

Yang, S., Hay, I. D., Cameron, D. R., Speir, M., Cui, B., Su, F., Peleg, A. Y., Lithgow, T. J., Deighton, M. A. & Qu, Y., 2015, In : Scientific Reports. 5, 11 p., 18578.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Assembly of the secretion pores GspD, Wza and CsgG into bacterial outer membranes does not require the Omp85 proteins BamA or TamA

Dunstan, R. A., Hay, I. D., Wilksch, J. J., Schittenhelm, R. B., Purcell, A. W., Clark, J. M., Costin, A., Ramm, G., Strugnell, R. A. & Lithgow, T. J., 2015, In : Molecular Microbiology. 97, 4, p. 616 - 629 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Conserved features in TamA enable interaction with TamB to drive the activity of the translocation and assembly module

Selkrig, J. P., Belousoff, M. J., Headey, S. J., Heinz, E., Shiota, T., Shen, H-H., Beckham, S. A., Bamert, R. S., Phan, M-D., Schembri, M. A., Wilce, M. C., Scanlon, M. J., Strugnell, R. A. & Lithgow, T. J., 2015, In : Scientific Reports. 5, 12 p., 12905.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Evidence of distinct channel conformations and substrate binding affinities for the mitochondrial outer membrane protein translocase pore Tom40

Kuszak, A. J., Jacobs, D., Gurnev, P. A., Shiota, T., Louis, J., Lithgow, T. J., Bezrukov, S. M., Rostovtseva, T. K. & Buchanan, S. K., 2015, In : Journal of Biological Chemistry. 290, 43, p. 26204 - 26217 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Evolution of the translocation and assembly module (TAM)

Heinz, E., Selkrig, J. P., Belousoff, M. J. & Lithgow, T. J., 2015, In : Genome Biology and Evolution. 7, 6, p. 1628 - 1643 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Identification of BamC on the Surface of E. coli

Webb, C. T. & Lithgow, T. J., 2015, The BAM Complex: Methods and Protocols. Buchanan, S. K. & Noinaj, N. (eds.). 1st ed. New York NY USA: Humana Press, p. 215 - 226 12 p. (Methods in Molecular Biology: Springer Protocols; vol. 1329).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

Light-triggered release of ciprofloxacin from an in situ forming click hydrogel for antibacterial wound dressings

Shi, Y., Truong, V. X., Kulkarni, K., Qu, Y., Simon, G. P., Boyd, R. L., Perlmutter, P., Lithgow, T. & Forsythe, J. S., 2015, In : Journal of Materials Chemistry B. 3, 45, p. 8771 - 8774 4 p.

Research output: Contribution to journalArticleOtherpeer-review