20092020

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

Filter
Article
2020

Complete genome sequence and genome-scale metabolic modelling of Acinetobacter baumannii type strain ATCC 19606

Zhu, Y., Lu, J., Zhao, J., Zhang, X., Yu, H. H., Velkov, T. & Li, J., Apr 2020, In : International Journal of Medical Microbiology. 310, 3, 11 p., 151412.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., Zhu, Y., Powell, D. R., Akutsu, T., Webb, G. I., Chou, K-C., Smith, A. I., Daly, R. J., Li, J. & Song, J., 21 May 2020, In : Briefings in Bioinformatics. 21, 3, p. 1047-1057 11 p., bbz041.

Research output: Contribution to journalArticleResearchpeer-review

16 Citations (Scopus)

Metabolomics Study of the Synergistic Killing of Polymyxin B in Combination with Amikacin against Polymyxin-Susceptible and -Resistant Pseudomonas aeruginosa

Hussein, M., Han, M-L., Zhu, Y., Zhou, Q. T., Lin, Y-W., Hancock, R. E. W., Hoyer, D., Creek, D. J., Li, J. & Velkov, T., Jan 2020, In : Antimicrobial Agents and Chemotherapy. 64, 1, 16 p., e01587-19.

Research output: Contribution to journalArticleResearchpeer-review

Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments

Li, M., Aye, S. M., Ahmed, M. U., Han, M-L., Li, C., Song, J., Boyce, J. D., Powell, D. R., Azad, M. A. K., Velkov, T., Zhu, Y. & Li, J., 22 May 2020, (Accepted/In press) In : Molecular Omics. 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Polymyxins Bind to the Cell Surface of Unculturable Acinetobacter baumannii and Cause Unique Dependent Resistance

Zhu, Y., Lu, J., Han, M-L., Jiang, X., Azad, M. A. K., Patil, N. A., Lin, Y-W., Zhao, J., Hu, Y., Yu, H. H., Chen, K., Boyce, J. D., Dunstan, R. A., Lithgow, T., Barlow, C. K., Li, W., Schneider-Futschik, E. K., Wang, J., Gong, B., Sommer, B. & 6 others, Creek, D. J., Fu, J., Wang, L., Schreiber, F., Velkov, T. & Li, J., 8 Jun 2020, (Accepted/In press) In : Advanced Science. 13 p., 2000704.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Li, F., Fan, C., Marquez-Lago, T. T., Leier, A., Revote, J., Jia, C., Zhu, Y., Smith, A. I., Webb, G. I., Liu, Q., Wei, L., Li, J. & Song, J., 21 May 2020, In : Briefings in Bioinformatics. 21, 3, p. 1069-1079 11 p.

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)
2019

Comparative metabolomics and transcriptomics reveal multiple pathways associated with polymyxin killing in pseudomonas aeruginosa

Han, M-L., Zhu, Y., Creek, D. J., Lin, Y-W., Gutu, A. D., Hertzog, P., Purcell, T., Shen, H-H., Moskowitz, S. M., Velkov, T. & Li, J., 1 Jan 2019, In : mSystems. 4, 1, 18 p., e00149-18.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
8 Citations (Scopus)

Comparative metabolomics reveals key pathways associated with the synergistic killing of colistin and sulbactam combination against multidrug-resistant Acinetobacter baumannii

Han, M-L., Liu, X., Velkov, T., Lin, Y-W., Zhu, Y., Creek, D. J., Barlow, C. K., Yu, H. H., Zhou, Z., Zhang, J. & Li, J., 4 Jul 2019, In : Frontiers in Pharmacology. 10, 11 p., 754.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Multifaceted mechanisms of colistin resistance revealed by genomic analysis of multidrug-resistant Klebsiella pneumoniae isolates from individual patients before and after colistin treatment

Zhu, Y., Galani, I., Karaiskos, I., Lu, J., Aye, S. M., Huang, J., Yu, H. H., Velkov, T., Giamarellou, H. & Li, J., 1 Oct 2019, In : Journal of Infection. 79, 4, p. 312-321 10 p.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Novel polymyxin combination with the antiretroviral zidovudine exerts synergistic killing against Ndm-producing multidrug-resistant klebsiella pneumoniae

Lin, Y-W., Rahim, N. A., Zhao, J., Han, M-L., Yu, H. H., Wickremasinghe, H., Chen, K., Wang, J., Paterson, D. L., Zhu, Y., Rao, G. G., Zhou, Q. T., Forrest, A., Velkov, T. & Li, J., 1 Apr 2019, In : Antimicrobial Agents and Chemotherapy. 63, 4, 11 p., e02176-18.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Synergistic Combination of Polymyxin B and Enrofloxacin Induced Metabolic Perturbations in Extensive Drug-resistant Pseudomonas aeruginosa

Lin, Y-W., Han, M-L., Zhao, J., Zhu, Y., Rao, G., Forrest, A., Song, J., Kaye, K. S., Hertzog, P., Purcell, A., Creek, D., Zhou, T. Q., Velkov, T. & Li, J., 3 Oct 2019, In : Frontiers in Pharmacology. 10, 11 p., 1146.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2018

A Comparative Study of Outer Membrane Proteome between Paired Colistin-Susceptible and Extremely Colistin-Resistant Klebsiella pneumoniae Strains

Jasim, R., Baker, M. A., Zhu, Y., Han, M., Schneider-Futschik, E. K., Hussein, M., Hoyer, D., Li, J. & Velkov, T., 2018, In : ACS Infectious Diseases. 4, 12, p. 1692-1704 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Alterations of Metabolic and Lipid Profiles in Polymyxin-Resistant Pseudomonas aeruginosa

Han, M-L., Zhu, Y., Creek, D. J., Lin, Y-W., Anderson, D., Shen, H-H., Tsuji, B., Gutu, A. D., Moskowitz, S. M., Velkov, T. & Li, J., 1 Jun 2018, In : Antimicrobial Agents and Chemotherapy. 62, 6, 14 p., e02656-17.

Research output: Contribution to journalArticleResearchpeer-review

11 Citations (Scopus)

Comparative analysis of phosphoethanolamine transferases involved in polymyxin resistance across 10 clinically relevant Gram-negative bacteria

Huang, J., Zhu, Y., Han, M., Li, M., Song, J., Velkov, T., Li, C. & Li, J., 1 Apr 2018, In : International Journal of Antimicrobial Agents. 51, 4, p. 586-593 8 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Dysregulation and dislocation of SFPQ disturbed DNA organization in Alzheimer's disease and frontotemporal dementia

Lu, J., Shu, R. & Zhu, Y., 23 Jan 2018, In : Journal of Alzheimer's Disease. 61, 4, p. 1311-1321 11 p.

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Enhanced uptake of potassium or glycine betaine or export of cyclic-di-AMP restores osmoresistance in a high cyclic-di-AMP Lactococcus lactis mutant

Pham, H. T., Nhiep, N. T. H., Vu, T. N. M., Huynh, T. A. N., Zhu, Y., Huynh, A. L. D., Chakrabortti, A., Marcellin, E., Lo, R., Howard, C. B., Bansal, N., Woodward, J. J., Liang, Z. X. & Turner, M. S., 3 Aug 2018, In : PLoS Genetics. 14, 8, 23 p., e1007574.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
15 Citations (Scopus)

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
File
9 Citations (Scopus)

Lipidomic analysis of the outer membrane vesicles from paired polymyxin-susceptible and -resistant Klebsiella pneumoniae clinical isolates

Jasim, R., Han, M-L., Zhu, Y., Hu, X., Hussein, M. H., Lin, Y-W., Zhou, T. Q., Dong, C. Y. D., Li, J. & Velkov, T., 10 Aug 2018, In : International Journal of Molecular Sciences. 19, 8, 13 p., 2356.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
5 Citations (Scopus)

Mechanistic Insights From Global Metabolomics Studies into Synergistic Bactericidal Effect of a Polymyxin B Combination With Tamoxifen Against Cystic Fibrosis MDR Pseudomonas aeruginosa

Hussein, M., Han, M-L., Zhu, Y., Schneider-Futschik, E. K., Hu, X., Zhou, Q. T., Lin, Y-W., Anderson, D., Creek, D. J., Hoyer, D., Li, J. & Velkov, T., 1 Jan 2018, In : Computational and Structural Biotechnology Journal. 16, p. 587-599 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2 Citations (Scopus)

Metabolic Analyses Revealed Time-Dependent Synergistic Killing by Colistin and Aztreonam Combination Against Multidrug-Resistant Acinetobacter baumannii

Han, M-L., Liu, X., Velkov, T., Lin, Y-W., Zhu, Y., Li, M., Yu, H. H., Zhou, Z., Creek, D. J., Zhang, J. & Li, J., 16 Nov 2018, In : Frontiers in Microbiology. 9, 12 p., 2776.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2 Citations (Scopus)

Polymyxin b in combination with enrofloxacin exerts synergistic killing against extensively drug-resistant pseudomonas aeruginosa

Lin, Y-W., Yu, H. H., Zhao, J., Han, M-L., Zhu, Y., Akter, J., Wickremasinghe, H., Walpola, H., Wirth, V., Rao, G. G., Forrest, A., Velkov, T. & Li, J., 1 Jun 2018, In : Antimicrobial Agents and Chemotherapy. 62, 6, 13 p., e00028-18.

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

Polymyxin-Induced Lipid A Deacylation in Pseudomonas aeruginosa Perturbs Polymyxin Penetration and Confers High-Level Resistance

Han, M-L., Velkov, T., Zhu, Y., Roberts, K. D., Le Brun, A. P., Chow, S. H., Gutu, A. D., Moskowitz, S. M., Shen, H-H. & Li, J., 19 Jan 2018, In : ACS Chemical Biology. 13, 1, p. 121-130 10 p.

Research output: Contribution to journalArticleResearchpeer-review

17 Citations (Scopus)
2017

Characterization of the Polymyxin D Synthetase Biosynthetic Cluster and Product Profile of Paenibacillus polymyxa ATCC 10401

Galea, C. A., Han, M., Zhu, Y., Roberts, K., Wang, J., Thompson, P. E., Li, J. & Velkov, T., 26 May 2017, In : Journal of Natural Products. 80, 5, p. 1264-1274 11 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Functional characterization of the unique terminal thioesterase domain from polymyxin synthetase

Galea, C., Roberts, K. D., Zhu, Y., Thompson, P. E., Li, J. & Velkov, T., 31 Jan 2017, In : Biochemistry. 56, 4, p. 657-668 12 p.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Investigating the Interaction of Octapeptin A3 with Model Bacterial Membranes

Han, M. L., Shen, H. H., Hansford, K. A., Schneider, E. K., Sivanesan, S., Roberts, K. D., Thompson, P. E., Le Brun, A. P., Zhu, Y., Sani, M-A., Separovic, F., Blaskovich, M. A. T., Baker, M. A., Moskowitz, S. M., Cooper, M. A., Li, J. & Velkov, T., 11 Aug 2017, In : ACS Infectious Diseases. 3, 8, p. 606-619 14 p.

Research output: Contribution to journalArticleResearchpeer-review

9 Citations (Scopus)

Plasma Protein Binding Structure-Activity Relationships Related to the N-Terminus of Daptomycin

Schneider, E. K., Huang, J. X., Carbone, V., Han, M., Zhu, Y., Nang, S., Khoo, K. K., Mak, J., Cooper, M. A., Li, J. & Velkov, T., 1 Feb 2017, In : ACS Infectious Diseases. 3, 3, p. 249-258 10 p.

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

Study of mcr-1 gene-mediated colistin resistance in enterobacteriaceae isolated from humans and animals in different countries

Hadjadj, L., Riziki, T., Zhu, Y., Li, J., Diene, S. M. & Rolain, J-M., 19 Dec 2017, In : Genes. 8, 12, 16 p., 394.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
22 Citations (Scopus)
2016

Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in lactococcus lactis

Zhu, Y., Pham, T. H., Nhiep, T. H. N., Vu, N. M. T., Marcellin, E., Chakrabortti, A., Wang, Y., Waanders, J., Lo, R., Huston, W. M., Bansal, N., Nielsen, L. K., Liang, Z. X. & Turner, M. S., Mar 2016, In : Molecular Microbiology. 99, 6, p. 1015-1027 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
24 Citations (Scopus)

Polymyxin resistance in Acinetobacter baumannii: genetic mutations and transcriptomic changes in response to clinically relevant dosage regimens

Cheah, S-E., Johnson, M. D., Zhu, Y., Tsuji, B. T., Forrest, A., Bulitta, J., Boyce, J. D., Nation, R. L. & Li, J., 19 May 2016, In : Scientific Reports. 6, 11 p., 26233.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
25 Citations (Scopus)

Toward community standards and software for whole-cell modeling

Waltemath, D., Karr, J. R., Bergmann, F. T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C. J., Pir, P., Alaybeyoglu, B., Aranganathan, N. K., Baghalian, K., Bittig, A. T., Burke, P. E. P., Cantarelli, M., Chew, Y. H., Costa, R. S., Cursons, J., Czauderna, T. & 37 others, Goldberg, A. P., Gomez, H. F., Hahn, J., Hameri, T., Gardiol, D. F. H., Kazakiewicz, D., Kiselev, I., Knight-Schrijver, V., Knupfer, C., Konig, M., Lee, D., Lloret-Villas, A., Mandrik, N., Medley, J. K., Moreau, B., Naderi-Meshkin, H., Palaniappan, S. K., Priego-Espinosa, D., Scharm, M., Sharma, M., Smallbone, K., Stanford, N. J., Song, J-H., Theile, T., Tokic, M., Tomar, N., Toure, V., Uhlendorf, J., Varusai, T. M., Watanabe, L. H., Wendland, F., Wolfien, M., Yurkovich, J. T., Zhu, Y., Zardilis, A., Zhukova, A. & Schreiber, F., 1 Oct 2016, In : IEEE Transactions on Biomedical Engineering. 63, 10, p. 2007-2014 8 p., 7489010.

Research output: Contribution to journalArticleResearchpeer-review

25 Citations (Scopus)
2015

Chemokine signaling controls integrity of radial glial scaffold in developing spinal cord and consequential proper position of boundary cap cells

Zhu, Y., Matsumoto, T., Nagasawa, T., Mackay, F. & Murakami, F., 17 Jun 2015, In : Journal of Neuroscience. 35, 24, p. 9211-9224 14 p.

Research output: Contribution to journalArticleResearchpeer-review

12 Citations (Scopus)
2014

Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

Bao, G., Dong, H., Zhu, Y., Mao, S., Zhang, T., Zhang, Y., Chen, Z. & Li, Y., 8 Aug 2014, In : Biochemical and Biophysical Research Communications. 450, 4, p. 1612-1618 7 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Discovery of a super-strong promoter enables efficient production of heterologous proteins in cyanobacteria

Zhou, J., Zhang, H., Meng, H., Zhu, Y., Bao, G., Zhang, Y., Li, Y. & Ma, Y., 28 Mar 2014, In : Scientific Reports. 4, 6 p., 4500.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
72 Citations (Scopus)

Metabolic changes in Klebsiella oxytoca in response to low oxidoreduction potential, as revealed by comparative proteomic profiling integrated with flux balance analysis

Zhu, Y., Li, D., Bao, G., Wang, S., Mao, S., Song, J., Li, Y. & Zhang, Y., 2014, In : Applied and Environmental Microbiology. 80, 9, p. 2833 - 2841 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
7 Citations (Scopus)
2013

Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

Zhu, Y., Song, J., Xu, Z., Sun, J., Zhang, Y., Li, Y. & Ma, Y., 2013, In : Biotechnology and Bioengineering. 110, 3, p. 914 - 923 10 p.

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Discovery of a novel gene involved in autolysis of Clostridium cells

Yang, L., Bao, G., Zhu, Y., Dong, H., Zhang, Y. & Li, Y., 2013, In : Protein & Cell. 4, 6, p. 467-474 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
4 Citations (Scopus)
2012

Controlling the oxidoreduction potential of the culture of Clostridium acetobutylicum leads to an earlier initiation of solventogenesis, thus increasing solvent productivity

Wang, S., Zhu, Y., Zhang, Y. & Li, Y., Feb 2012, In : Applied Microbiology and Biotechnology. 93, 3, p. 1021-1030 10 p.

Research output: Contribution to journalArticleResearchpeer-review

40 Citations (Scopus)

Introducing a single secondary alcohol dehydrogenase into butanol-tolerant Clostridium acetobutylicum Rh8 switches ABE fermentation to high level IBE fermentation

Dai, Z., Dong, H., Zhu, Y., Zhang, Y., Li, Y. & Ma, Y., 28 Jun 2012, In : Biotechnology for Biofuels. 5, 10 p., 44.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
46 Citations (Scopus)
2011

Formic acid triggers the "acid crash" of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum

Wang, S., Zhang, Y., Dong, H., Mao, S., Zhu, Y., Wang, R., Luan, G. & Li, Y., Mar 2011, In : Applied and Environmental Microbiology. 77, 5, p. 1674-1680 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
76 Citations (Scopus)

Group II intron-anchored gene deletion in Clostridium

Jia, K., Zhu, Y., Zhang, Y. & Li, Y., 31 Jan 2011, In : PLoS ONE. 6, 1, 10 p., e16693.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
20 Citations (Scopus)
2010

Proteome reference map and comparative proteomic analysis between a wild type clostridium acetobutylicumDSM 1731 and its mutant with enhanced butanol tolerance and butanol yield

Mao, S., Luo, Y., Zhang, T., Li, J., Bao, G., Zhu, Y., Chen, Z., Zhang, Y., Li, Y. & Ma, Y., 4 Jun 2010, In : Journal of Proteome Research. 9, 6, p. 3046-3061 16 p.

Research output: Contribution to journalArticleResearchpeer-review

96 Citations (Scopus)

Proteome reference map and comparative proteomic analysis between a wild type Clostridium acetobutylicum DSM 1731 and its mutant with enhanced butanol tolerance and butanol yield

Mao, S., Luo, Y., Zhang, Y., Zhang, T., Li, J., Bao, G., Zhu, Y., Chen, Z., Zhang, Y., Li, Y. & Ma, Y., 2010, In : Journal of Proteome Research.

Research output: Contribution to journalArticleResearchpeer-review

Proteomic analyses to reveal the protective role of glutathione in resistance of lactococcus lactis to osmotic stress

Zhang, Y., Zhang, Y., Zhu, Y., Mao, S. & Li, Y., 1 May 2010, In : Applied and Environmental Microbiology. 76, 10, p. 3177-3186 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
45 Citations (Scopus)
2009

The importance of engineering physiological functionality into microbes

Zhang, Y., Zhu, Y., Zhu, Y. & Li, Y., 1 Dec 2009, In : Trends in Biotechnology. 27, 12, p. 664-672 9 p.

Research output: Contribution to journalArticleResearchpeer-review

56 Citations (Scopus)