Publications

Independent publications

48. Clark, C. M.; Kwan, J. C. Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene bioRxiv 2024, DOI: 10.1101/2024.08.16.608329.

47. Uppal, S.; Woolet, J.; Venkateshwaran, M.; Baxer, C.; Johnson, Y.; Tung, A.; Yu, C.S.; Whitman, T.; Kwan, J. C. A granular view of the traits controlling soil bacterial community reconstruction following a prescribed burn bioRxiv 2024, DOI: 10.1101/2024.06.20.599938.

46. Uppal, S.; Waterworth, S. C.; Nick, A.; Vogel, H.; Flórez, L.; Kaltenpoth, M.; Kwan, J. C. Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles ISME Journal 2024, DOI: 10.1093/ismejo/wrae211.

45. Neuhaus, G. F.; Aron, A. T.; Isemonger, E. W.; Petras, D.; Waterworth, S. C.; Madonseia, L. S.; Gentry, E. C.; Noundou, X. S.; Kalinski, J.-C. J.; Polyzois, A.; Habiyaremye, J. C.; Redick, M. A.; Kwan, J. C.; Dorrington, R. A.; Dorrestein, P. C.; McPhail, K. L. Environmental metabolomics characterization of modern stromatolites and annotation of ibhayipeptolides PLoS ONE 2024, 19, e0303273.

44. Fergusson, C. H.; Saulog, J.; Paulo, B. S.; Wilson, D. M.; Liu, D. Y.; Morghouse, N. J.; Waterworth, S.; Barkei, J.; Gray, L. A.; Kwan, J. C.; Eustaquio, A. S.; Linington, R. Discovery of the polyketide lagriamide B by integrated genome mining, isotope labeling, and untargeted metabolomics Chemical Science 2024, 15, 8089-8096.

43. Rees, E. R.; Uppal, S.; Clark, C. M.; Lail, A. J.; Waterworth, S. C.; Roesemann, S. D.; Wolf, K. A.; Kwan, J. C. Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities bioRxiv 2023, DOI: 10.1101/2023.09.01.555939.

42. Rees, E. R.; Waterworth, S. C.; Chanana, S. C.; Kwan, J. C. Automappa: An interactive interface for metagenome-derived genome bins bioRxiv 2023, DOI: 10.1101/2023.08.25.554826.

41. Waterworth, S. C.; Rees, E. R.; Clark, C.; Carlson, S.; Miller, I. J.; Puglisi, M.; Kwan, J. C. Elevated expression of srp RiPPs across bacterial phyla in marine sponges bioRxiv 2023, DOI: 10.1101/2023.06.09.544420.

40. Uppal, S.; Metz, J. L.; Xavier, R. K. M.; Nepal, K.; Xu, D.; Wang, G.; Kwan, J. C. Uncovering lasonolide A biosynthesis using genome-resolved metagenomics mBio 2022, 13, e01524-22.

39. Wolf, K. A.; Kwan, J. C.; Kamil, J. P. Structural dynamics and molecular evolution of the SARS-CoV-2 spike protein mBio 2022, 13, e02030-21e02030-21.

38. Meyer, F.; Fritz, A.; Deng, Z.-L.; Koslicki, D.; Gurevich, A.; Robertson, G.; Alser, M.; Antipov, D.; Beghini, F.; Bertrand, D.; Brito, J. J.; Brown, C. T.; Buchmann, J.; Buluç, A.; Chen, B.; Chikhi, R.; Clausen, P. T.; Cristian, A.; Dabrowski, P. W.; Darling, A. E.; Egan, R.; Eskin, E.; Georganas, E.; Goltsman, E.; Gray, M. A.; Hansen, L. H.; Hofmeyr, S.; Huang, P.; Irber, L.; Jia, H.; Jørgensen, T. S.; Kieser, S. D.; Klemetsen, T.; Kola, A.; Kolmogorov, M.; Korobeynikov, A.; Kwan, J.; LaPierre, N.; Lemaitre, C.; Li, C.; Limasset, A.; Malcher-Miranda, F.; Mangul, S.; Marcelino, V. R.; Marchet, C.; Marijon, P.; Meleshko, D.; Mende, D. R.; Milanese, A.; Nagarajan, N.; Nissen, J.; Nurk, S.; Oliker, L.; Paoli, L.; Peterlongo, P.; Piro, V. C.; Porter, J. S.; Rasmussen, S.; Rees, E. R.; Reinert, K.; Renard, B.; Robertsen, E. M.; Rosen, G. L.; Ruscheweyh, H.-J.; Sarwal, V.; Segata, N.; Seiler, E.; Shi, L.; Sun, F.; Sunagawa, S.; Sørensen, S. J.; Thomas, A.; Tong, C.; Trajkovski, M.; Tremblay, J.; Uritskiy, G.; Vicedomini, R.; Wang, Zi; Wang, Zhe; Wang, Zho; Warren, A.; Willassen, N. P.; Yelick, K.; You, R.; Zeller, G.; Zhao, Z.; Zhu, S.; Zhu, J.; Garrido-Oter, R.; Gastmeier, P.; Hacquard, S.; Häußler, S.; Khaledi, A.; Maechler, F.; Mesny, F.; Radutoiu, S.; Schulze-Lefert, P.; Smit, N.; Strowig, T.; Bremges, A.; Sczyrba, A.; McHardy, A. C. Critical assessment of metagenome interpretation-the second round of challenges Nature Methods 2022, 19, 429-440.

37. Waterworth, S. C.; Parker-Nance, S.; Kwan, J. C.; Dorrington, R. A. Comparative genomics provides insight into the function of broad-host range sponge symbionts mBio 2021, 12, e01577-21.

36. Waterworth, S. C.; Isemonger, E. W.; Rees, E. R.; Dorrington, R. A.; Kwan, J. C. Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds. Environmental Microbiology Reports 2020, 13, 126–137.

35. Rayko, M.; Komissarov, A.; Kwan, J. C.; Lim-Fong, G.; Rhodes, A. C.; Kliver, S.; Kuchur, P.; O'Brien, S. J.; Lopez, J. V. Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines Scientific Data 2020, 7, 356.

34. Waterworth, S. C.; Flórez, L. V.; Rees, E. R.; Hertweck, C.; Kaltenpoth, M.; Kwan, J. C. Horizontal gene transfer to a defensive symbiont with a reduced genome in a multipartite beetle microbiome. mBio 2020, 11, e02430-19.

33. Acharya, D. D.; Miller, I. J.; Cui, Y.; Braun, D.; Berres, M.; Styles, M.; Li, L.; Kwan, J.; Rajski, S.; Blackwell, H. E.; Bugni, T. S. Omics technologies to understand silent biosynthetic gene cluster activation in Micromonospora sp. WMMB235. ACS Chemical Biology 2019, 14, 1260–1270.

32. Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R.; Rey, F.; Kwan, J. C. Autometa: Automated extraction of genomes from host-associated metagenomes. Nucleic Acids Research 2019, 47, e57.

31. Flórez, L. V.; Scherlach, K.; Miller, I. J.; Rodrigues, A.; Kwan, J. C.; Hertweck, C.; Kaltenpoth, M. An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles. Nature Communications 2018, 9, 2478.

30. Seal, B.; Drider, D.; Oakley, B.; Brüssow, H.; Bikard, D.; Rich, J.; Miller, S.; Devillard, E.; Kwan, J.; Bertin, G.; Reeves, S.; Swift, S.; Raicek, M.; Gay, C. Microbial-derived products as potential new antibiotics: A report from the second Alternatives to Antibiotics Symposium. Veterinary Research 2018, 49, 66.

29. Kwan, J. C. The who, why and how of small molecule production in invertebrate microbiomes - basic insights into drug discovery. mSystems 2018, 3, e00187-17.

28. Lopera, J.; Miller, I. J.; McPhail, K.; Kwan, J. C. Increased biosynthetic gene dosage in a genome-reduced defensive bacterial symbiont. mSystems 2017, 2, e00096-17.

27. Miller, I. J.; Chevrette, M. G.; Kwan, J. C. Interpreting microbial biosynthesis in the genomic age: Biological and practical considerations. Marine Drugs 2017, 15, 165.

26. Miller, I. J.; Vanee, N.; Fong, S. S.; Lim-Fong, G.; Kwan, J. C. Lack of overt genome reduction in the bryostatin-producing bryozoan symbiont 'Candidatus Endobugula sertula'. Applied and Environmental Microbiology 2016, 82, 6573–6583.

25. Miller, I. J.; Weyna, T. R.; Fong, S. S.; Lim-Fong, G.; Kwan, J. C. Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. Scientific Reports 2016, 6, 34362.

Publications based on work prior to joining UW-Madison

24. Liang, X.; Chen, Q.-Y.; Seabra, G. M.; Matthew, S.; Kwan, J. C.; Li, C.; Paul, V. J.; Luesch, H. Bifunctional doscadenamides activate quorum sensing in Gram-negative bacteria and synergize with TRAIL to induce apoptosis in cancer cells Journal of Natural Products 2021, 84, 779-789.

23. Liang, X.; Matthew, S.; Chen, Q.-Y.; Kwan, J. C.; Paul, V.; Luesch, H. Discovery and total synthesis of doscadenamide A: A quorum sensing signaling molecule from a marine cyanobacterium Organic Letters 2019, 21, 7274–7278.

22. Al-Awadhi, F. H.; Gao, B.; Rezaei, M. A.; Kwan, J. C.; Li, C.; Ye, T.; Paul, V. J.; Luesch, H. Discovery, synthesis, pharmacological profiling and biological characterization of brintonamides A–E, novel dual protease and GPCR modulators from a marine cyanobacterium. Journal of Medicinal Chemistry 2018, 61, 6374–6378.

21. Smith, J. E.; Pond, C. D.; Pierce, E.; Harmer, Z. P.; Kwan, J.; Zachariah, M.; Harper, M. K.; Wyche, T. P.; Matainaho, T. K.; Bugni, T. S.; Barrows, L. R.; Ireland, C. M.; Schmidt, E. W. Accessing chemical diversity from the uncultivated symbionts of small marine animals. Nature Chemical Biology 2018, 14, 179–185.

20. Torres, J. P.; Tianero, M. D.; Robes, J. M. D.; Kwan, J. C.; Biggs, J. S.; Concepcion, G. P.; Olivera, B. M.; Haygood, M. G.; Schmidt, E. W Stenotrophomonas-like bacteria are widespread symbionts of cone snail venom ducts. Applied and Environmental Microbiology 2017, 83, e01418-17.

19. Lin, Z.; Torres, J.; Tianero, D.; Kwan, J.; Schmidt, E. W. Origin of chemical diversity in the Prochloron-tunicate symbiosis. Applied and Environmental Microbiology 2016, 82, 3450–3460.

18. Tianero, M. D. B.; Kwan, J. C.; Wyche, T.; Koch, M.; Barrows, L. R.; Bugni, T. S.; Schmidt, E. W. Species specificity of symbiosis and secondary metabolism in ascidians ISME Journal 2015, 9, 615–628.

17. Kim, B.; Park, H.; Salvador, L. A.; Serrano, P. E.; Kwan, J. C.; Zeller, S. L.; Chen, Q.-Y.; Ryu, S.; Liu, Y.; Byeon, S.; Luesch, H.; Hong, J. Evaluation of class I HDAC isoform selectivity of largazole analogues. Bioorganic & Medicinal Chemistry Letters 2014, 24, 3728–3731.

16. Kwan, J. C.; Tianero, M. D. B.; Donia, M. S.; Wyche, T. P.; Bugni, T. S.; Schmidt, E. W. Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella. PLoS ONE 2014, 9, e95850.

15. Kwan, J. C.; Liu, Y.; Ratnayake, R.; Hatano, R.; Kuribana, A.; Morimoto, C.; Ohnuma, K.; Paul, V. J.; Ye, T.; Luesch, H. Grassypeptolides as natural inhibitors of dipeptidyl peptidase 8 and T-cell activation. ChemBioChem 2014, 15, 799−804.

14. Kwan, J. C.; Schmidt, E. W. Bacterial endosymbiosis in a chordate host: Long-term co-evolution and conservation of secondary metabolism. PLoS ONE 2013, 8, e80822.

13. Lin, Z.; Torres, J. P.; Ammon, M. A.; Marett, L.; Teichert, R. W.; Reilly, C. A.; Kwan, J. C.; Hughen, R. W.; Flores, M.; Peraud, O.; Cox, J. E.; Light, A.; Villaraza, J. L.; Haygood, M. G.; Concepcion, G. P.; Olivera, B. M.; Schmidt, E. W. A bacterial source for mollusk pyrone polyketides. Chemistry & Biology 2013, 20, 73−81.

12. Kwan, J. C.; Donia, M. S.; Han, A. W.; Hirose, E.; Haygood, M. G.; Schmidt, E. W. Genome streamlining and chemical defense in a coral reef symbiosis. Proceedings of the National Academy of Sciences of the United States of America 2012, 109, 20655−20660.

11. Hou, Y.; Tianero, M. D. B.; Kwan, J. C.; Wyche, T. P.; Michel, C. R.; Ellis, G. A.; Vasquez-Rivera, E.; Braun, D. R.; Rose, W.; Schmidt, E. W.; Bugni, T. S. Structure and biosynthesis of bottromycin D. Organic Letters 2012, 14, 5050−5053.

10. Kwan, J. C.; Schmidt, E. W. Cleaning up polyketide synthases. Chemistry & Biology 2012, 19, 309−311.

9. Kwan, J. C.; Meickle, T.; Ladwa, D. H.; Teplitski, M.; Paul, V. J.; Luesch, H. Lyngbyoic acid, a ‘tagged’ fatty acid from a marine cyanobacterium, disrupts quorum sensing in Pseudomonas aeruginosa. Molecular BioSystems 2011, 7, 1205−1216.

8. Kwan, J. C.; Abboud, K. A.; Paul, V. J. Luesch, H. Grassypeptolides A−C, cytotoxic bis-thiazoline containing marine cyclodepsipeptides. Journal of Organic Chemistry 2010, 75, 8012−8023.

7. Liu, Y.; Salvador, L. A.; Byeon, S.; Ying, Y.; Kwan, J. C.; Law, B. K.; Hong, J.; Luesch, H. Anti-colon cancer activity of largazole, a marine-derived tunable histone deacetylase inhibitor. Journal of Pharmacology and Experimental Therapeutics 2010, 335, 351−361.

6. Kwan, J. C.; Luesch, H. Weapons in disguise − Activating mechanisms and protecting group chemistry in nature. Chemistry – A European Journal 2010, 16, 13020−13029.

5. Kwan, J. C.; Teplitski, M.; Gunasekera, S. P.; Paul, V. J.; Luesch, H. Isolation and biological evaluation of 8-epi-malyngamide C from the Floridian marine cyanobacterium Lyngbya majuscula. Journal of Natural Products 2010, 73, 463−466.

4. Gunasekera, S. P.; Miller, M. W.; Kwan, J. C.; Luesch, H.; Paul, V. J. Molassamide, a depsipeptide serine protease inhibitor from the marine cyanobacterium Dichothrix utahensis. Journal of Natural Products 2010, 73, 459−462.

3. Kwan, J. C.; Taori, K.; Paul, V. J.; Luesch, H. Lyngbyastatins 8−10, elastase inhibitors with cyclic depsipeptide scaffolds isolated from the marine cyanobacterium Lyngbya semiplena. Marine Drugs 2009, 7, 528−538.

2. Kwan, J. C.; Eksioglu, E. A.; Liu, C.; Paul, V. J.; Luesch, H. Grassystatins A−C from marine cyanobacteria, potent cathepsin E inhibitors that reduce antigen presentation. Journal of Medicinal Chemistry 2009, 52, 5732−5747.

1. Kwan, J. C.; Rocca, J. R.; Abboud, K. A.; Paul, V. J.; Luesch, H. Total structure determination of grassypeptolide, a new marine cyanobacterial cytotoxin. Organic Letters 2008, 10, 789−792.

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