Bacterial Group

  1. Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity. 
    Charlop-Powers Z, Pregitzer CC, Lemetre C, Ternei MA, Maniko J, Hover BM, Calle PY, McGuire KL, Garbarino J, Forgione HM, Charlop-Powers S, Brady SF.
    Proc Natl Acad Sci USA. 2016 Dec 20;113(51):14811-14816. doi: 10.1073/pnas.1615581113. PMID: 27911822
  2. Multiplexed CRISPR/Cas9- and TAR-Mediated Promoter Engineering of Natural Product Biosynthetic Gene Clusters in Yeast.
    Kang HS, Charlop-Powers Z, Brady SF.
    ACS Synth Biol. 2016 Sep 16;5(9):1002-10. doi: 10.1021/acssynbio.6b00080. PMID: 27197732
  3. Natural Product Discovery through Improved Functional Metagenomics in Streptomyces.
    Iqbal HA, Low-Beinart L, Obiajulu JU, Brady SF.
    J Am Chem Soc. 2016 Aug 3;138(30):9341-4. doi: 10.1021/jacs.6b02921. PMID: 27447056
  4. phylogeo: an R package for geographic analysis and visualization of microbiome data.
    Charlop-Powers Z, Brady SF.
    Bioinformatics. 2015 Sep 1;31(17):2909-11. doi: 10.1093/bioinformatics/btv269. PMID: 25913208
  5. Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters.
    Montiel D, Kang HS, Chang FY, Charlop-Powers Z, Brady SF.
    Proc Natl Acad Sci USA. 2015 Jul 21;112(29):8953-8. doi: 10.1073/pnas.1507606112. PMID: 26150486

Fungal Group

  1. HEx: a heterologous expression platform for the discovery of fungal natural products.
    Colin JB Harvey, Mancheng Tang, Ulrich Schlecht, Joe Horecka, Curt R Fischer, Hsiao-ching Lin, Jian Li, Brian Naughton, James Cherry, Molly Miranda, Yong Fuga Li, Angela M Chu, James R Hennessy, Gergana A Vandova, Diane Inglis, Raeka Aiyar, Lars M Steinmetz, Ronald W Davis, Marnix H Medema, Elizabeth Sattely, Chaitan Khosla, Robert P St. Onge, Yi Tang, Maureen E Hillenmeyer.
    bioRxiv preprint 2018 Jan 15. (peer-reviewed version accepted, pending publication)
  2. Engineering the biocatalytic selectivity of iridoid production in Saccharomyces cerevisiae.
    Billingsley JM, DeNicola AB, Barber JS, Tang MC, Horecka J, Chu A, Garg NK, Tang Y.
    Metab Eng. 2017 Nov;44:117-125. PMID: 28939278
  3. Reversible Product Release and Recapture by a Fungal Polyketide Synthase Using a Carnitine Acyltransferase Domain.
    Hang L, Tang MC, Harvey CJB, Page CG, Li J, Hung YS, Liu N, Hillenmeyer ME, Tang Y.
    Angew Chem Int Ed Engl. 2017 Aug 1;56(32):9556-9560. PMID: 28679030
  4. Quantitative analysis of protein interaction network dynamics in yeast.
    Celaj A, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP, St Onge RP.
    Mol Syst Biol. 2017 Jul 13;13(7):934. PMID: 28705884
  5. Heterologous expression of diverse propionyl-CoA carboxylases affects polyketide production in Escherichia coli.
    Vandova GA, O'Brien RV, Lowry B, Robbins TF, Fischer CR, Davis RW, Khosla C, Harvey CJ, Hillenmeyer ME.
    J Antibiot (Tokyo). 2017 Jul;70(7):859-863. PMID: 28400575
  6. A Method for High-throughput Production of Sequence-verified DNA Libraries and Strain Collections. 
    Smith JD, Schlecht U, Xu W, Suresh S, Horecka J, Proctor MJ, Aiyar RS, Bennett RA, Chu A, Li YF, Roy K, Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP. 
    Molecular Systems Biology 2017 Feb 13;13(2):913 PMID: 28193641
  7. Oxidative Cyclization in Natural Product Biosynthesis. 
    Tang MC, Zou Y, Watanabe K, Walsh CT, Tang Y.
    Chem Rev. 2016 Dec 12. PMID: 27936626.
  8. Technology development for natural product biosynthesis in Saccharomyces cerevisiae. 
    Billingsley JM, DeNicola AB, Tang Y.
    Curr Opin Biotechnol. 2016 Dec;42:74-83. PMID: 26994377
  9. Distinct patterns of Cas9 mismatch tolerance in vitro and in vivo. 
    Fu BX, St Onge RP, Fire AZ, Smith JD. 
    Nucleic Acids Res. 2016 Jun 20;44(11):5365-77. PMID: 27198218
  10. Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. 
    Li YF, Tsai KJ, Harvey CJ, Li JJ, Ary BE, Berlew EE, Boehman BL, Findley DM, Friant AG, Gardner CA, Gould MP, Ha JH, Lilley BK, McKinstry EL, Nawal S, Parry RC, Rothchild KW, Silbert SD, Tentilucci MD, Thurston AM, Wai RB, Yoon Y, Aiyar RS, Medema MH, Hillenmeyer ME, Charkoudian LK.
    Fungal Genet Biol. 2016 Apr;89:18-28. doi: 10.1016/j.fgb.2016.01.012. Epub 2016 Jan 22. PMID: 26808821
  11. Saccharomyces cerevisiae as a tool for mining, studying and engineering fungal polyketide synthases. 
    Bond C, Tang Y, Li L. 
    Fungal Genet Biol. 2016 Apr;89:52-61 PMID: 26850128
  12. Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP.
    Genome Biol. 2016 Mar 8;17(1):45. doi: 10.1186/s13059-016-0900-9. PMID: 26956608
  13. Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters. 
    Hillenmeyer ME, Vandova GA, Berlew EE, Charkoudian LK.
    Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13952-7. doi: 10.1073/pnas.1511688112. Epub 2015 Oct 23. PMID: 26499248
  14. Discovery of Unclustered Fungal Indole Diterpene Biosynthetic Pathways through Combinatorial Pathway Reassembly in Engineered Yeast. 
    Tang MC, Lin HC, Li D, Zou Y, Li J, Xu W, Cacho RA, Hillenmeyer ME, Garg NK, Tang Y.
     J Am Chem Soc. 2015 Nov 4;137(43):13724-7. doi: 10.1021/jacs.5b06108. Epub 2015 Oct 21. PMID: 26469304
  15. Computational identification and analysis of orphan assembly-line polyketide synthases. 
    O'Brien RV, Davis RW, Khosla C, Hillenmeyer ME. 
    J Antibiot (Tokyo). 2014 Jan;67(1):89-97. doi: 10.1038/ja.2013.125. Epub 2013 Dec 4. PMID: 24301183 

Plant Group

  1. Diverged Plant Terpene Synthases Reroute the Carbocation Cyclization Path towards the Formation of Unprecedented 6/11/5 and 6/6/7/5 Sesterterpene Scaffolds.
    Huang AC, Hong YJ, Bond AD, Tantillo DJ, Osbourn A.
    Angew Chem Int Ed Engl. 2018 Jan 26;57(5):1291-1295. doi: 10.1002/anie.201711444. Epub 2017 Dec 28. PubMed PMID: 29194888.
  2. Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution.
    Huang AC, Kautsar SA, Hong YJ, Medema MH, Bond AD, Tantillo DJ, Osbourn A.
    Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E6005-E6014. doi: 10.1073/pnas.1705567114. Epub 2017 Jul 3. PubMed PMID: 28673978; PubMed Central PMCID: PMC5530694.
  3. plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters.
    Kautsar SA, Suarez Duran HG, Blin K, Osbourn A, Medema MH.
    Nucleic Acids Res. 2017 Apr 27. doi: 10.1093/nar/gkx305. PubMed PMID: 28453650; PubMed Central PMCID: PMC5570173.
  4. Harnessing plant metabolic diversity.
    Owen C, Patron NJ, Huang A, Osbourn A.
    Curr Opin Chem Biol. 2017 May 17;40:24-30. doi: 10.1016/j.cbpa.2017.04.015. Review. PubMed PMID: 28527344.
  5. Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites.
    Chavali AK, Rhee SY.
    Brief Bioinform. 2017 Apr 7. doi: 10.1093/bib/bbx020. [Epub ahead of print] PubMed PMID: 28398567.
  6. Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.
    Schläpfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, Dreher K, Chavali AK, Nilo-Poyanco R, Bernard T, Kahn D, Rhee SY.
    Plant Physiol. 2017 Apr;173(4):2041-2059. doi: 10.1104/pp.16.01942. Epub 2017 Feb 22. PubMed PMID: 28228535; PubMed Central PMCID: PMC5373064.
  7. Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.
    Medema MH, Osbourn A.
    Nat Prod Rep. 2016 Aug 27;33(8):951-62. doi: 10.1039/c6np00035e. Epub 2016 Jun 20. Review. PubMed PMID: 27321668; PubMed Central PMCID: PMC4987707.
  8. The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize.
    Walsh JR, Schaeffer ML, Zhang P, Rhee SY, Dickerson JA, Sen TZ.
    BMC Syst Biol. 2016 Nov 29;10(1):129. PubMed PMID: 27899149; PubMed Central PMCID: PMC5129634
  9. A glimpse into the future of genome-enabledplant biology from the shores of Cold Spring Harbor.
    Rhee SY, Parker JE, Mockler TC.
    Genome Biol. 2016 Jan 11;17:3. doi: 10.1186/s13059-016-0870-y. PubMed PMID: 26754022; PubMed CentralPMCID: PMC4707773.
  10. Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways.
    Medema MH, Osbourn A.
    Nat Prod Rep. 2016 Aug 27;33(8):951-62. doi: 10.1039/c6np00035e. Epub 2016 Jun 20.PMID: 27321668
  11. Plant metabolic clusters - from genetics to genomics.
    Nützmann HW, Huang A, Osbourn A.
    New Phytol. 2016 Apr 26. doi: 10.1111/nph.13981. PMID: 27112429
  12. Engineering biosynthesis of the anticancer alkaloid noscapine in yeast.
    Li Y, Smolke CD.
    Nat Commun. 2016 Jul 5;7:12137. doi: 10.1038/ncomms12137. PMID: 27378283
  13. Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae.
    Zhou Y., Ma Y., Zeng J., Duan L., Xue X., Wang H., Lin T., Liu Z., Zeng K., Zhong Y., Zhang S., Hu Q., Liu M., Zhang H., Reed J., Moses T., Liu X., Huang P., Qing Z., Liu X., Tu P., Kuang H., Zhang Z., Osbourn A., Ro D. K., Shang Y., Huang S.
    Nat Plants 2016 Nov 28;2:16183. doi: 10.1038/nplants.2016.183. PMID: 27892922