Varigen Scientist Publications

Discovery of Novel Biosynthetic Gene Cluster Diversity from a Soil Metagenomic Library. Santana-Pereira ALR, Sandoval-Powers M, Monsma S, Zhou J, Santos SR, Mead DA, Liles MR. Front Microbiol. 2020 Dec 7;11:585398. doi: 10.3389/fmicb.2020.585398

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase. Palmer M, Hedlund BP, Roux S, Tsourkas PK, Doss RK, Stamereilers C, Mehta A, Dodsworth JA, Lodes M, Monsma S, Glavina del Rio T, Schoenfeld TW, Eloe-Fadrosh EA, Mead DA. Front Microbiol. 2020; 11: 583361. doi: 10.3389/fmicb.2020.583361

Chloramphenicol Derivatives with Antibacterial Activity Identified by Functional Metagenomics. Nasrin S, Ganji S, Kakirde KS, Jacob MR, Wang M, Ravu RR, Cobine PA, Khan IA, Wu CC, Mead DA, Li XC, Liles MR. J Nat Prod. 2018 Jun 22;81(6):1321-1332.

Challenges and Opportunities in the Discovery of Secondary Metabolites Using a Functional Metagenomics Approach. Pereira A, Liles MR, In: Functional Metagenomics: Tools and Applications, edited by Charles T, Liles MR, and Sessitch A. pp. 119-138. (2017) Berlin Heidelberg: Springer-Verlag.

Meeting Report for Synthetic Biology for Natural Products 2017: The Interface of (Meta)Genomics, Machine Learning, and Natural Product Discovery. Smanski MJ, Mead D, Gustafsson C, Thomas MG. ACS Synth Biol. 2017 May 19;6(5):737-743.

Fungal artificial chromosomes for mining of the fungal secondary metabolome. Bok JW, Ye R, Clevenger KD, Mead D, Wagner M, Krerowicz A, Albright JC, Goering AW, Thomas PM, Kelleher NL, Keller NP, Wu CC. BMC Genomics. 2015 Apr 29;16:343. doi: 10.1186/s12864-015-1561-x.

Bacillusin A, an Antibacterial Macrodiolide from Bacillus amyloliquefaciens AP183. Ravu RR, Jacob MR, Chen X, Wang M, Nasrin S, Kloepper JW, Liles MR, Mead DA, Khan IA, Li XC. J Nat Prod. 2015 Apr 24;78(4):924-8.

Draft genome sequence of Bacillus amyloliquefaciens AP183 with antibacterial activity against methicillin-resistant Staphylococcus aureus. Nasrin S, Hossain MJ, and Liles MR (2015) Genome Announcements, 3(2). pii: e00162-15.

Biological agents for control of disease in aquaculture. Carrias A, Ran C, Terhune J, and Liles MR (2012), pp. 353-393. In: Infectious Diseases in Aquaculture, S. Austin (Ed.). London: Woodhead Publishing.

Recovery of as-yet-uncultured soil Acidobacteria on dilute solid media. George IF, Hartmann M, Liles MR, and Agathos SN. (2011) Applied & Environmental Microbiology, 77(22):8184-8188.

Polyketide synthase pathways identified from a metagenomic library are derived from soil Acidobacteria. Parsley LC, Goode AM, Becklund K, George I, Linneman J, Lopanik NB, Goodman RM, and Liles MR. (2011) FEMS Microbiology Ecology, 78(1):176-187.

Gram-negative shuttle BAC vector for heterologous expression of metagenomic libraries. Kakirde KS, Wild J, Godiska R, Mead D, Wiggins AG, Szybalski W, and Liles MR. (2011) Gene, 475(2):57-62.

Size Does Matter: Application-driven Approaches for Soil Metagenomics. Kakirde KS, Parsley LC, and Liles MR. (2010) Soil Biology and Biochemistry, 42(11):1911-1923.

Isolation and cloning of high molecular weight metagenomic DNA from soil microorganisms.  Liles M R, Williamson LL, Rodbumrer J, Parsley L, Torsvik V, Goodman RM, and Handelsman J. (2009) Cold Spring Harbor Protocols, doi:10.1101/pdb.prot5271.

Recovery, purification, and cloning of high molecular weight genomic DNA from soil microorganisms. Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, and Handelsman J. (2008) Applied and Environmental Microbiology, 74:3302-3305.

Isolation of high molecular weight genomic DNA from soil bacteria for genomic library construction.  Liles MR, Williamson LL, Goodman RM, and Handelsman J.  (2004) In: Molecular Methods in Environmental Microbiology, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD. (Eds.), pp. 839-852.

Cloning the metagenome: Culture-independent access to the diversity and functions of the uncultivated microbial world. Handelsman J, Liles MR, Mann D, Riesenfeld C, and Goodman RM. (2002) Methods in Microbiology, 33:241-255.

Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J. (2002). Applied and Environmental Microbiology, 68:4301-4306.

Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osbourne MS, Clardy J, Handelsman J, and Goodman RM  (2000) Applied and Environmental Microbiology, 66 (6): 2541-2547.

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Varigen™ Biosciences, Natural Products by Design™  is an NIH- and NSF-funded effort to harness naturally occurring microbial diversity to develop the next generation of natural products through genomics and metagenomics. Varigen's team is led by researchers with over 125 years of combined experience.