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    Froula, Jeff

    TitleBusiness/Systems Analyst 3
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5775
    vCardDownload vCard

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Kamke J, Soni P, Li Y, Ganesh S, Kelly WJ, Leahy SC, Shi W, Froula J, Rubin EM, Attwood GT. Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep. BMC Res Notes. 2017 Aug 08; 10(1):367. PMID: 28789673.
        View in: PubMed
      2. Peng Z, Nath N, Zhao Z, Froula J, Cheng JF, Chen F. Preparing Mate-Paired Illumina Libraries Using Cre Recombinase. Methods Mol Biol. 2017; 1642:247-261. PMID: 28815505.
        View in: PubMed
      3. Peng Z, Froula J, Cheng JF. Preparing Fosmid Mate-Paired Libraries Using Cre-LoxP Recombination. Methods Mol Biol. 2017; 1642:263-284. PMID: 28815506.
        View in: PubMed
      4. Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ. The Epigenomic Landscape of Prokaryotes. PLoS Genet. 2016 Feb; 12(2):e1005854. PMID: 26870957; PMCID: PMC4752239.
      5. Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 2016 Jul; 10(7):1589-601. PMID: 26744812; PMCID: PMC4918448.
      6. Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015; 3:e1165. PMID: 26336640; PMCID: PMC4556158.
      7. Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res. 2014 Sep; 24(9):1517-25. PMID: 24907284; PMCID: PMC4158751.
      8. Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP, Hess M. Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation. Biotechnol Bioeng. 2014 Aug; 111(8):1550-65. PMID: 24728961.
        View in: PubMed
      9. Peng Z, Zhao Z, Nath N, Froula J, Clum A, Zhang T, Cheng JF, Copeland AC, Pennacchio LA, Chen F. Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS One. 2012; 7(1):e29437. PMID: 22253722; PMCID: PMC3253782.
      10. He S, Wurtzel O, Singh K, Froula J, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods. 2010 Oct; 7(10):807-12. PMID: 20852648.
        View in: PubMed
      11. Vaishampayan PA, Kuehl JV, Froula J, Morgan JL, Ochman H, Francino MP. Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol. 2010 Jan 06; 2:53-66. PMID: 20333224; PMCID: PMC2839348.
      12. Froula J, Francino MP. Selection against spurious promoter motifs correlates with translational efficiency across bacteria. PLoS One. 2007 Aug 15; 2(8):e745. PMID: 17710145; PMCID: PMC1939733.
      13. Collins C, Rommens JM, Kowbel D, Godfrey T, Tanner M, Hwang SI, Polikoff D, Nonet G, Cochran J, Myambo K, Jay KE, Froula J, Cloutier T, Kuo WL, Yaswen P, Dairkee S, Giovanola J, Hutchinson GB, Isola J, Kallioniemi OP, Palazzolo M, Martin C, Ericsson C, Pinkel D, Albertson D, Li WB, Gray JW. Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast carcinoma. Proc Natl Acad Sci U S A. 1998 Jul 21; 95(15):8703-8. PMID: 9671742; PMCID: PMC21140.
      14. Nau R, Schmidt T, Kaye K, Froula J, Täuber MG. Quinolone antibiotics in therapy of experimental pneumococcal meningitis in rabbits. Antimicrob Agents Chemother. 1995 Mar; 39(3):593-7. PMID: 7793857; PMCID: PMC162589.
      15. Schmidt T, Froula J, Täuber MG. Clarithromycin lacks bactericidal activity in cerebrospinal fluid in experimental pneumococcal meningitis. J Antimicrob Chemother. 1993 Oct; 32(4):627-32. PMID: 8288505.
        View in: PubMed

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