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    22833 Publications
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    24 Edited Profiles

    Banfield, Jillian

    TitleGeological Scientist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentEarth Sciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/642-9488

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Zhang H, Waychunas GA, Banfield JF. Molecular Dynamics Simulation Study of the Early Stages of Nucleation of Iron Oxyhydroxide Nanoparticles in Aqueous Solutions. J Phys Chem B. 2015 Aug 20; 119(33):10630-42.
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      2. De Yoreo JJ, Gilbert PU, Sommerdijk NA, Penn RL, Whitelam S, Joester D, Zhang H, Rimer JD, Navrotsky A, Banfield JF, Wallace AF, Michel FM, Meldrum FC, Cölfen H, Dove PM. CRYSTAL GROWTH. Crystallization by particle attachment in synthetic, biogenic, and geologic environments. Science. 2015 Jul 31; 349(6247):aaa6760.
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      3. Young JC, Pan C, Adams RM, Brooks B, Banfield JF, Morowitz MJ, Hettich RL. Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case. Proteomics. 2015 Oct; 15(20):3463-73.
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      4. Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front Microbiol. 2015; 6:654.
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      5. Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 2015 Jul 9; 523(7559):208-11.
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      6. Andrade K, Logemann J, Heidelberg KB, Emerson JB, Comolli LR, Hug LA, Probst AJ, Keillar A, Thomas BC, Miller CS, Allen EE, Moreau JW, Brocks JJ, Banfield JF. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME J. 2015 Dec; 9(12):2697-711.
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      7. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF. CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus. MBio. 2015; 6(2).
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      8. Aliaga Goltsman DS, Comolli LR, Thomas BC, Banfield JF. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J. 2015; 9:1014-23.
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      9. Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. Elife. 2015; 4.
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      10. Luef B, Frischkorn KR, Wrighton KC, Holman HY, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun. 2015; 6:6372.
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      11. Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 2015 Mar 16; 25(6):690-701.
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      12. Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res. 2015 Apr; 25(4):534-43.
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      13. Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe SG, Banfield JF. Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J. 2015 Aug; 9(8):1846-56.
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      14. Tully BJ, Emerson JB, Andrade K, Brocks JJ, Allen EE, Banfield JF, Heidelberg KB. De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape. Archaea. 2015; 2015:875784.
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      15. Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics. 2014; 15(1):1107.
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      16. Probst AJ, Weinmaier T, Raymann K, Perras A, Emerson JB, Rattei T, Wanner G, Klingl A, Berg IA, Yoshinaga M, Viehweger B, Hinrichs KU, Thomas BC, Meck S, Auerbach AK, Heise M, Schintlmeister A, Schmid M, Wagner M, Gribaldo S, Banfield JF, Moissl-Eichinger C. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat Commun. 2014; 5:5497.
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      17. Legg BA, Zhu M, Comolli LR, Gilbert B, Banfield JF. Impacts of ionic strength on three-dimensional nanoparticle aggregate structure and consequences for environmental transport and deposition. Environ Sci Technol. 2014 Dec 2; 48(23):13703-10.
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      18. Xiong W, Giannone RJ, Morowitz MJ, Banfield JF, Hettich RL. Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J Proteome Res. 2015 Jan 2; 14(1):133-41.
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      19. Legg BA, Zhu M, Comolli LR, Gilbert B, Banfield JF. Determination of the three-dimensional structure of ferrihydrite nanoparticle aggregates. Langmuir. 2014 Aug 26; 30(33):9931-40.
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      20. Li Z, Wang Y, Yao Q, Justice NB, Ahn TH, Xu D, Hettich RL, Banfield JF, Pan C. Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat Commun. 2014; 5:4405.
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      21. Comolli LR, Banfield JF. Inter-species interconnections in acid mine drainage microbial communities. Front Microbiol. 2014; 5:367.
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      22. Mosier AC, Li Z, Thomas BC, Hettich RL, Pan C, Banfield JF. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J. 2015 Jan; 9(1):180-94.
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      23. Zhang H, Banfield JF. Structural Characteristics and Mechanical and Thermodynamic Properties of Nanocrystalline TiO2. Chem Rev. 2014 Oct 8; 114(19):9613-44.
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      24. Zhang H, De Yoreo JJ, Banfield JF. A unified description of attachment-based crystal growth. ACS Nano. 2014 Jul 22; 8(7):6526-30.
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      25. Justice NB, Li Z, Wang Y, Spaudling SE, Mosier AC, Hettich RL, Pan C, Banfield JF. (15) N- and (2) H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity. Environ Microbiol. 2014 Oct; 16(10):3224-37.
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      26. Hanke A, Hamann E, Sharma R, Geelhoed JS, Hargesheimer T, Kraft B, Meyer V, Lenk S, Osmers H, Wu R, Makinwa K, Hettich RL, Banfield JF, Tegetmeyer HE, Strous M. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Front Microbiol. 2014; 5:231.
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      27. Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE, Banfield JF. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points. Environ Microbiol. 2015 Mar; 17(3):622-36.
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      28. Nielsen MH, Li D, Zhang H, Aloni S, Han TY, Frandsen C, Seto J, Banfield JF, Cölfen H, De Yoreo JJ. Investigating Processes of Nanocrystal Formation and Transformation via Liquid Cell TEM. Microsc Microanal. 2014 Apr; 20(2):425-36.
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      29. Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, Handley KM, Mullin SW, Nicora CD, Singh A, Lipton MS, Long PE, Williams KH, Banfield JF. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 2014 Jul; 8(7):1452-63.
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      30. Brooks B, Firek BA, Miller CS, Sharon I, Thomas BC, Baker R, Morowitz MJ, Banfield JF. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome. 2014; 2(1):1.
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      31. Pan C, Banfield JF. Quantitative metaproteomics: functional insights into microbial communities. Methods Mol Biol. 2014; 1096:231-40.
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      32. Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome. 2013; 1(1):30.
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      33. Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. 2014 May; 8(5):979-90.
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      34. Sharon I, Banfield JF. Microbiology. Genomes from metagenomics. Science. 2013 Nov 29; 342(6162):1057-8.
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      35. Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R. Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus. PLoS One. 2013; 8(11):e78237.
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      36. Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, Thomas BC, Banfield JF. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio. 2013; 4(5):e00708-13.
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      37. Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF, Ley RE. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife. 2013; 2:e01102.
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      38. Emerson JB, Thomas BC, Andrade K, Heidelberg KB, Banfield JF. New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake. Appl Environ Microbiol. 2013 Nov; 79(21):6755-64.
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      39. Wallace AF, Hedges LO, Fernandez-Martinez A, Raiteri P, Gale JD, Waychunas GA, Whitelam S, Banfield JF, De Yoreo JJ. Microscopic evidence for liquid-liquid separation in supersaturated CaCO3 solutions. Science. 2013 Aug 23; 341(6148):885-9.
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      40. Zhang H, Finnegan MP, Banfield JF. Titania nanorods curve to lower their energy. Nanoscale. 2013 Aug 7; 5(15):6742-6.
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      41. Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe SG, Banfield JF. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome. 2013; 1(1):22.
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      42. Garrity GM, Banfield J, Eisen J, van der Lelie N, McMahon T, Rusch D, Delong E, Moran MA, Currie C, Furhman J, Hallam S, Hugenholtz P, Moran N, Nelson K, Roberts R, Stepanauskas R. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013. Stand Genomic Sci. 2013 Jul 30; 8(3):561-70.
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      43. Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics. 2013; 14:485.
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      44. Emerson JB, Andrade K, Thomas BC, Norman A, Allen EE, Heidelberg KB, Banfield JF. Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea. 2013; 2013:370871.
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      45. Yelton AP, Williams KH, Fournelle J, Wrighton KC, Handley KM, Banfield JF. Vanadate and acetate biostimulation of contaminated sediments decreases diversity, selects for specific taxa, and decreases aqueous V5+ concentration. Environ Sci Technol. 2013 Jun 18; 47(12):6500-9.
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      46. Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF. Stable-isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific. ACS Chem Biol. 2013 Aug 16; 8(8):1755-63.
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      47. Goltsman DS, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF. New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS". Appl Environ Microbiol. 2013 Sep; 79(17):5384-93.
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      48. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One. 2013; 8(4):e61692.
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      49. Moreau JW, Fournelle JH, Banfield JF. Quantifying heavy metals sequestration by sulfate-reducing bacteria in an Acid mine drainage-contaminated natural wetland. Front Microbiol. 2013; 4:43.
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      50. Mosier AC, Justice NB, Bowen BP, Baran R, Thomas BC, Northen TR, Banfield JF. Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics. MBio. 2013; 4(2):e00484-12.
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      51. Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science. 2013 Mar 8; 339(6124):1207-10.
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      52. Wilkins MJ, Wrighton KC, Nicora CD, Williams KH, McCue LA, Handley KM, Miller CS, Giloteaux L, Montgomery AP, Lovley DR, Banfield JF, Long PE, Lipton MS. Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface. PLoS One. 2013; 8(3):e57819.
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      53. Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS One. 2013; 8(2):e56018.
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      54. Paez-Espino D, Morovic W, Sun CL, Thomas BC, Ueda K, Stahl B, Barrangou R, Banfield JF. Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun. 2013; 4:1430.
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      55. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013; 4:2120.
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      56. Handley KM, VerBerkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, Frischkorn KR, Chourey K, Thomas BC, Shah MB, Long PE, Hettich RL, Banfield JF. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J. 2013 Apr; 7(4):800-16.
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      57. Sun CL, Barrangou R, Thomas BC, Horvath P, Fremaux C, Banfield JF. Phage mutations in response to CRISPR diversification in a bacterial population. Environ Microbiol. 2013 Feb; 15(2):463-70.
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      58. Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing KH, Long PE, Comolli LR, Banfield JF. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. ISME J. 2013 Feb; 7(2):338-50.
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      59. Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, Wilkins MJ, Hettich RL, Lipton MS, Williams KH, Long PE, Banfield JF. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012 Sep 28; 337(6102):1661-5.
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      60. Justice NB, Pan C, Mueller R, Spaulding SE, Shah V, Sun CL, Yelton AP, Miller CS, Thomas BC, Shah M, VerBerkmoes N, Hettich R, Banfield JF. Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl Environ Microbiol. 2012 Dec; 78(23):8321-30.
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      61. Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res. 2012 Nov 1; 40(20):10554-66.
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      62. Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013 Jan; 23(1):111-20.
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      63. Cruz-Martínez K, Rosling A, Zhang Y, Song M, Andersen GL, Banfield JF. Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities. Appl Environ Microbiol. 2012 Nov; 78(21):7587-95.
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      64. Zhu M, Legg B, Zhang H, Gilbert B, Ren Y, Banfield JF, Waychunas GA. Early stage formation of iron oxyhydroxides during neutralization of simulated acid mine drainage solutions. Environ Sci Technol. 2012 Aug 7; 46(15):8140-7.
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      65. Emerson JB, Thomas BC, Andrade K, Allen EE, Heidelberg KB, Banfield JF. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol. 2012 Sep; 78(17):6309-20.
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      66. Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, Verberkmoes NC. Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One. 2012; 7(5):e38077.
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      67. Li D, Nielsen MH, Lee JR, Frandsen C, Banfield JF, De Yoreo JJ. Direction-specific interactions control crystal growth by oriented attachment. Science. 2012 May 25; 336(6084):1014-8.
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      68. Schmidt MC, Rocha AM, Padmanabhan K, Shpanskaya Y, Banfield J, Scott K, Mihelcic JR, Samatova NF. NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems. PLoS Comput Biol. 2012; 8(5):e1002490.
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      69. Denef VJ, Banfield JF. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science. 2012 Apr 27; 336(6080):462-6.
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      70. Weinberger AD, Sun CL, Plucinski MM, Denef VJ, Thomas BC, Horvath P, Barrangou R, Gilmore MS, Getz WM, Banfield JF. Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput Biol. 2012; 8(4):e1002475.
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      71. Handley KM, Wrighton KC, Piceno YM, Andersen GL, DeSantis TZ, Williams KH, Wilkins MJ, N'Guessan AL, Peacock A, Bargar J, Long PE, Banfield JF. High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. FEMS Microbiol Ecol. 2012 Jul; 81(1):188-204.
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      72. Singer DM, Chatman SM, Ilton ES, Rosso KM, Banfield JF, Waychunas GA. U(VI) sorption and reduction kinetics on the magnetite (111) surface. Environ Sci Technol. 2012 Apr 3; 46(7):3821-30.
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      73. Singer DM, Chatman SM, Ilton ES, Rosso KM, Banfield JF, Waychunas GA. Identification of simultaneous U(VI) sorption complexes and U(IV) nanoprecipitates on the magnetite (111) surface. Environ Sci Technol. 2012 Apr 3; 46(7):3811-20.
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      74. Comolli LR, Duarte R, Baum D, Luef B, Downing KH, Larson DM, Csencsits R, Banfield JF. A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments. Microsc Res Tech. 2012 Jun; 75(6):829-36.
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      75. Yelton AP, Thomas BC, Simmons SL, Wilmes P, Zemla A, Thelen MP, Justice N, Banfield JF. A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Comput Biol. 2011 Oct; 7(10):e1002230.
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      76. Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res. 2011 Dec; 39(22):9695-704.
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      77. Knierim B, Luef B, Wilmes P, Webb RI, Auer M, Comolli LR, Banfield JF. Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities. Environ Microbiol Rep. 2012 Feb; 4(1):36-41.
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      78. Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 2012 Jan; 6(1):81-93.
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      79. Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF, Thelen MP. Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol. 2011 Aug; 77(15):5230-7.
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      80. Bowen BP, Fischer CR, Baran R, Banfield JF, Northen T. Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics. 2011; 12 Suppl 1:S6.
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      81. Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011; 12(5):R44.
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      82. Mueller RS, Dill BD, Pan C, Belnap CP, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ Microbiol. 2011 Aug; 13(8):2279-92.
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      83. Pan C, Fischer CR, Hyatt D, Bowen BP, Hettich RL, Banfield JF. Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics. 2011 Apr; 10(4):M110.006049.
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      84. Belnap CP, Pan C, Denef VJ, Samatova NF, Hettich RL, Banfield JF. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J. 2011 Jul; 5(7):1152-61.
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      85. Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A. 2011 Jan 18; 108(3):1128-33.
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      86. Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA. Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res. 2011 Jan; 21(1):126-36.
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      87. Callister SJ, Wilkins MJ, Nicora CD, Williams KH, Banfield JF, VerBerkmoes NC, Hettich RL, N'Guessan L, Mouser PJ, Elifantz H, Smith RD, Lovley DR, Lipton MS, Long PE. Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles. Environ Sci Technol. 2010 Dec 1; 44(23):8897-903.
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      88. Wilmes P, Bowen BP, Thomas BC, Mueller RS, Denef VJ, VerBerkmoes NC, Hettich RL, Northen TR, Banfield JF. Metabolome-proteome differentiation coupled to microbial divergence. MBio. 2010; 1(5).
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      89. Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF. Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol Syst Biol. 2010 Jun 8; 6:374.
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      90. Singer SW, Erickson BK, VerBerkmoes NC, Hwang M, Shah MB, Hettich RL, Banfield JF, Thelen MP. Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities. ISME J. 2010 Nov; 4(11):1398-409.
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      91. Moreau JW, Zierenberg RA, Banfield JF. Diversity of dissimilatory sulfite reductase genes (dsrAB) in a salt marsh impacted by long-term acid mine drainage. Appl Environ Microbiol. 2010 Jul; 76(14):4819-28.
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      92. Erickson BK, Mueller RS, VerBerkmoes NC, Shah M, Singer SW, Thelen MP, Banfield JF, Hettich RL. Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community. J Proteome Res. 2010 May 7; 9(5):2148-59.
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      93. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF. Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8806-11.
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      94. Jiao Y, Cody GD, Harding AK, Wilmes P, Schrenk M, Wheeler KE, Banfield JF, Thelen MP. Characterization of extracellular polymeric substances from acidophilic microbial biofilms. Appl Environ Microbiol. 2010 May; 76(9):2916-22.
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      95. Pan C, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF. A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. BMC Bioinformatics. 2010; 11:118.
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      96. Denef VJ, Mueller RS, Banfield JF. AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J. 2010 May; 4(5):599-610.
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      97. Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A. 2010 Feb 9; 107(6):2383-90.
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      98. Belnap CP, Pan C, VerBerkmoes NC, Power ME, Samatova NF, Carver RL, Hettich RL, Banfield JF. Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME J. 2010 Apr; 4(4):520-30.
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      99. Banfield JF, Young M. Microbiology. Variety--the splice of life--in microbial communities. Science. 2009 Nov 27; 326(5957):1198-9.
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      100. Williams KH, Kemna A, Wilkins MJ, Druhan J, Arntzen E, N'Guessan AL, Long PE, Hubbard SS, Banfield JF. Geophysical monitoring of coupled microbial and geochemical processes during stimulated subsurface bioremediation. Environ Sci Technol. 2009 Sep 1; 43(17):6717-23.
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      101. Wilkins MJ, Verberkmoes NC, Williams KH, Callister SJ, Mouser PJ, Elifantz H, N'guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovley DR, Hettich RL, Long PE, Banfield JF. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol. 2009 Oct; 75(20):6591-9.
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      102. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 2009; 10(8):R85.
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      103. Brocks JJ, Banfield J. Unravelling ancient microbial history with community proteogenomics and lipid geochemistry. Nat Rev Microbiol. 2009 Aug; 7(8):601-9.
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      104. Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol. 2009 Jul; 75(13):4599-615.
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      105. Cruz-Martínez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J. 2009 Jun; 3(6):738-44.
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      106. VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol. 2009 Mar; 7(3):196-205.
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      107. Zhang H, Chen B, Banfield JF. The size dependence of the surface free energy of titania nanocrystals. Phys Chem Chem Phys. 2009 Apr 14; 11(14):2553-8.
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      108. Baker BJ, Tyson GW, Goosherst L, Banfield JF. Insights into the diversity of eukaryotes in acid mine drainage biofilm communities. Appl Environ Microbiol. 2009 Apr; 75(7):2192-9.
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      109. Wilmes P, Simmons SL, Denef VJ, Banfield JF. The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev. 2009 Jan; 33(1):109-32.
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      110. Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF. Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J. 2009 Feb; 3(2):159-67.
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      111. Wilmes P, Remis JP, Hwang M, Auer M, Thelen MP, Banfield JF. Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME J. 2009 Feb; 3(2):266-70.
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      112. Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol. 2009 Feb; 11(2):313-25.
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      113. Simmons SL, Dibartolo G, Denef VJ, Goltsman DS, Thelen MP, Banfield JF. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol. 2008 Jul 22; 6(7):e177.
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      114. Andersson AF, Banfield JF. Virus population dynamics and acquired virus resistance in natural microbial communities. Science. 2008 May 23; 320(5879):1047-50.
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      115. Singer SW, Chan CS, Zemla A, VerBerkmoes NC, Hwang M, Hettich RL, Banfield JF, Thelen MP. Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community. Appl Environ Microbiol. 2008 Jul; 74(14):4454-62.
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      116. Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC, Banfield JF. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J. 2008 Aug; 2(8):853-64.
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      117. Jeans C, Singer SW, Chan CS, Verberkmoes NC, Shah M, Hettich RL, Banfield JF, Thelen MP. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2008 May; 2(5):542-50.
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      118. Eppley JM, Tyson GW, Getz WM, Banfield JF. Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics. 2007; 8:398.
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      119. Tyson GW, Banfield JF. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol. 2008 Jan; 10(1):200-7.
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      120. Eppley JM, Tyson GW, Getz WM, Banfield JF. Genetic exchange across a species boundary in the archaeal genus ferroplasma. Genetics. 2007 Sep; 177(1):407-16.
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      121. Denef VJ, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF. Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis. J Proteome Res. 2007 Aug; 6(8):3152-61.
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      122. Moreau JW, Weber PK, Martin MC, Gilbert B, Hutcheon ID, Banfield JF. Extracellular proteins limit the dispersal of biogenic nanoparticles. Science. 2007 Jun 15; 316(5831):1600-3.
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      123. Zhang H, Rustad JR, Banfield JF. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations. J Phys Chem A. 2007 Jun 14; 111(23):5008-14.
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      124. Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature. 2007 Mar 29; 446(7135):537-41.
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      125. Chen B, Zhang H, Gilbert B, Banfield JF. Mechanism of inhibition of nanoparticle growth and phase transformation by surface impurities. Phys Rev Lett. 2007 Mar 9; 98(10):106103.
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      126. Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF. Genome dynamics in a natural archaeal population. Proc Natl Acad Sci U S A. 2007 Feb 6; 104(6):1883-8.
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      127. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. Lineages of acidophilic archaea revealed by community genomic analysis. Science. 2006 Dec 22; 314(5807):1933-5.
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      128. Guzman KA, Finnegan MP, Banfield JF. Influence of surface potential on aggregation and transport of titania nanoparticles. Environ Sci Technol. 2006 Dec 15; 40(24):7688-93.
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      129. Whitaker RJ, Banfield JF. Population genomics in natural microbial communities. Trends Ecol Evol. 2006 Sep; 21(9):508-16.
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      130. Gilbert B, Huang F, Lin Z, Goodell C, Zhang H, Banfield JF. Surface chemistry controls crystallinity of ZnS nanoparticles. Nano Lett. 2006 Apr; 6(4):605-10.
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      131. Guzmán KA, Taylor MR, Banfield JF. Environmental risks of nanotechnology: National Nanotechnology Initiative funding, 2000-2004. Environ Sci Technol. 2006 Mar 1; 40(5):1401-7.
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      132. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol. 2005 Oct; 71(10):6319-24.
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      133. Williams KH, Ntarlagiannis D, Slater LD, Dohnalkova A, Hubbard SS, Banfield JF. Geophysical imaging of stimulated microbial biomineralization. Environ Sci Technol. 2005 Oct 1; 39(19):7592-600.
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      134. Tyson GW, Banfield JF. Cultivating the uncultivated: a community genomics perspective. Trends Microbiol. 2005 Sep; 13(9):411-5.
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      135. Naicker PK, Cummings PT, Zhang H, Banfield JF. Characterization of titanium dioxide nanoparticles using molecular dynamics simulations. J Phys Chem B. 2005 Aug 18; 109(32):15243-9.
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      136. Allen EE, Banfield JF. Community genomics in microbial ecology and evolution. Nat Rev Microbiol. 2005 Jun; 3(6):489-98.
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      137. Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC, Shah M, Hettich RL, Banfield JF. Community proteomics of a natural microbial biofilm. Science. 2005 Jun 24; 308(5730):1915-20.
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      138. Suzuki Y, Kelly SD, Kemner KM, Banfield JF. Direct microbial reduction and subsequent preservation of uranium in natural near-surface sediment. Appl Environ Microbiol. 2005 Apr; 71(4):1790-7.
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      139. Huang F, Banfield JF. Size-dependent phase transformation kinetics in nanocrystalline ZnS. J Am Chem Soc. 2005 Mar 30; 127(12):4523-9.
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      140. Baumler DJ, Jeong KC, Fox BG, Banfield JF, Kaspar CW. Sulfate requirement for heterotrophic growth of "Ferroplasma acidarmanus" strain fer1. Res Microbiol. 2005 May; 156(4):492-8.
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      141. Banfield JF, Verberkmoes NC, Hettich RL, Thelen MP. Proteogenomic approaches for the molecular characterization of natural microbial communities. OMICS. 2005; 9(4):301-33.
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      142. Baker BJ, Lutz MA, Dawson SC, Bond PL, Banfield JF. Metabolically active eukaryotic communities in extremely acidic mine drainage. Appl Environ Microbiol. 2004 Oct; 70(10):6264-71.
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      143. Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF. Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid. Extremophiles. 2004 Oct; 8(5):411-9.
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      144. Gilbert B, Huang F, Zhang H, Waychunas GA, Banfield JF. Nanoparticles: strained and stiff. Science. 2004 Jul 30; 305(5684):651-4.
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      145. Gilbert B, Zhang H, Huang F, Banfield JF, Ren Y, Haskel D, Lang JC, Srajer G, Jürgensen A, Waychunas GA. Analysis and simulation of the structure of nanoparticles that undergo a surface-driven structural transformation. J Chem Phys. 2004 Jun 22; 120(24):11785-95.
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      146. Huang F, Gilbert B, Zhang H, Banfield JF. Reversible, surface-controlled structure transformation in nanoparticles induced by an aggregation state. Phys Rev Lett. 2004 Apr 16; 92(15):155501.
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      147. Chan CS, De Stasio G, Welch SA, Girasole M, Frazer BH, Nesterova MV, Fakra S, Banfield JF. Microbial polysaccharides template assembly of nanocrystal fibers. Science. 2004 Mar 12; 303(5664):1656-8.
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      148. Labrenz M, Banfield JF. Sulfate-reducing bacteria-dominated biofilms that precipitate ZnS in a subsurface circumneutral-pH mine drainage system. Microb Ecol. 2004 Apr; 47(3):205-17.
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      149. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004 Mar 4; 428(6978):37-43.
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      150. Baker BJ, Hugenholtz P, Dawson SC, Banfield JF. Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol. 2003 Sep; 69(9):5512-8.
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      151. Zhang H, Gilbert B, Huang F, Banfield JF. Water-driven structure transformation in nanoparticles at room temperature. Nature. 2003 Aug 28; 424(6952):1025-9.
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      152. Baker BJ, Banfield JF. Microbial communities in acid mine drainage. FEMS Microbiol Ecol. 2003 May 1; 44(2):139-52.
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      153. Suzuki Y, Kelly SD, Kemner KM, Banfield JF. Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment. Appl Environ Microbiol. 2003 Mar; 69(3):1337-46.
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      154. Gihring TM, Bond PL, Peters SC, Banfield JF. Arsenic resistance in the archaeon "Ferroplasma acidarmanus": new insights into the structure and evolution of the ars genes. Extremophiles. 2003 Apr; 7(2):123-30.
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      155. Crocetti GR, Banfield JF, Keller J, Bond PL, Blackall LL. Glycogen-accumulating organisms in laboratory-scale and full-scale wastewater treatment processes. Microbiology. 2002 Nov; 148(Pt 11):3353-64.
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      156. Suzuki Y, Kelly SD, Kemner KM, Banfield JF. Nanometre-size products of uranium bioreduction. Nature. 2002 Sep 12; 419(6903):134.
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      157. Newman DK, Banfield JF. Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science. 2002 May 10; 296(5570):1071-7.
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      158. Ranade MR, Navrotsky A, Zhang HZ, Banfield JF, Elder SH, Zaban A, Borse PH, Kulkarni SK, Doran GS, Whitfield HJ. Energetics of nanocrystalline TiO2. Proc Natl Acad Sci U S A. 2002 Apr 30; 99 Suppl 2:6476-81.
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      159. Gihring TM, Banfield JF. Arsenite oxidation and arsenate respiration by a new Thermus isolate. FEMS Microbiol Lett. 2001 Nov 13; 204(2):335-40.
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      160. Gihring TM, Druschel GK, McCleskey RB, Hamers RJ, Banfield JF. Rapid arsenite oxidation by Thermus aquaticus and Thermus thermophilus: field and laboratory investigations. Environ Sci Technol. 2001 Oct 1; 35(19):3857-62.
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      161. Banfield JF, Moreau JW, Chan CS, Welch SA, Little B. Mineralogical biosignatures and the search for life on Mars. Astrobiology. 2001; 1(4):447-65.
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      162. Labrenz M, Druschel GK, Thomsen-Ebert T, Gilbert B, Welch SA, Kemner KM, Logan GA, Summons RE, De Stasio G, Bond PL, Lai B, Kelly SD, Banfield JF. Formation of sphalerite (ZnS) deposits in natural biofilms of sulfate-reducing bacteria. Science. 2000 Dec 1; 290(5497):1744-7.
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      163. Bond PL, Druschel GK, Banfield JF. Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl Environ Microbiol. 2000 Nov; 66(11):4962-71.
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      164. Bond PL, Smriga SP, Banfield JF. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl Environ Microbiol. 2000 Sep; 66(9):3842-9.
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      165. Banfield JF, Welch SA, Zhang H, Ebert TT, Penn RL. Aggregation-based crystal growth and microstructure development in natural iron oxyhydroxide biomineralization products. Science. 2000 Aug 4; 289(5480):751-4.
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      166. Edwards KJ, Bond PL, Banfield JF. Characteristics of attachment and growth of Thiobacillus caldus on sulphide minerals: a chemotactic response to sulphur minerals? Environ Microbiol. 2000 Jun; 2(3):324-32.
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      167. Edwards KJ, Bond PL, Gihring TM, Banfield JF. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science. 2000 Mar 10; 287(5459):1796-9.
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      168. Banfield JF, Marshall CR. Perspectives: earth science and evolution. Genomics and the geosciences. Science. 2000 Jan 28; 287(5453):605-6.
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      169. Edwards KJ, Gihring TM, Banfield JF. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment. Appl Environ Microbiol. 1999 Aug; 65(8):3627-32.
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      170. Banfield JF, Barker WW, Welch SA, Taunton A. Biological impact on mineral dissolution: application of the lichen model to understanding mineral weathering in the rhizosphere. Proc Natl Acad Sci U S A. 1999 Mar 30; 96(7):3404-11.
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      171. Skinner HC, Banfield JF. Microbes all around. Geotimes. 1997 Aug; 42(8):16-9.
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      172. Veblen DR, Banfield JF, Guthrie GD, Heaney PJ, Ilton ES, Livi KJ, Smelik EA. High-resolution and analytical transmission electron microscopy of mineral disorder and reactions. Science. 1993 Jun 4; 260(5113):1465-72.
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