Publications

(Descending Chronology; * = senior and/or corresponding author)

Also see Google Scholar: James R. Brown

  1. Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE Gardiner DF, Brown JR*. 2021. Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944). BMC Microbiology 21:181. https://doi.org/10.1186/s12866-021-02245-8
  2. Nuzzo A, Saha S, Berg E, Jayawickreme C, Tocker J, Brown JR*. 2021. Expanding the drug discovery space with predicted metabolite-target interactions. Communications Biology (Nature). 4:288. https://doi.org/10.1038/s42003-021-01822-x
  3. Inflammatory endotype associated airway microbiome in COPD clinical stability and exacerbations. 2020. Wang Z, Locantore N, Haldar K, Ramsheh MY, Beech AS, Ma W, Brown JR, Tal-Singer R, Barer MR, Bafadhel M, Donaldson GC, Wedzicha JA, Singh D, Wilkinson TMA, Miller BE, Brightling CE. American Journal of Respiratory And Critical Care Medicine. https://doi.org/10.1164/rccm.202009-3448OC
  4. Wang Z, Yang Y, Yan Z, Liu H, Chen B, Liang Z, Wang F, Miller BE, Tal-Singer R, Yi X, Li J-t, Stampfli MR, Zhou H, Brightling CE, Brown JR, Wu M, Chen R, Shu W. 2020. Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. The ISME Journal. https://doi.org/10.1038/s41396-020-0727-y
  5. Haldar K, George L, Wang Z, Mistry V, Ramsheh MY, Free RC, John C, Reeve NF, Miller BE, Tal-Singer R, Webb AJ, Brookes AJ, Tobin MD, Singh D, Donaldson GC, Wedzicha JA, Brown JR, Barer MR, Brightling CE. 2020. The sputum microbiome is distinct between COPD and health, independent of smoking history. BMC Respiratory Research. 21:183. https://doi.org/10.1186/s12931-020-01448-3
  6. Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. 2020. PICRUSt2: An improved and extensible approach for metagenome inference. Nature Biotechnology. 38:685-88. https://doi.org/10.1038/s41587-020-0548-6.
  7. Nuzzo A, Brown JR*. 2020. Microbiome metabolite mimics accelerate drug discovery. Trends in Molecular Medicine. 26:435-437 https://doi.org/10.1016/j.molmed.2020.03.006
  8. Nuzzo A, Brown JR*. 2020. The microbiome factor in drug discovery and development. Chemical Research in Toxicology. https://doi.org/10.1021/acs.chemrestox.9b00333
  9. Scangarella-Oman N, Ingraham K, Tiffany C, Tomsho L, Van Horn S, Mayhew D, Perry C, Ashton T, Dumont E, Huang J, Brown JR, Miller L. 2020. In vitro activity and microbiological efficacy of gepotidacin from a Phase 2, randomized, multicenter, dose-ranging study in patients with acute bacterial skin and skin structure infections. Antimicrobial Agents and Chemotherapy. 64:e01301-19.
  10. Washburn WL, Wang Z, Walton AH, Goedegebuure SP, Figueroa DJ, Van Horn S, Grossman J, Remlinger K, Madsen H, Brown JR, Srinivasan R, Wolf AI, Berger SB, Yi V, Hawkins WG, Fields RC, Hotchkiss RS. 2019. T cell and monocyte specific RNAseq analysis in septic and non-septic critically-ill patients and in patients with cancer. Journal of Immunology. 203:1897 https://doi.org/10.4049/jimmunol.1900560.
  11. Michalovich D, Rodriguez-Perez N, Smolinska S, Pirozynski M, Mayhew D, Uddin S, Van Horn S, Sokolowska M, Altunbulakli C, Eljaszewicz A, Pugin B, Barcik W, Kurnik-Lucka M, Saunders K, Simpson K, Schmid-Grendelmeier P, Ferstl R, Frei R, Sievi N, Kohler M, Gajdanowicz P, Graversen K, Bøgh K, Jutel M, Brown JR, Akdis C, Hessel E, O’Mahony L. 2019. Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients. Nature Communications. 10:5711. https://doi.org/10.1038/s41467-019-13751-9.
  12. Costa Sa AC, Madsen H, Brown JR*. 2019. Shared molecular signatures across neurodegenerative diseases and herpes virus infections highlights potential mechanisms for maladaptive innate immune responses. Scientific Reports (Nature). 9:8795. https://doi.org/10.1038/s41598-019-45129-8.
  13. Wang Z, Maschera B, Lea S, Kolsum U, Michalovich D, Van Horn S, Traini C, Brown JR*, Hessel EM, Singh D. 2019. Airway host-microbiome interactions in chronic obstructive pulmonary disease. BMC Respiratory Research. 20:113.  https://doi.org/10.1186/s12931-019-1085-z.
  14. Brown JR*, Baker SJ, Barros-Aquirre D, Payne D. 2018. The ninth commandment — Better incentives to promote investment for new drugs and improving existing ones. Microbiologist, Society for Applied Microbiology. 19:42.
  15. Wang Z, Arat S, Magid-Slav M, Brown JR*. 2018. Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets. BMC Systems Biology. 12:3. https://doi.org/10.1186/s12918-017-0524-z.
  16. Mayhew D, Devos N, Lambert C, Brown JR, Clarke S, Kim V, Magid-Slav M, Miller BE, Ostridge K, Patel R, Sathe G, Simola DF, Staples KJ, Sung R, Tal-Singer R, Tuck AC, Van Horn S, Weynants V, Williams N, Devaster J-M, Wilkinson TM. 2018. Lung microbiome analysis and stochastic modeling of COPD exacerbations in the AERIS study. Thorax. https://doi.org/10.1136/thoraxjnl2017-210741.
  17. Wang Z, Saha S, Van Horn S, Thomas E, Traini C, Sathe G, Rajpal DK, Brown JR*. 2017. Gut microbiome differences between metformin and liraglutide treated T2DM subjects. Endocrinology, Diabetes & Metabolism https://doi.org/10.1002/edm2.9.
  18. Wang Z, Singh R, Miller BE, Tal-Singer R, Van Horn S, Tomsho L, Mackay A, Allinson JP, Webb AJ, Brookes AJ, George LM, Barker B, Kolsum U, Donnelly LE, Belchamber K, Barnes PJ, Singh D, Brightling CE, Donaldson GC, Wedzicha JA, Brown JR*. 2017. Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study. Thorax 73:331-338 https://doi.org/10.1136/thoraxjnl-2017-210741.
  19. Brown JR*. 2017. The Microbiome in Health and Disease. In Bornstein MH, ed. The SAGE Encyclopedia of Lifespan and Human Development.
  20. Saha S, Rajpal DK, Brown JR*. 2016. Human microbial metabolites as a source of new drugs. Drug Discovery Today. 21: 692-698. DOI: 1016/j.drudis.2016.02.009
  21. Wang Z, Bafadhel M, Haldar K, Spivak A, Mayhew D, Miller BE, Tal-Singer R, Johnston SL, Ramsheh MY, Barer MR, Brightling CE, Brown JR*. 2016. Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations. European Respiratory Journal. 47:1082-92.
  22. Rajpal D, Klein J-L, Mayhew D, Boucheron J, Spivak A, Kumar V, Ingraham K, Paulik M, Chen L, Van Horn S, Thomas E, Sathe G, Livi GP, Holmes DJ, Brown JR*. 2015. Selective spectrum antibiotic modulation of the gut microbiome in obesity and diabetes rodent models. PLoS One. 10: e0145499.
  23. Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, Castro-Pichel J, Martínez-Jiménez F, Papadatos G, Mugumbate G, Kumar V, Colmenarejo G, Hurle M, Barroso V, Young R, Bates RH. Maria Lopez-Roman E, Mendoza-Losana A, Brown JR, Alvarez-Ruiz E, Marti-Renom MA, Overington JP, Cammack N, Ballell L, Barros D. 2015. Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery. PLoS One 10:e0142293.
  24. Peña I, Manzano MP, Cantizani J, Kessler A, Alonso-Padilla J, Bardera AI, Alvarez E, Colmenarejo G, Cotillo I, Roquero I, de Dios-Anton F, Barroso V, Rodriguez A, Gray DW, Navarro M, Kumar V, Sherstnev A, Drewry D, Brown JR, Fiandor JM, Martin JJ. 2015. New compound sets identified from high throughput phenotypic screening against three kinetoplastid parasites: An open resource. Scientific Reports (Nature). 5:8771.
  25. Arat S, Spivak A, Van Horn S, Thomas E, Traini C, Sathe G, Livi GP, Ingraham K, Jones L, Aubart K, Holmes DJ, Naderer O, Brown JR. 2015. Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase. Antimicrobial Agents and Chemotherapy. 59:1182-1192.
  26. O’Dwyer K, Spivak A, Ingraham K, Min S, Holmes DJ, Jakielaszek C, Rittenhouse S, Kwan A, Livi GP, Sathe G, Thomas E, Van Horn S, Miller LA, Twynholm M, Tomayko J, Dalessandro M, Caltabiano M, Scangarella-Oman NE, Brown JR*. 2015. Bacterial resistance to leucyl-tRNA synthetase inhibitor GSK2251052 develops during treatment of complicated urinary tract infections. Antimicrobial Agents and Chemotherapy. 59:289-298.
  27. Brown JR, Drewry D, Gamo F-J, Garcia-Bustos JF. 2015. Kinase inhibitors among hits from malaria cellular screens. In Doerig C, Wiese M, Spaeth G, ed. Protein phosphorylation in eukaryotic parasites: potential for chemotherapy. Wiley-Blackwell.
  28. Napolitano A, Miller S, Nicholls AW, Baker D, Van Horn S, Thomas E, Rajpal D, Spivak A, Brown JR*, Nunez DJ. 2014. Novel gut-based pharmacology of metformin in patients with Type 2 Diabetes Mellitus. PLoS One. 9:e100778.
  29. Irlbeck DM, Vernon SD, McCleary KK, Bateman L, Klimas NG, Lapp CW, Peterson DL , Brown JR, Wilfret DA, Gerondelis P. 2014. No association found between the detection of either Xenotropic Murine Leukemia Virus-Related Virus or Polytropic Murine Leukemia Virus and Chronic Fatigue Syndrome in a blinded, multi-site, prospective study. BMC Research Notes. 7:461.
  30. Ross LL, Horton J, Hasan S, Brown JR, Murphy D, DeJesus E, Potter M, LaMarca A, MelendezRivera I, Ward D, Uy J, Shaefer MS. 2014. HIV-1 transmission patterns in antiretroviral therapy naïve, HIV-infected North Americans based on phylogenetic analysis by population level and ultra-deep DNA sequencing. PLoS One. 9:e89611.
  31. Smith SB, Magid-Slav M, Brown JR*. 2013. Host response to respiratory bacterial pathogens as identified by integrated analysis of human gene expression data. PLoS One. 8:e75607.
  32. Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. 2013. Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Computational Biology. 9:e1003253.
  33. Rajpal DK, Brown JR*. 2013. The microbiome as a therapeutic target for metabolic diseases. Drug Development Research. 74:376-394.
  34. Rajpal DK, Brown JR*. 2013. Modulating the human gut microbiome as an emerging therapeutic paradigm. Science Progress. 96:224-236.
  35. Vamathevan JJ, Hall MD, Hasan S, Woollard PM, Xu M, Yang Y, Li X, Wang X, Kenny S, Brown JR, Huxley-Jones J, Lyon J, Haselden J, Min J, Sanseau P. 2013. Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development. Toxicology and Applied Pharmacology. 270:149-157.
  36. Brown JR, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley, TD, Raes J, Turnbaugh, P. 2013 Translating the human microbiome. Nature Biotechnology. 31:304–308.
  37. Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR*. 2012. Data mining the human gut microbiota for therapeutic targets. Briefings in Bioinformatics. Mar. 24 EPub.
  38. Smith SB, Dampier W, Tozeren A, Brown JR*, Magid-Slav M. 2012. Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis. PLoS One. 7(3):e33174.
  39. Kumar V, Sun P, Vamathevan J, Li Y, Ingraham K, Palmer L, Huang J, Brown JR*. 2011. Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles. Antimicrobial Agents and Chemotherapy. 55:4267-4276.
  40. Brown JR*, Magid-Slav M, Sanseau P, Rajpal D. 2011. Computational biology approaches for selecting host-pathogen drug targets. Drug Discovery Today. 16:229-236.
  41. Brown JR*, Auger KR. 2011. Phylogenomics of phosphoinositide lipid kinases: Perspectives on the evolution of second messenger signaling and drug discovery. BMC Evolutionary Biology. 11:4.
  42. Gamo F-J, Sanz LM, Vidal J, de Cozar C, Alvarez E, Lavandera J-L, Vanderwall DE, Green DVS, Kumar V, Hasan S, Brown JR, Peishoff CE, Cardon LR, Garcia-Bustos JF. 2010. Thousands of chemical starting points for antimalarial lead identification. Nature. 465:305-310.
  43. Zhang Y, Italia MJ, Auger KR, Halsey WS, Van Horn SF, Sathe GM, Magid-Slav M, Brown JR*, Holbrook JD. 2010. Molecular evolutionary analysis of cancer cell lines. Molecular Cancer Therapeutics. 9:279-291.
  44. Brown JR*. 2010. Next generation sequencing for antibacterial drug discovery. International Drug Discovery. 6:42-45.
  45. Brown JR*, Deharo S, Dancis B, Barnes MR, Sanseau P. 2007. Non-coding RNA bioinformatics. In Barnes MR, Gray IC, ed. Bioinformatics for Geneticists 2nd edition. Wiley Press.
  46. Murphy DM, Dancis B, Brown JR*. 2006. Evolution of MicroRNA Biogenesis. In Clarke N, Sanseau P, ed. microRNAs: Biology, Function and Expression. DNA Press.
  47. Brown JR*, Murphy DM. 2009. Computational biology in anti-tuberculosis drug discovery. Infectious Disorders – Drug targets. 9:319-326.
  48. Murphy DM, Brown JR*. 2008. Novel drug target strategies against Mycobacterium tuberculosis. Current Opinion Microbiology. 11:422-427.
  49. Murphy DM, Dancis B, Brown JR*. The evolution of core proteins involved in microRNA biogenesis. BMC Evolutionary Biology. 8:92.
  50. Brown JR*, Editor. 2008. Comparative Genomics: Basic and Applied Research. CRC / Taylor and Francis Press. 383 pages.
  51. Brown JR*. 2008. The Broad Horizons of Comparative Genomics. In Brown, JR, ed. Comparative Genomics: Basic and Applied Research. CRC/Taylor & Francis Press.
  52. Brown JR*. 2008. Comparative Genomics in Drug Discovery. In Brown, JR, ed. Comparative Genomics: Basic and Applied Research. CRC/Taylor & Francis Press.
  53. Murphy DM, Brown JR*. 2007. Identification of gene targets against dormant phase Mycobacterium tuberculosis BMC Infectious Diseases 7:84.
  54. Barnes MR, Deharo S, Grocock RJ, Brown JR, Sanseau P. 2007 The micro RNA target paradigm: a fundamental and polymorphic control layer of cellular expression. Expert Opinion Biol. Ther. 9:1387-99.
  55. Huang J, Van Aller GS, Taylor AN, Kerrigan JJ, Liu W-S, Trulli JM, Lai Z, Holmes D, Payne DJ, Aubart KM, Brown JR, Zalacain M. 2006. Phylogenomic and biochemical characterization of three Legionella pneumophila polypeptide deformylases. Bacteriol. 188:5249-5257.
  56. Stanhope MJ, Walsh SL, Becker JA, Italia MJ, Ingraham KA, Gwynn MN, Mathie T, Poupard JA, Miller LA, Brown JR, Amrine-Madsen H. 2005. Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread. Antimicrobial Agents and Chemotherapy. 49:4315-4326.
  57. Brown JR, Sanseau P. 2005. A computational view of microRNAs and their targets. Drug Discovery Today 10:595-601.
  58. Brown JR*, Koretke KK, Birkeland ML, Sanseau P, Patrick, DR. 2004. Aurora kinase evolution: Implications for model organism studies and the development of anti-cancer drugs. BMC Evolutionary Biology 4:39.
  59. Brown JR*, Volker CJ. 2004. Phylogeny of g-proteobacteria: resolution of one branch of the universal tree? BioEssays. 26:463-468.
  60. Stanhope MJ, Brown JR, Armine-Madsen H. 2004. Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of the SARS virus. Infection, Genetics and Evolution. 4:15-19.
  61. Brown JR*. 2004. Putting the “Bio” back in bioinformatics. The Scientist 18:44-45.
  62. Brown JR*. 2004. Horizontal Gene Transfer and Bacterial Genomic Legacies. In Mullany L. The Dynamic Bacterial Genome and its Biological Consequences. Advances in Molecular and Cellular Microbiology. Cambridge University Press.
  63. Brown JR*. 2003. Ancient horizontal gene transfer. Nature Reviews Genetics. 4:119-130.
  64. Brown JR*, Gentry DR, Becker JA, Ingraham K, Holmes DJ, Stanhope MJ. 2003. Horizontal transfer of drug resistant aminoacyl-tRNA synthetases of anthrax and Gram-positive pathogens. EMBO reports. 4:692-698.
  65. Zalacain M, Biswas S, Ingraham KA, Ambrad J, Bryant A, Chalker AF, Iordanescu S, Fan J, Fan F, Lunsford RD, O’Dwyer K, Palmer LM, So C, Sylvester D, Volker C, Warren P, McDevitt D, Brown JR, Holmes DJ, Burnham MKR. 2003. A global approach to identify novel broad spectrum antibacterial targets among proteins of unknown function. J Molecular Microbiology and Biotechnology. 6:109-126.
  66. Choudhry AE, Mandichak TL, Broskey JP, Egolf RW, Kinsland C, Begley TP, Seefeld MA, Ku TW, Brown JR, Zalacain M, Ratnam K. 2003. Inhibitors of pantothenate kinase: novel antibiotics for Staphylococcal infections. Antimicrobial Agents and Chemotherapy. 47:2051-2055.
  67. Gentry DR, Ingraham KA, Stanhope MJ, Rittenhouse S, Jarvest RL, O’Hanlon PJ, Brown JR, Holmes DJ. 2003. Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals sub populations of Streptococcus pneumoniae with two distinct methionyl tRNA synthetase genes. Antimicrobial Agents and Chemotherapy. 47:1784-1789.
  68. Brown JR*. 2003. Reconstructing the universal tree of life. In Ribas de Pouplana L, ed. The Genetic Code and the Origin of Life. Landes Biosciences Press.
  69. Volker CJ, Brown JR*. 2002. Bioinformatics and the discovery of novel anti-microbial targets. Current Drug Targets – Infectious Disorders. 2:279-290.
  70. Noordewier M, Brown JR*. 2002. Comparing the genomes of Salmonella enterica serovars: Differences and similarities among the closest of relatives. Trends in Pharmacological Sciences. 23:397-399.
  71. Poupard J, Brown JR, Gagnon R, Stanhope M, Stewart C. 2002. Methods of data mining from large multi-national surveillance studies. Antimicrobial Agents and Chemotherapy. 46:24092419.
  72. Sousa S, McLaughlin MM, Pereira SA, VanHorn S, Knowlton R, Brown JR, Nicholas RO, Livi GP. The ARO4 gene of Candida albicans encodes a tyrosine-sensitive DAHP synthase: evolution, functional conservation and phenotype of Aro3p, /Aro4p-deficient mutants. Microbiology. 148:1291-1303.
  73. Brown JR*, Italia MJ, Douady CJ, Stanhope MJ. 2002. Horizontal gene transfer and the universal tree of life. pp. 305-349. In Syvanen M, Kado CI. Horizontal Gene Transfer, 2nd Edition. Academic Press.
  74. Stanhope MJ, Lupas A, Italia MJ, Koretke K, Volker C, Brown JR. 2001. Phylogenetic analyses of genomic and EST sequences do not support horizontal gene transfers between bacteria and vertebrates. Nature 411:940-944.
  75. Brown JR*, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. 2001. Universal trees based on large combined protein sequence datasets. Nature Genetics. 28:281-285.
  76. Brown JR*. 2001. Genomic and phylogenetic perspectives on the evolution of prokaryotes. Systematic Biology. 50:497-512.
  77. Ribas de Pouplana L, Brown JR, Schimmel P. 2001. Structure-based phylogeny of class IIa tRNA synthetases in relation to an unusual biochemistry. Molecular Evolution. 53:261-268.
  78. Petit, CM, Brown JR, Ingraham K, Bryant AP, Holmes D. 2001. Lipid modification of prelipoproteins is dispensable for growth in vitro but essential for virulence in Streptococcus pneumoniae. FEMS Microbiology Letters. 9987:1-5.
  79. Savopoulos JW, Hibbs M, Jones EJ, Mensah L, Richardson C, Fosberry A, Downes R, Fox SG, Brown JR, Jenkins O. 2001. Identification, cloning and expression of a functional phenylalanyltRNA synthetase (pheRS) from Staphylococcus aureus. Protein Expression and Purification. 21:470-484.
  80. Chalker AF, Minehart HW, Birks NJ, Koretke KK, Lonetto MA, Warren PV, Stanhope MJ, Lupas AN, Brinkmann K, Brown JR, Hoffman PS. 2001. Systematic identification of unique essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis. Bacteriol. 183:1259-1268.
  81. Robb FT, Maeder DL, Brown JR, Weiss RB, DiRuggiero J, Dunn DM, Yeh RK. 2001. The genomic sequence of the hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. pp. 134-157. In Adams, MWW, Kelly RM. Hyperthermophilic Enzymes Pt A. Methods in Enzymology. Academic Press.
  82. Chihade J, Brown JR, Schimmel P, Ribas de Pouplana L. Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. 2000. Proceedings of the National Academy of Sciences USA. 97:12153-12157.
  83. Koretke KK, Lupas AN, Warren PV, Rosenberg M, Brown JR*. 2000. Evolution of two component signal transduction. Biol. Evol. 17:1956-1970.
  84. Du W, Brown JR, Sylvester DR, Huang J, Chalker AF, So C-Y, Holmes DJ, Payne DJ, Wallis NG. 2000. Two active forms of UDP-N-acetylglucosamine enolpyruvyl transferase in Gram-positive bacteria. Bacteriology 182:4146-4152.
  85. Wilding EI, Brown JR, Bryant A, Chalker AF, Holmes D, Ingraham K, So CY, Iordanescu S, Rosenberg M, Gwynn MN. 2000. Identification, essentiality and evolution of the mevalonate pathway for isopentenyl diphosphate biosynthesis in Gram-positive cocci. Bacteriology 182:4319-4327.
  86. Throup JP, Koretke KK, Bryant AP, Ingraham K.A., Chalker AF, Ge Y, Marra A, Wallis NG, Brown JR, Holmes DJ, Rosenberg M, Burnham, MKR. 2000. A genomic analysis of two component signal transduction in Streptococcus pneumoniae. Molecular Microbiology 35:566-576.
  87. Brown JR*, Koretke KK. 2000. Universal trees: discovering the archaeal and bacterial legacies. pp. 19-55. In Priest FG, Goodfellow M. Applied Microbial Systematics. Chapman and Hall Publishers.
  88. Leroux MR, Fändrich M, Klunker D, Siegers K, Lupas AN, Brown JR, Schiebel E, Dobson CM, Hartl FU. 1999. MtGimC, a novel archaeal chaperone related to the eukaryotic chaperonin cofactor GimC/prefoldin. EMBO J. 18:6730-43.
  89. Brown JR*, Doolittle WF. 1999. Gene descent, duplication and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. Molecular Evolution 49:485-495.
  90. DiRuggiero J, Brown JR, Bogert AM, Robb FT. 1999. DNA repair systems in Archaea: mechanisms from the last universal common ancestor? J. Molecular Evolution 49:474-484.
  91. Brown JR*. 1999. Universal tree of life. In the Encyclopedia of Life Sciences. Nature Publishing Group, London, www.els.net.
  92. Brown JR*, Warren PV. 1998. Antibiotic discovery: Is it in the genes? Drug Discovery Today. 3:564-566.
  93. Brown JR*, Lupas AN. 1998. What makes a thermophile? Trends in Microbiology. 6:349-351.
  94. Brown JR*, Zhang J, Hodgson JE. 1998. A bacterial antibiotic resistance gene with eukaryotic origins. Current Biology. 8:R365-R367.
  95. Brown JR*. Aminoacyl-tRNA synthetases: Evolution of a troubled family. pp. 217-230. In Wiegel J, Adams M. Thermophiles – the keys to molecular evolution and the origin of life? Taylor and Francis Group.
  96. Brown JR*, Doolittle WF. 1997. Archaea and the prokaryote-eukaryote transition. Microbiology and Molecular Biology Reviews. 61:456-502.
  97. Brown JR*, Robb FT, Weiss R, Doolittle WF. 1997. Evidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases. Molecular Evolution. 45:9-16.
  98. Charlebois RL, Sensen CW, Doolittle WF, Brown JR*. 1997. Evolutionary analysis of the hisCGABdFDoDaEHI operon from the archaeon Sulfolobus solfataricus J. Bacteriology 179: 4429-4432.
  99. Bochar D, Brown JR, Doolittle WF, Klenk H-P, Lam W, Schenk M, Stauffacher CV, Rodwell VM. Cloning, sequencing, and expression in Escherichia coli of the biosynthetic HMGCoA reductase of Sulfolobus solfataricus. J. Bacteriology. 179:3632-3638.
  100. Crnogorac-Jurcevic T, Brown JR, Lehrach H, Schalkwyk L. 1997. Tetraodon fluviatilis, an additional puffer fish model for genome studies. Genomics. 41:177-184.
  101. Brown JR* Preparing for the flood: evolutionary biology in the age of genomics. Trends in Ecology and Evolution. 11:510-513.
  102. Roger A, Brown JR*. 1996. A chimeric origin for eukaryotes re-examined. Trends in Biochemical Sciences. 21:370-371.
  103. Brown JR*, Beckenbach K, Beckenbach AT, Smith MJ. 1996. Length variation, heteroplasmy and sequence divergence in the mitochondrial DNA of four species of sturgeon (Acipenser). Genetics 142:525-535.
  104. Brown JR*, Doolittle WF. 1995. Root of the universal tree of life based on ancient aminoacyltRNA synthetase gene duplications. Proceedings of the National Academy of Sciences USA. 92:2441-2445.
  105. Doolittle WF, Brown JR*. 1994. Tempo, mode, the progenote and the universal root. Proceedings of the National Academy of Sciences USA 91:6721-6728.
  106. Brown JR*, Masuchi Y, Robb FT,. Doolittle WF. 1994. Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. Molecular Evolution 38:566-576.
  107. Doolittle WF, Brown JR*. 1994. Tempo, mode, the progenote and the universal root. pp. 3-24. In Fitch WM and Ayala FJ. Tempo and Mode in Evolution. National Academy Press.
  108. Brown JR*, Beckenbach AT, Smith MJ. 1993. Intraspecific DNA sequence variation of the mitochondrial D-loop region of the white sturgeon (Acipenser transmontanus). Molecular Biology and Evolution 10:326-341.
  109. Brown JR*, Beckenbach AT, Smith MJ. 1992. Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus). Genetics 132:221228.
  110. Brown JR*, Beckenbach AT, Smith MJ. 1992. The effects of Pleistocene glaciations and human intervention upon mitochondrial DNA diversity in white sturgeon (Acipenser transmontanus) populations. Canadian Fisheries and Aquatic Sciences 49:358-367.
  111. Buroker NE, Brown JR*, Gilbert TL, O’Hara PJ, Beckenbach AT, Thomas WK, Smith MJ. 1990. Length heteroplasmy of sturgeon mtDNA: an illegitimate elongation model. Genetics 124:157163.
  112. Brown JR*, Gilbert TL, Kowbel DJ, O’Hara PJ, Buroker NE, Beckenbach AT, Smith MJ. 1989. Nucleotide sequence of the apocytochrome B gene in white sturgeon mitochondrial DNA. Nucleic Acids Res. 17:4389.
  113. Gilbert TL, Brown JR*, O’Hara PJ, Buroker NE, Beckenbach AT, Smith MJ. 1988. Sequence of tRNA(Thr) and tRNA(Pro) from white sturgeon (Acipenser transmontanus) mitochondria. Nucleic Acids Res. 16:11825.
  114. Roland WG, Brown JR*. 1990. A production model for suspended culture of the Pacific oyster, (Crassostrea gigas). Aquaculture 87:35-52.
  115. Brown JR*. Multivariate analyses of the role of environmental factors in seasonal and siterelated growth variation in the Pacific oyster, Crassostrea gigas. Marine Ecology Progress Series 45:225-236.
  116. Brown JR*, Hartwick EB. 1988. Influences of temperature, salinity and available food upon suspended culture of the Pacific oyster, Crassostrea gigas: I. Absolute and allometric growth. Aquaculture 70:231-251.
  117. Brown JR*, Hartwick EB. 1988. Influences of temperature, salinity and available food upon suspended culture of the Pacific oyster, Crassostrea gigas: II. Condition and survival. Aquaculture 70:253-267.
  118. Brown JR*, Hartwick EB. 1988. A habitat suitability index model for suspended tray culture of the Pacific oyster, Crassostrea gigas Thunberg. Aquaculture and Fisheries Management 19:107124.