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    Bowen, Benjamin

    TitleBioinformaticist Research SE
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
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      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. Swenson TL, Karaoz U, Swenson JM, Bowen B, Northen TR. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. Nat Commun. 2018 01 02; 9(1):19. PMID: 29296020.
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      2. Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen B, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin AP, Zhou J. Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. MBio. 2017 Nov 14; 8(6). PMID: 29138306.
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      3. Lubbe A, Bowen B, Northen T. Exometabolomic Analysis of Cross-Feeding Metabolites. Metabolites. 2017 Oct 04; 7(4). PMID: 28976938.
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      4. Rubel O, Bowen B. BASTet: Shareable and reproducible analysis and visualization of mass spectrometry imaging data via OpenMSI. IEEE Trans Vis Comput Graph. 2017 Aug 29. PMID: 28866551.
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      5. Xie X, Sinha S, Yi Z, Langlais PR, Madan M, Bowen B, Willis W, Meyer C. Role of adipocyte mitochondria in inflammation, lipemia and insulin sensitivity in humans: effects of pioglitazone treatment. Int J Obes (Lond). 2017 Aug 14. PMID: 29087390.
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      6. Gao J, Louie KB, Steinke P, Bowen B, Raad M, Zuckermann RN, Siuzdak G, Northen TR. Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry. Anal Chem. 2017 Jun 20; 89(12):6521-6526. PMID: 28520405.
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      7. Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen B, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. Widespread adenine N6-methylation of active genes in fungi. Nat Genet. 2017 Jun; 49(6):964-968. PMID: 28481340.
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      8. Erbilgin O, Bowen B, Kosina SM, Jenkins S, Lau RK, Northen TR. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BMC Bioinformatics. 2017 Jan 23; 18(1):57. PMID: 28114881.
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      9. Baran R, Lau R, Bowen B, Diamond S, Jose N, Garcia-Pichel F, Northen TR. Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D2O) Stable Isotope Probing. ACS Chem Biol. 2017 Mar 17; 12(3):674-681. PMID: 28068058.
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      10. Shih PM, Vuu K, Mansoori N, Ayad L, Louie KB, Bowen B, Northen TR, Loqué D. A robust gene-stacking method utilizing yeast assembly for plant synthetic biology. Nat Commun. 2016 Oct 26; 7:13215. PMID: 27782150.
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      11. Xie X, Yi Z, Sinha S, Madan M, Bowen B, Langlais P, Ma D, Mandarino L, Meyer C. Proteomics analyses of subcutaneous adipocytes reveal novel abnormalities in human insulin resistance. Obesity (Silver Spring). 2016 Jul; 24(7):1506-14. PMID: 27345962; PMCID: PMC4926648 [Available on 07/01/17].
      12. Bouskill NJ, Wood TE, Baran R, Ye Z, Bowen B, Lim H, Zhou J, Nostrand JD, Nico P, Northen TR, Silver WL, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Front Microbiol. 2016; 7:525. PMID: 27148214; PMCID: PMC4837414.
      13. Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen B, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Front Microbiol. 2016; 7:323. PMID: 27014243; PMCID: PMC4791749.
      14. Gao J, de Raad M, Bowen B, Zuckermann RN, Northen TR. Application of Black Silicon for Nanostructure-Initiator Mass Spectrometry. Anal Chem. 2016 Feb 02; 88(3):1625-30. PMID: 26741735.
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      15. Deng K, Guenther JM, Gao J, Bowen B, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol. 2015; 3:153. PMID: 26528471; PMCID: PMC4603251.
      16. Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Da Rocha UN, Chakraborty R, Bowen B, Karaoz U, Cadillo-Quiroz H, Garcia-Pichel F, Northen TR. Exometabolite niche partitioning among sympatric soil bacteria. Nat Commun. 2015 Sep 22; 6:8289. PMID: 26392107; PMCID: PMC4595634.
      17. Fischer CR, Ruebel O, Bowen B. An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses. Arch Biochem Biophys. 2016 Jan 01; 589:18-26. PMID: 26365033.
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      18. Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, García-Cerdán JG, Pratap A, Wang M, Lim J, Tice H, Daum C, Xu J, Northen T, Visel A, Bristow J, Niyogi KK, Wei CL. Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nat Plants. 2015 Jul 27; 1:15107. PMID: 27250540.
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      19. Yao Y, Sun T, Wang T, Ruebel O, Northen T, Bowen B. Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases. Metabolites. 2015 Jul 20; 5(3):431-42. PMID: 26287255; PMCID: PMC4588804.
      20. McLean CS, Mielke C, Cordova JM, Langlais PR, Bowen B, Miranda D, Coletta DK, Mandarino LJ. Gene and MicroRNA Expression Responses to Exercise; Relationship with Insulin Sensitivity. PLoS One. 2015; 10(5):e0127089. PMID: 25984722; PMCID: PMC4436215.
      21. Dalisay DS, Kim KW, Lee C, Yang H, Rübel O, Bowen B, Davin LB, Lewis NG. Dirigent Protein-Mediated Lignan and Cyanogenic Glucoside Formation in Flax Seed: Integrated Omics and MALDI Mass Spectrometry Imaging. J Nat Prod. 2015 Jun 26; 78(6):1231-42. PMID: 25981198.
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      22. Miquel S, Leclerc M, Martin R, Chain F, Lenoir M, Raguideau S, Hudault S, Bridonneau C, Northen T, Bowen B, Bermúdez-Humarán LG, Sokol H, Thomas M, Langella P. Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii. MBio. 2015 Apr 21; 6(2). PMID: 25900655; PMCID: PMC4453580.
      23. Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen B, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Front Microbiol. 2015; 6:277. PMID: 25926821; PMCID: PMC4396413.
      24. Yang J, Rübel O, Mahoney MW, Bowen B. Identifying important ions and positions in mass spectrometry imaging data using CUR matrix decompositions. Anal Chem. 2015; 87(9):4658-66. PMID: 25825055.
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      25. Castellanos-Martín A, Castillo-Lluva S, Sáez-Freire Mdel M, Blanco-Gómez A, Hontecillas-Prieto L, Patino-Alonso C, Galindo-Villardon P, Pérez Del Villar L, Martín-Seisdedos C, Isidoro-Garcia M, Abad-Hernández MM, Cruz-Hernández JJ, Rodríguez-Sánchez CA, González-Sarmiento R, Alonso-López D, De Las Rivas J, García-Cenador B, García-Criado J, Lee DY, Bowen B, Reindl W, Northen T, Mao JH, Pérez-Losada J. Unraveling heterogeneous susceptibility and the evolution of breast cancer using a systems biology approach. Genome Biol. 2015 Feb 21; 16:40. PMID: 25853295; PMCID: PMC4389302.
      26. Wang Y, Kora G, Bowen B, Pan C. MIDAS: a database-searching algorithm for metabolite identification in metabolomics. Anal Chem. 2014 Oct 07; 86(19):9496-503. PMID: 25157598.
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      27. Heins RA, Cheng X, Nath S, Deng K, Bowen B, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 ß-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol. 2014 Sep 19; 9(9):2082-91. PMID: 24984213; PMCID: PMC4168791.
      28. Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal ß-glucosidase production. Front Microbiol. 2013; 4:365. PMID: 24367356; PMCID: PMC3854461.
      29. Louie KB, Bowen B, Cheng X, Berleman JE, Chakraborty R, Deutschbauer A, Arkin A, Northen TR. "Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. Anal Chem. 2013 Nov 19; 85(22):10856-62. PMID: 24111681.
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      30. Rübel O, Greiner A, Cholia S, Louie K, Bethel EW, Northen TR, Bowen B. OpenMSI: a high-performance web-based platform for mass spectrometry imaging. Anal Chem. 2013 Nov 05; 85(21):10354-61. PMID: 24087878.
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      31. Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen B, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J. 2013 Nov; 7(11):2178-91. PMID: 23739051; PMCID: PMC3806265.
      32. Fischer CR, Bowen B, 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. PMID: 23713674.
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      33. Ho JC, Storm P, Rydström A, Bowen B, Alsin F, Sullivan L, Ambite I, Mok KH, Northen T, Svanborg C. Lipids as tumoricidal components of human a-lactalbumin made lethal to tumor cells (HAMLET): unique and shared effects on signaling and death. J Biol Chem. 2013 Jun 14; 288(24):17460-71. PMID: 23629662; PMCID: PMC3682546.
      34. Mosier AC, Justice NB, Bowen B, 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 Mar 12; 4(2):e00484-12. PMID: 23481603; PMCID: PMC3604775.
      35. Wattacheril J, Seeley EH, Angel P, Chen H, Bowen B, Lanciault C, Caprioli RM, Abumrad N, Flynn CR. Differential intrahepatic phospholipid zonation in simple steatosis and nonalcoholic steatohepatitis. PLoS One. 2013; 8(2):e57165. PMID: 23451176; PMCID: PMC3581520.
      36. Louie KB, Bowen B, McAlhany S, Huang Y, Price JC, Mao JH, Hellerstein M, Northen TR. Mass spectrometry imaging for in situ kinetic histochemistry. Sci Rep. 2013; 3:1656. PMID: 23584513; PMCID: PMC3625901.
      37. Baran R, Bowen B, Price MN, Arkin AP, Deutschbauer AM, Northen TR. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chem Biol. 2013 Jan 18; 8(1):189-99. PMID: 23082955.
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      38. Lee DY, Bowen B, Nguyen DH, Parsa S, Huang Y, Mao JH, Northen TR. Low-dose ionizing radiation-induced blood plasma metabolic response in a diverse genetic mouse population. Radiat Res. 2012 Dec; 178(6):551-5. PMID: 23051006.
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      39. Lee DY, Platt V, Bowen B, Louie K, Canaria CA, McMurray CT, Northen T. Resolving brain regions using nanostructure initiator mass spectrometry imaging of phospholipids. Integr Biol (Camb). 2012 Jun; 4(6):693-9. PMID: 22543711; PMCID: PMC3698601.
      40. Greving M, Cheng X, Reindl W, Bowen B, Deng K, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, Northen T. Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Anal Bioanal Chem. 2012 May; 403(3):707-11. PMID: 22407334.
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      41. Tamboli RA, Hajri T, Jiang A, Marks-Shulman PA, Williams DB, Clements RH, Melvin W, Bowen B, Shyr Y, Abumrad NN, Flynn CR. Reduction in inflammatory gene expression in skeletal muscle from Roux-en-Y gastric bypass patients randomized to omentectomy. PLoS One. 2011; 6(12):e28577. PMID: 22194858; PMCID: PMC3241684.
      42. Baran R, Bowen B, Northen TR. Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002. Mol Biosyst. 2011 Dec; 7(12):3200-6. PMID: 21935552.
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      43. Ghosh S, Lertwattanarak R, Lefort N, Molina-Carrion M, Joya-Galeana J, Bowen B, Garduno-Garcia Jde J, Abdul-Ghani M, Richardson A, DeFronzo RA, Mandarino L, Van Remmen H, Musi N. Reduction in reactive oxygen species production by mitochondria from elderly subjects with normal and impaired glucose tolerance. Diabetes. 2011 Aug; 60(8):2051-60. PMID: 21677280; PMCID: PMC3142073.
      44. Bowen B, Fischer CR, Baran R, Banfield JF, Northen T. Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics. 2011 Jun 15; 12 Suppl 1:S6. PMID: 21810208; PMCID: PMC3223729.
      45. Storm P, Aits S, Puthia MK, Urbano A, Northen T, Powers S, Bowen B, Chao Y, Reindl W, Lee DY, Sullivan NL, Zhang J, Trulsson M, Yang H, Watson JD, Svanborg C. Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis. Oncogene. 2011 Dec 01; 30(48):4765-79. PMID: 21643007; PMCID: PMC4041205.
      46. Pan C, Fischer CR, Hyatt D, Bowen B, Hettich RL, Banfield JF. Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics. 2011 Apr; 10(4):M110.006049. PMID: 21285414; PMCID: PMC3069347.
      47. Reindl W, Bowen B, Balamotis MA, Green JE, Northen TR. Multivariate analysis of a 3D mass spectral image for examining tissue heterogeneity. Integr Biol (Camb). 2011 Apr; 3(4):460-7. PMID: 21212877; PMCID: PMC3495549.
      48. Wilmes P, Bowen B, Thomas BC, Mueller RS, Denef VJ, VerBerkmoes NC, Hettich RL, Northen TR, Banfield JF. Metabolome-proteome differentiation coupled to microbial divergence. MBio. 2010 Oct 26; 1(5). PMID: 20978538; PMCID: PMC2962434.
      49. Baran R, Bowen B, Bouskill NJ, Brodie EL, Yannone SM, Northen TR. Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assisted metabolite profiling. Anal Chem. 2010 Nov 01; 82(21):9034-42. PMID: 20945921.
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      50. Lopes LB, Brophy CM, Flynn CR, Yi Z, Bowen B, Smoke C, Seal B, Panitch A, Komalavilas P. A novel cell permeant peptide inhibitor of MAPKAP kinase II inhibits intimal hyperplasia in a human saphenous vein organ culture model. J Vasc Surg. 2010 Dec; 52(6):1596-607. PMID: 20864298; PMCID: PMC3005888.
      51. Xie X, Yi Z, Bowen B, Wolf C, Flynn CR, Sinha S, Mandarino LJ, Meyer C. Characterization of the Human Adipocyte Proteome and Reproducibility of Protein Abundance by One-Dimensional Gel Electrophoresis and HPLC-ESI-MS/MS. J Proteome Res. 2010 Sep 03; 9(9):4521-34. PMID: 20812759; PMCID: PMC2935302.
      52. Lefort N, Glancy B, Bowen B, Willis WT, Bailowitz Z, De Filippis EA, Brophy C, Meyer C, Højlund K, Yi Z, Mandarino LJ. Increased reactive oxygen species production and lower abundance of complex I subunits and carnitine palmitoyltransferase 1B protein despite normal mitochondrial respiration in insulin-resistant human skeletal muscle. Diabetes. 2010 Oct; 59(10):2444-52. PMID: 20682693; PMCID: PMC3279558.
      53. Lee DY, Bowen B, Northen TR. Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and imaging. Biotechniques. 2010 Aug; 49(2):557-65. PMID: 20701590; PMCID: PMC2967016.
      54. Bowen B, Northen TR. Dealing with the unknown: metabolomics and metabolite atlases. J Am Soc Mass Spectrom. 2010 Sep; 21(9):1471-6. PMID: 20452782.
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      55. Podolnikova NP, Yermolenko IS, Fuhrmann A, Lishko VK, Magonov S, Bowen B, Enderlein J, Podolnikov AV, Ros R, Ugarova TP. Control of integrin alphaIIb beta3 outside-in signaling and platelet adhesion by sensing the physical properties of fibrin(ogen) substrates. Biochemistry. 2010 Jan 12; 49(1):68-77. PMID: 19929007; PMCID: PMC4530791.
      56. Højlund K, Yi Z, Lefort N, Langlais P, Bowen B, Levin K, Beck-Nielsen H, Mandarino LJ. Human ATP synthase beta is phosphorylated at multiple sites and shows abnormal phosphorylation at specific sites in insulin-resistant muscle. Diabetologia. 2010 Mar; 53(3):541-51. PMID: 20012595.
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      57. Højlund K, Bowen B, Hwang H, Flynn CR, Madireddy L, Geetha T, Langlais P, Meyer C, Mandarino LJ, Yi Z. In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS. J Proteome Res. 2009 Nov; 8(11):4954-65. PMID: 19764811; PMCID: PMC2783959.
      58. Hwang H, Bowen B, Lefort N, Flynn CR, De Filippis EA, Roberts C, Smoke CC, Meyer C, Højlund K, Yi Z, Mandarino LJ. Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes. Diabetes. 2010 Jan; 59(1):33-42. PMID: 19833877; PMCID: PMC2797941.
      59. Lefort N, Yi Z, Bowen B, Glancy B, De Filippis EA, Mapes R, Hwang H, Flynn CR, Willis WT, Civitarese A, Højlund K, Mandarino LJ. Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS. J Proteomics. 2009 Aug 20; 72(6):1046-60. PMID: 19567276; PMCID: PMC2774790.
      60. Woo HK, Go EP, Hoang L, Trauger SA, Bowen B, Siuzdak G, Northen TR. Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom. 2009 Jun; 23(12):1849-55. PMID: 19449318; PMCID: PMC3052201.
      61. Yi Z, Bowen B, Hwang H, Jenkinson CP, Coletta DK, Lefort N, Bajaj M, Kashyap S, Berria R, De Filippis EA, Mandarino LJ. Global relationship between the proteome and transcriptome of human skeletal muscle. J Proteome Res. 2008 Aug; 7(8):3230-41. PMID: 18613714; PMCID: PMC2755516.
      62. Højlund K, Yi Z, Hwang H, Bowen B, Lefort N, Flynn CR, Langlais P, Weintraub ST, Mandarino LJ. Characterization of the human skeletal muscle proteome by one-dimensional gel electrophoresis and HPLC-ESI-MS/MS. Mol Cell Proteomics. 2008 Feb; 7(2):257-67. PMID: 17911086; PMCID: PMC3836591.
      63. Bowen B, Enderlein J, Woodbury NW. Single-molecule fluorescence spectroscopy of TOTO on poly-AT and poly-GC DNA. Photochem Photobiol. 2003 Dec; 78(6):576-81. PMID: 14743865.
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      64. Bowen B, Woodbury NW. TOTO binding affinity analysis using single-molecule fluorescence spectroscopy. Photochem Photobiol. 2003 Dec; 78(6):582-6. PMID: 14743866.
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      65. Montaño GA, Bowen B, LaBelle JT, Woodbury NW, Pizziconi VB, Blankenship RE. Characterization of Chlorobium tepidum chlorosomes: a calculation of bacteriochlorophyll c per chlorosome and oligomer modeling. Biophys J. 2003 Oct; 85(4):2560-5. PMID: 14507718; PMCID: PMC1303479.
      66. Bowen B, Woodbury N. Single-molecule fluorescence lifetime and anisotropy measurements of the red fluorescent protein, DsRed, in solution. Photochem Photobiol. 2003 Apr; 77(4):362-9. PMID: 12733647.
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      67. Franklin AE, McElver J, Sunjevaric I, Rothstein R, Bowen B, Cande WZ. Three-dimensional microscopy of the Rad51 recombination protein during meiotic prophase. Plant Cell. 1999 May; 11(5):809-24. PMID: 10330467; PMCID: PMC144225.
      68. Grotewold E, Chamberlin M, Snook M, Siame B, Butler L, Swenson J, Maddock S, St Clair G, Bowen B. Engineering secondary metabolism in maize cells by ectopic expression of transcription factors. Plant Cell. 1998 May; 10(5):721-40. PMID: 9596632; PMCID: PMC144024.

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