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    Brian Palenik

    SchoolUniversity of California, San Diego
    DepartmentCenter for Marine Biotechnology and Biomedecine
    Address9500 Gilman Drive #0202
    CA La Jolla 92093
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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. Paerl RW, Bouget FY, Lozano JC, Vergé V, Schatt P, Allen EE, Palenik B, Azam F. Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. 2017 Mar; 11(3):753-765. PMID: 27935586.
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      2. Ma Y, Allen LZ, Palenik B. Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environ Microbiol Rep. 2014 Dec; 6(6):583-94. PMID: 25756111.
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      3. Dupont CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Venter JC, Allen AE. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 2015 May; 9(5):1076-92. PMID: 25333462; PMCID: PMC4410273.
      4. Palenik B. Molecular mechanisms by which marine phytoplankton respond to their dynamic chemical environment. Ann Rev Mar Sci. 2015; 7:325-40. PMID: 25195866.
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      5. Taton A, Unglaub F, Wright NE, Zeng WY, Paz-Yepes J, Brahamsha B, Palenik B, Peterson TC, Haerizadeh F, Golden SS, Golden JW. Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. Nucleic Acids Res. 2014; 42(17):e136. PMID: 25074377; PMCID: PMC4176158.
      6. Foflonker F, Price DC, Qiu H, Palenik B, Wang S, Bhattacharya D. Genome of the halotolerant green alga Picochlorum sp. reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiol. 2015 Feb; 17(2):412-26. PMID: 24965277.
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      7. Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AG, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014 Jun; 12(6):e1001889. PMID: 24959919; PMCID: PMC4068987.
      8. Wang S, Lambert W, Giang S, Goericke R, Palenik B. Microalgal assemblages in a poikilohaline pond. J Phycol. 2014 Apr; 50(2):303-9. PMID: 26988187.
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      9. Tetu SG, Johnson DA, Varkey D, Phillippy K, Stuart RK, Dupont CL, Hassan KA, Palenik B, Paulsen IT. Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Front Microbiol. 2013; 4:232. PMID: 23966990; PMCID: PMC3744912.
      10. Paz-Yepes J, Brahamsha B, Palenik B. Role of a microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus. Proc Natl Acad Sci U S A. 2013 Jul 16; 110(29):12030-5. PMID: 23818639; PMCID: PMC3718166.
      11. Prather KA, Bertram TH, Grassian VH, Deane GB, Stokes MD, Demott PJ, Aluwihare LI, Palenik B, Azam F, Seinfeld JH, Moffet RC, Molina MJ, Cappa CD, Geiger FM, Roberts GC, Russell LM, Ault AP, Baltrusaitis J, Collins DB, Corrigan CE, Cuadra-Rodriguez LA, Ebben CJ, Forestieri SD, Guasco TL, Hersey SP, Kim MJ, Lambert WF, Modini RL, Mui W, Pedler BE, Ruppel MJ, Ryder OS, Schoepp NG, Sullivan RC, Zhao D. Bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol. Proc Natl Acad Sci U S A. 2013 May 07; 110(19):7550-5. PMID: 23620519; PMCID: PMC3651460.
      12. Stuart RK, Brahamsha B, Busby K, Palenik B. Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress. ISME J. 2013 Jun; 7(6):1139-49. PMID: 23344240; PMCID: PMC3660668.
      13. Dupont CL, Johnson DA, Phillippy K, Paulsen IT, Brahamsha B, Palenik B. Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102. Appl Environ Microbiol. 2012 Nov; 78(22):7822-32. PMID: 22904052; PMCID: PMC3485950.
      14. Ma Y, Paulsen IT, Palenik B. Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environ Microbiol. 2012 Feb; 14(2):453-66. PMID: 22059529.
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      15. Tai V, Poon AF, Paulsen IT, Palenik B. Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. PLoS One. 2011; 6(9):e24249. PMID: 21931665; PMCID: PMC3170327.
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      17. Apple JK, Strom SL, Palenik B, Brahamsha B. Variability in protist grazing and growth on different marine Synechococcus isolates. Appl Environ Microbiol. 2011 May; 77(9):3074-84. PMID: 21398485; PMCID: PMC3126417.
      18. Rynearson TA, Palenik B. Learning to read the oceans genomics of marine phytoplankton. Adv Mar Biol. 2011; 60:1-39. PMID: 21962749.
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      19. Mao X, Olman V, Stuart R, Paulsen IT, Palenik B, Xu Y. Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. BMC Genomics. 2010 May 10; 11:291. PMID: 20459751; PMCID: PMC2874817.
      20. Ostrowski M, Mazard S, Tetu SG, Phillippy K, Johnson A, Palenik B, Paulsen IT, Scanlan DJ. PtrA is required for coordinate regulation of gene expression during phosphate stress in a marine Synechococcus. ISME J. 2010 Jul; 4(7):908-21. PMID: 20376102.
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      21. Mayali X, Palenik B, Burton RS. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environ Microbiol. 2010 Apr; 12(4):975-89. PMID: 20105218.
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      22. Tai V, Paulsen IT, Phillippy K, Johnson DA, Palenik B. Whole-genome microarray analyses of Synechococcus-Vibrio interactions. Environ Microbiol. 2009 Oct; 11(10):2698-709. PMID: 19659554.
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      23. Snyder DS, Brahamsha B, Azadi P, Palenik B. Structure of compositionally simple lipopolysaccharide from marine synechococcus. J Bacteriol. 2009 Sep; 191(17):5499-509. PMID: 19581366; PMCID: PMC2725629.
      24. Stuart RK, Dupont CL, Johnson DA, Paulsen IT, Palenik B. Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains. Appl Environ Microbiol. 2009 Aug; 75(15):5047-57. PMID: 19502430; PMCID: PMC2725496.
      25. Thomas EV, Phillippy KH, Brahamsha B, Haaland DM, Timlin JA, Elbourne LD, Palenik B, Paulsen IT. Statistical analysis of microarray data with replicated spots: a case study with synechococcus WH8102. Comp Funct Genomics. 2009; 950171. PMID: 19404483; PMCID: PMC2673484.
      26. Tai V, Palenik B. Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site. ISME J. 2009 Aug; 3(8):903-15. PMID: 19360028.
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      27. Tetu SG, Brahamsha B, Johnson DA, Tai V, Phillippy K, Palenik B, Paulsen IT. Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp. WH8102. ISME J. 2009 Jul; 3(7):835-49. PMID: 19340084.
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      28. Palenik B, Ren Q, Tai V, Paulsen IT. Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ Microbiol. 2009 Feb; 11(2):349-59. PMID: 19196269.
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      29. Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik B, Paulsen IT, de Marsac NT, Wincker P, Dossat C, Ferriera S, Johnson J, Post AF, Hess WR, Partensky F. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 2008; 9(5):R90. PMID: 18507822; PMCID: PMC2441476.
      30. Dupont CL, Neupane K, Shearer J, Palenik B. Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases. Environ Microbiol. 2008 Jul; 10(7):1831-43. PMID: 18412551.
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      31. Davis AK, Palenik B. Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonana. Protist. 2008 Apr; 159(2):195-207. PMID: 18162437.
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      32. Dupont CL, Barbeau K, Palenik B. Ni uptake and limitation in marine Synechococcus strains. Appl Environ Microbiol. 2008 Jan; 74(1):23-31. PMID: 17951444; PMCID: PMC2223220.
      33. Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A. 2007 May 01; 104(18):7705-10. PMID: 17460045; PMCID: PMC1863510.
      34. Dupont CL, Yang S, Palenik B, Bourne PE. Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17822-7. PMID: 17098870; PMCID: PMC1635651.
      35. Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci U S A. 2006 Sep 05; 103(36):13555-9. PMID: 16938853; PMCID: PMC1569201.
      36. Davis AK, Hildebrand M, Palenik B. Gene expression induced by copper stress in the diatom Thalassiosira pseudonana. Eukaryot Cell. 2006 Jul; 5(7):1157-68. PMID: 16835459; PMCID: PMC1489294.
      37. Su Z, Mao F, Dam P, Wu H, Olman V, Paulsen IT, Palenik B, Xu Y. Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res. 2006; 34(3):1050-65. PMID: 16473855; PMCID: PMC1363776.
      38. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 2004 Oct 01; 306(5693):79-86. PMID: 15459382.
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      39. Chen X, Su Z, Dam P, Palenik B, Xu Y, Jiang T. Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. Nucleic Acids Res. 2004; 32(7):2147-57. PMID: 15096577; PMCID: PMC407844.
      40. Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. The genome of a motile marine Synechococcus. Nature. 2003 Aug 28; 424(6952):1037-42. PMID: 12917641.
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      41. Su Z, Dam P, Chen X, Olman V, Jiang T, Palenik B, Xu Y. Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102. Genome Inform. 2003; 14:3-13. PMID: 15706515.
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      42. Palenik B. The genomics of symbiosis: hosts keep the baby and the bath water. Proc Natl Acad Sci U S A. 2002 Sep 17; 99(19):11996-7. PMID: 12221298; PMCID: PMC129385.
      43. Heffelfinger GS, Martino A, Gorin A, Xu Y, Rintoul MD, Geist A, Al-Hashimi HM, Davidson GS, Faulon JL, Frink LJ, Haaland DM, Hart WE, Jakobsson E, Lane T, Li M, Locascio P, Olken F, Olman V, Palenik B, Plimpton SJ, Roe DC, Samatova NF, Shah M, Shoshoni A, Strauss CE, Thomas EV, Timlin JA, Xu D. Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling. OMICS. 2002; 6(4):305-30. PMID: 12626091.
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      44. Palenik B. Chromatic adaptation in marine Synechococcus strains. Appl Environ Microbiol. 2001 Feb; 67(2):991-4. PMID: 11157276; PMCID: PMC92680.
      45. Toledo G, Palenik B, Brahamsha B. Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group. Appl Environ Microbiol. 1999 Dec; 65(12):5247-51. PMID: 10583972; PMCID: PMC91712.
      46. Collier JL, Brahamsha B, Palenik B. The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amidohydrolase, EC to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme. Microbiology. 1999 Feb; 145 ( Pt 2):447-59. PMID: 10075427.
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      47. Toledo G, Palenik B. Synechococcus diversity in the California current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains. Appl Environ Microbiol. 1997 Nov; 63(11):4298-303. PMID: 9361417; PMCID: PMC168750.
      48. Palenik B, Koke JA. Characterization of a nitrogen-regulated protein identified by cell surface biotinylation of a marine phytoplankton. Appl Environ Microbiol. 1995 Sep; 61(9):3311-5. PMID: 16535120.
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      49. Palenik B. Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis. Appl Environ Microbiol. 1994 Sep; 60(9):3212-9. PMID: 7944363; PMCID: PMC201791.
      50. Pantoja S, Lee C, Marecek JF, Palenik B. Synthesis and use of fluorescent molecular probes for measuring cell-surface enzymatic oxidation of amino acids and amines in seawater. Anal Biochem. 1993 Jun; 211(2):210-8. PMID: 8317696.
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      51. Palenik B. Polymerase evolution and organism evolution. Curr Opin Genet Dev. 1992 Dec; 2(6):931-6. PMID: 1477538.
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      52. Palenik B, Haselkorn R. Multiple evolutionary origins of prochlorophytes, the chlorophyll b-containing prokaryotes. Nature. 1992 Jan 16; 355(6357):265-7. PMID: 1731224.
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      53. Palenik B, Morel FM. Amine oxidases of marine phytoplankton. Appl Environ Microbiol. 1991 Aug; 57(8):2440-3. PMID: 16348545.
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      54. Palenik B, Price NM, Morel FM. Potential effects of UV-B on the chemical environment of marine organisms: a review. Environ Pollut. 1991; 70(2):117-30. PMID: 15092139.
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