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    Auer, Manfred

    TitleBiophysicist Staff Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ 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. Belsom A, Mudd G, Giese SH, Auer M, Rappsilber J. A complimentary benzophenone cross-linking/mass spectrometry photochemistry. Anal Chem. 2017 Apr 21. PMID: 28430416.
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      2. Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci. 2017; 12:23. PMID: 28194258.
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      3. Kim KH, Brown RC, Daugaard T, Tivol WF, Auer M, Simmons B, Singh S. Strategy for extending the stability of bio-oil derived phenolic oligomer via mild hydrotreatment with ionic liquid stabilized nanoparticles. ChemSusChem. 2016 Dec 19. PMID: 27992678.
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      4. Shamir ER, Coutinho K, Georgess D, Auer M, Ewald AJ. Twist1-positive epithelial cells retain adhesive and proliferative capacity throughout dissemination. Biol Open. 2016 Sep 15; 5(9):1216-28. PMID: 27402962.
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      5. Jorgens DM, Inman JL, Wojcik M, Robertson C, Palsdottir H, Tsai WT, Huang H, Bruni-Cardoso A, López CS, Bissell MJ, Xu K, Auer M. Deep nuclear invaginations are linked to cytoskeletal filaments - integrated bioimaging of epithelial cells in 3D culture. J Cell Sci. 2017 Jan 01; 130(1):177-189. PMID: 27505896.
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      6. Mori H, Bhat R, Bruni-Cardoso A, Chen EI, Jorgens DM, Coutinho K, Louie K, Bowen BB, Inman JL, Tecca V, Lee SJ, Becker-Weimann S, Northen T, Seiki M, Borowsky AD, Auer M, Bissell MJ. New insight into the role of MMP14 in metabolic balance. PeerJ. 2016; 4:e2142. PMID: 27478693; PMCID: PMC4950575.
      7. Berleman JE, Zemla M, Remis JP, Liu H, Davis AE, Worth AN, West Z, Zhang A, Park H, Bosneaga E, van Leer B, Tsai W, Zusman DR, Auer M. Exopolysaccharide microchannels direct bacterial motility and organize multicellular behavior. ISME J. 2016 Nov; 10(11):2620-2632. PMID: 27152937.
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      8. Bhattacharya P, Barnebey A, Zemla M, Goodwin L, Auer M, Yannone SM. Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33. Stand Genomic Sci. 2015; 10:74. PMID: 26445627; PMCID: PMC4595116.
      9. Sun L, Singh S, Joo M, Vega-Sanchez M, Ronald P, Simmons BA, Adams P, Auer M. Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnol Bioeng. 2016 Jan; 113(1):82-90. PMID: 26137889.
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      10. Yamashita T, Hakizimana P, Wu S, Hassan A, Jacob S, Temirov J, Fang J, Mellado-Lagarde M, Gursky R, Horner L, Leibiger B, Leijon S, Centonze VE, Berggren PO, Frase S, Auer M, Brownell WE, Fridberger A, Zuo J. Outer Hair Cell Lateral Wall Structure Constrains the Mobility of Plasma Membrane Proteins. PLoS Genet. 2015 Sep; 11(9):e1005500. PMID: 26352669; PMCID: PMC4564264.
      11. Koos B, Cane G, Grannas K, Löf L, Arngården L, Heldin J, Clausson CM, Klaesson A, Hirvonen MK, de Oliveira FM, Talibov VO, Pham NT, Auer M, Danielson UH, Haybaeck J, Kamali-Moghaddam M, Söderberg O. Proximity-dependent initiation of hybridization chain reaction. Nat Commun. 2015 Jun 12; 6:7294. PMID: 26065580; PMCID: PMC4490387.
      12. Gregoire P, Engelbrektson A, Hubbard CG, Metlagel Z, Csencsits R, Auer M, Conrad ME, Thieme J, Northrup P, Coates JD. Control of sulfidogenesis through bio-oxidation of H2S coupled to (per)chlorate reduction. Environ Microbiol Rep. 2014 Dec; 6(6):558-64. PMID: 25756108.
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      13. Sarkar P, Bosneaga E, Yap EG, Das J, Tsai WT, Cabal A, Neuhaus E, Maji D, Kumar S, Joo M, Yakovlev S, Csencsits R, Yu Z, Bajaj C, Downing KH, Auer M. Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ. PLoS One. 2014; 9(9):e106928. PMID: 25207917; PMCID: PMC4160213.
      14. Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A, Cunha J, Hadi MZ, Zusman DR, Northen TR, Witkowska HE, Auer M. The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front Microbiol. 2014; 5:474. PMID: 25250022; PMCID: PMC4158809.
      15. Tsai WT, Hassan A, Sarkar P, Correa J, Metlagel Z, Jorgens DM, Auer M. From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data. J Vis Exp. 2014 Aug 13; (90):e51673. PMID: 25145678; PMCID: PMC4448944.
      16. Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ, Hess M. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Front Microbiol. 2014; 5:307. PMID: 25101058; PMCID: PMC4106096.
      17. Dougherty MJ, Tran HM, Stavila V, Knierim B, George A, Auer M, Adams PD, Hadi MZ. Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size. PLoS One. 2014; 9(6):e100836. PMID: 24971883; PMCID: PMC4074075.
      18. Schaudinn C, Stoodley P, Hall-Stoodley L, Gorur A, Remis J, Wu S, Auer M, Hertwig S, Guerrero-Given D, Hu FZ, Ehrlich GD, Costerton JW, Robinson DH, Webster P. Death and transfiguration in static Staphylococcus epidermidis cultures. PLoS One. 2014; 9(6):e100002. PMID: 24964210; PMCID: PMC4070908.
      19. Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson JJ, Auer M, Wall JD, Mukhopadhyay A. Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. Front Microbiol. 2014; 5:77. PMID: 24639670; PMCID: PMC3944678.
      20. Shamir ER, Pappalardo E, Jorgens DM, Coutinho K, Tsai WT, Aziz K, Auer M, Tran PT, Bader JS, Ewald AJ. Twist1-induced dissemination preserves epithelial identity and requires E-cadherin. J Cell Biol. 2014 Mar 03; 204(5):839-56. PMID: 24590176; PMCID: PMC3941052.
      21. Antonellis PJ, Pollock LM, Chou SW, Hassan A, Geng R, Chen X, Fuchs E, Alagramam KN, Auer M, McDermott BM. ACF7 is a hair-bundle antecedent, positioned to integrate cuticular plate actin and somatic tubulin. J Neurosci. 2014 Jan 01; 34(1):305-12. PMID: 24381291; PMCID: PMC3866489.
      22. Oh JW, Chung WJ, Heo K, Jin HE, Lee BY, Wang E, Zueger C, Wong W, Meyer J, Kim C, Lee SY, Kim WG, Zemla M, Auer M, Hexemer A, Lee SW. Biomimetic virus-based colourimetric sensors. Nat Commun. 2014; 5:3043. PMID: 24448217.
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      23. Remis JP, Wei D, Gorur A, Zemla M, Haraga J, Allen S, Witkowska HE, Costerton JW, Berleman JE, Auer M. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environ Microbiol. 2014 Feb; 16(2):598-610. PMID: 23848955; PMCID: PMC4234120.
      24. Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol. 2013 Sep; 15(9):2573-87. PMID: 23763762.
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      25. Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams PD, Scheller HV, Ronald PC. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci. 2013; 4:83. PMID: 23596448; PMCID: PMC3622038.
      26. Neng L, Zhang W, Hassan A, Zemla M, Kachelmeier A, Fridberger A, Auer M, Shi X. Isolation and culture of endothelial cells, pericytes and perivascular resident macrophage-like melanocytes from the young mouse ear. Nat Protoc. 2013 Apr; 8(4):709-20. PMID: 23493068; PMCID: PMC3740596.
      27. Varanasi P, Singh P, Auer M, Adams PD, Simmons BA, Singh S. Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels. 2013 Jan 28; 6(1):14. PMID: 23356589; PMCID: PMC3579681.
      28. Shin JB, Krey JF, Hassan A, Metlagel Z, Tauscher AN, Pagana JM, Sherman NE, Jeffery ED, Spinelli KJ, Zhao H, Wilmarth PA, Choi D, David LL, Auer M, Barr-Gillespie PG. Molecular architecture of the chick vestibular hair bundle. Nat Neurosci. 2013 Mar; 16(3):365-74. PMID: 23334578; PMCID: PMC3581746.
      29. Berleman J, Auer M. The role of bacterial outer membrane vesicles for intra- and interspecies delivery. Environ Microbiol. 2013 Feb; 15(2):347-54. PMID: 23227894.
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      30. Petersen PD, Lau J, Ebert B, Yang F, Verhertbruggen Y, Kim JS, Varanasi P, Suttangkakul A, Auer M, Loqué D, Scheller HV. Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants. Biotechnol Biofuels. 2012 Nov 26; 5(1):84. PMID: 23181474; PMCID: PMC3537538.
      31. Chen X, Vega-Sánchez ME, Verhertbruggen Y, Chiniquy D, Canlas PE, Fagerström A, Prak L, Christensen U, Oikawa A, Chern M, Zuo S, Lin F, Auer M, Willats WG, Bartley L, Harholt J, Scheller HV, Ronald PC. Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification. Mol Plant. 2013 Mar; 6(2):570-3. PMID: 23180670.
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      32. Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tang K, Auer M, Scheller HV, Loqué D. Engineering secondary cell wall deposition in plants. Plant Biotechnol J. 2013 Apr; 11(3):325-35. PMID: 23140549; PMCID: PMC3644865.
      33. Loss LA, Bebis G, Chang H, Auer M, Sarkar P, Parvin B. Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography. ACM BCB. 2012 Oct; 2012:170-177. PMID: 28090597.
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      34. Varanasi P, Singh P, Arora R, Adams PD, Auer M, Simmons BA, Singh S. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour Technol. 2012 Dec; 126:156-61. PMID: 23073103.
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      35. Zhang W, Dai M, Fridberger A, Hassan A, Degagne J, Neng L, Zhang F, He W, Ren T, Trune D, Auer M, Shi X. Perivascular-resident macrophage-like melanocytes in the inner ear are essential for the integrity of the intrastrial fluid-blood barrier. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):10388-93. PMID: 22689949; PMCID: PMC3387119.
      36. Baelum J, Borglin S, Chakraborty R, Fortney JL, Lamendella R, Mason OU, Auer M, Zemla M, Bill M, Conrad ME, Malfatti SA, Tringe SG, Holman HY, Hazen TC, Jansson JK. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol. 2012 Sep; 14(9):2405-16. PMID: 22616650.
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      37. Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, Heazlewood JL. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol. 2012 May; 159(1):12-26. PMID: 22430844; PMCID: PMC3375956.
      38. Vega-Sánchez ME, Verhertbruggen Y, Christensen U, Chen X, Sharma V, Varanasi P, Jobling SA, Talbot M, White RG, Joo M, Singh S, Auer M, Scheller HV, Ronald PC. Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice. Plant Physiol. 2012 May; 159(1):56-69. PMID: 22388489; PMCID: PMC3375985.
      39. Ewald AJ, Huebner RJ, Palsdottir H, Lee JK, Perez MJ, Jorgens DM, Tauscher AN, Cheung KJ, Werb Z, Auer M. Mammary collective cell migration involves transient loss of epithelial features and individual cell migration within the epithelium. J Cell Sci. 2012 Jun 01; 125(Pt 11):2638-54. PMID: 22344263; PMCID: PMC3403234.
      40. Carlson HK, Iavarone AT, Gorur A, Yeo BS, Tran R, Melnyk RA, Mathies RA, Auer M, Coates JD. Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria. Proc Natl Acad Sci U S A. 2012 Jan 31; 109(5):1702-7. PMID: 22307634; PMCID: PMC3277152.
      41. Chhabra SR, Butland G, Elias DA, Chandonia JM, Fok OY, Juba TR, Gorur A, Allen S, Leung CM, Keller KL, Reveco S, Zane GM, Semkiw E, Prathapam R, Gold B, Singer M, Ouellet M, Szakal ED, Jorgens D, Price MN, Witkowska HE, Beller HR, Arkin AP, Hazen TC, Biggin MD, Auer M, Wall JD, Keasling JD. Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Appl Environ Microbiol. 2011 Nov; 77(21):7595-604. PMID: 21908633; PMCID: PMC3209177.
      42. 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. PMID: 23757227; PMCID: PMC4444221.
      43. Yin L, Verhertbruggen Y, Oikawa A, Manisseri C, Knierim B, Prak L, Jensen JK, Knox JP, Auer M, Willats WG, Scheller HV. The cooperative activities of CSLD2, CSLD3, and CSLD5 are required for normal Arabidopsis development. Mol Plant. 2011 Nov; 4(6):1024-37. PMID: 21471331.
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      44. Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons BA, Adams PD, Singh AK. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresour Technol. 2011 Jan; 102(2):1329-37. PMID: 20884206.
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      45. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 2010 Oct 08; 330(6001):204-8. PMID: 20736401.
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      46. Remis JP, Costerton JW, Auer M. Biofilms: structures that may facilitate cell-cell interactions. ISME J. 2010 Sep; 4(9):1085-7. PMID: 20631806.
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      47. Li C, Knierim B, Manisseri C, Arora R, Scheller HV, Auer M, Vogel KP, Simmons BA, Singh S. Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification. Bioresour Technol. 2010 Jul; 101(13):4900-6. PMID: 19945861.
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      48. Sarkar P, Bosneaga E, Auer M. Plant cell walls throughout evolution: towards a molecular understanding of their design principles. J Exp Bot. 2009; 60(13):3615-35. PMID: 19687127.
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      49. DeBolt S, Scheible WR, Schrick K, Auer M, Beisson F, Bischoff V, Bouvier-Navé P, Carroll A, Hematy K, Li Y, Milne J, Nair M, Schaller H, Zemla M, Somerville C. Mutations in UDP-Glucose:sterol glucosyltransferase in Arabidopsis cause transparent testa phenotype and suberization defect in seeds. Plant Physiol. 2009 Sep; 151(1):78-87. PMID: 19641030; PMCID: PMC2735980.
      50. Palsdottir H, Remis JP, Schaudinn C, O'Toole E, Lux R, Shi W, McDonald KL, Costerton JW, Auer M. Three-dimensional macromolecular organization of cryofixed Myxococcus xanthus biofilms as revealed by electron microscopic tomography. J Bacteriol. 2009 Apr; 191(7):2077-82. PMID: 19168614; PMCID: PMC2655519.
      51. Shawkey MD, Saranathan V, Pálsdóttir H, Crum J, Ellisman MH, Auer M, Prum RO. Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure. J R Soc Interface. 2009 Apr 06; 6 Suppl 2:S213-20. PMID: 19158016; PMCID: PMC2706473.
      52. 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. PMID: 18843299.
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      53. Triffo WJ, Palsdottir H, McDonald KL, Lee JK, Inman JL, Bissell MJ, Raphael RM, Auer M. Controlled microaspiration for high-pressure freezing: a new method for ultrastructural preservation of fragile and sparse tissues for TEM and electron tomography. J Microsc. 2008 May; 230(Pt 2):278-87. PMID: 18445158; PMCID: PMC2734140.
      54. Auer M, Koster AJ, Ziese U, Bajaj C, Volkmann N, Wang da N, Hudspeth AJ. Three-dimensional architecture of hair-bundle linkages revealed by electron-microscopic tomography. J Assoc Res Otolaryngol. 2008 Jun; 9(2):215-24. PMID: 18421501; PMCID: PMC2504599.
      55. Downing KH, Sui H, Auer M. Electron tomography: a 3D view of the subcellular world. Anal Chem. 2007 Nov 01; 79(21):7949-57. PMID: 18044021.
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      56. Persson S, Paredez A, Carroll A, Palsdottir H, Doblin M, Poindexter P, Khitrov N, Auer M, Somerville CR. Genetic evidence for three unique components in primary cell-wall cellulose synthase complexes in Arabidopsis. Proc Natl Acad Sci U S A. 2007 Sep 25; 104(39):15566-71. PMID: 17878302; PMCID: PMC2000526.
      57. Schaber JA, Triffo WJ, Suh SJ, Oliver JW, Hastert MC, Griswold JA, Auer M, Hamood AN, Rumbaugh KP. Pseudomonas aeruginosa forms biofilms in acute infection independent of cell-to-cell signaling. Infect Immun. 2007 Aug; 75(8):3715-21. PMID: 17562773; PMCID: PMC1952004.
      58. McDonald KL, Auer M. High-pressure freezing, cellular tomography, and structural cell biology. Biotechniques. 2006 Aug; 41(2):137, 139, 141 passim. PMID: 16925014.
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      59. Bajaj C, Yu Z, Auer M. Volumetric feature extraction and visualization of tomographic molecular imaging. J Struct Biol. 2003 Oct-Nov; 144(1-2):132-43. PMID: 14643216.
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