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Chemical and Biological Process Development

Jon Magnuson

Jon Magnuson

Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352


Jon Magnuson is a biochemist with more than 20 years of research experience studying enzymes and metabolic pathways in bacteria and fungi. Dr. Magnuson is currently part of a team utilizing filamentous fungi in the development of processes for converting renewable biomass to fuels, chemicals and enzymes. This research involves the discovery and manipulation of genes encoding the enzymes of biosynthetic pathways or the regulation of those pathways. Complementary to this work is his major interest in fungal genomics. He is involved in the annotation and analysis of many fungal genomes with particular focus on the enzymes involved in the breakdown of plant biomass into sugars. Another area of his research is developing tools to assess and understand the diversity of fungi and other eukaryotic microbes found in different natural environments. This research has culminated in the development of a microarray based on a highly variable region of the ribosomal RNA gene, which is useful for the study of the diverse fungi, diatoms and green algae found in soils, sediments and natural biofilms.

PNNL Patents

Education and Credentials

  • Ph.D., Biochemistry, University of Minnesota, 1993
  • B.S., Biochemistry, University of Minnesota, 1986

PNNL Publications


  • Dai Z, S Deng, DE Culley, KS Bruno, and JK Magnuson. 2017. "Agrobacterium tumefaciens-mediated transformation of oleaginous yeast Lipomyces species." Applied Microbiology and Biotechnology 101(15):6099-6110.  doi:10.1007/s00253-017-8357-7
  • Mondo SJ, RO Dannebaum, RC Kuo, KB Louie, AJ Bewick, KM LaButti, S Haridas, A Kuo, A Salamov, S Ahrendt, R Lau, BP Bowen, A Lipzen, W Sullivan, WB Andreopoulos, A Clum, E Lindquist, C Daum, TR Northen, GK Ramamoorthy, RJ Schmitz, A Gryganskyi, DE Culley, JK Magnuson, T James, MA O'Malley, JE Stajich, J Spatafora, A Visel, and IV Grigoriev. 2017. "Widespread Adenine N6-methylation of Active Genes in Fungi." Nature Genetics 49(6):964-968.  doi:10.1038/ng.3859
  • Unkefer CJ, RT Sayre, JK Magnuson, DB Anderson, I Baxter, IK Blaby, JK Brown, M Carleton, RA Cattolico, T Dale, TP Devarenne, CM Downes, SK Dutcher, DT Fox, UW Goodenough, J Jaworski, JE Holladay, DM Kramer, AT Koppisch, MS Lipton, BL Marrone, MM Mccormick, I Molnar, JB Mott, KL Ogden, EA Panisko, M Pellegrini, JE Polle, JW Richardson, M Sabarskyo, SR Starkenburg, GD Stormo, M Teshima, S Twary, PJ Unkefer, J Yuan, and JéA Olivares. 2017. "Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts." Algal Research 22:187-215.  doi:10.1016/j.algal.2016.06.002


  • Elliott DC, TR Hart, GG Neuenschwander, LJ Rotness, Jr, G Roesijadi, AH Zacher, and JK Magnuson. 2014. "Hydrothermal Processing of Macroalgal Feedstocks in Continuous-Flow Reactors ." ACS Sustainable Chemistry & Engineering 2(2):207-215.  doi:10.1021/sc400251p
  • Jambovane SR, SA Prost, AM Sheen, JK Magnuson, and RT Kelly. 2014. "ON-DEMAND SERIAL DILUTION USING QUANTIZED NANO/PICOLITER-SCALE DROPLETS." In Proceedings of the 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2014), October 26-30, 2014, San Antonio, Texas, pp. 1247-1249.  Chemical and Biological Microsystems Society, San Diego, CA. 


  • Meyer P, IJ Tews, JK Magnuson, SA Karagiosis, and SB Jones. 2013. "Techno-economic analysis of corn stover fungal fermentation to ethanol." Applied Energy 111:657-668.  doi:10.1016/j.apenergy.2013.04.085
  • Meyer PA, IJ Tews, JK Magnuson, SA Karagiosis, and SB Jones. 2013. "Techno-economic analysis of corn stover fungal fermentation to ethanol." Applied Energy 111:657-668.  doi:10.1016/j.apenergy.2013.04.085
  • Dai Z, UK Aryal, AK Shukla, W Qian, RD Smith, JK Magnuson, WS Adney, GT Beckham, R Brunecky, ME Himmel, SR Decker, X Ju, X Zhang, and SE Baker. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61:120-132.  doi:10.1016/j.fgb.2013.09.004
  • Simmons BA, and JK Magnuson. 2013. "A Conversation with Blake Simmons, Vice President, Deconstruction Division, and Jon Magnuson, Director, Fungal Biotechnology Group, Joint BioEnergy Institute, Emeryville, CA." Industrial Biotechnology 9(3):108-112.  doi:10.1089/ind.2013.1568


  • Andersen MR, M Salazar, P Schaap, P van de Vondervoort, DE Culley, J Thykaer, JC Frisvad, KF Nielsen, R Albang, K Albermann, R Berka, G Braus, SA Braus-Stromeyer, L Corrochano, Z Dai, P van Dijck, G Hofmann, LL Lasure, JK Magnuson, H Menke, M Meijer, S Meijer, JB Nielsen, ML Nielsen, A van Ooyen, HJ Pel, L Poulsen, R Samson, H Stam, A Tsang, JM van den Brink, A ATkins, A Aerts, H Shapiro, J Pangilinan, A Salamov, Y Lou, E Lindquist, S Lucas, J Grimwood, IV Grigoriev, CP Kubicek, D Martinez, N van Peij, JA Roubos, JB Nielsen, and SE Baker. 2011. "Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88." Genome Research 21(6):885-897.  doi:10.1101/gr.112169.110
  • Berka R, IV Grigoriev, RP Otillar, A Salamov, J Grimwood, I Reid, N Ishmael, john, C Darmond, MC Moisan, B Henrissat, PM Coutinho, V Lombard, DO Natvig, E Lindquist, J Schmutz, S Lucas, P Harris, J Powlowski, A Bellemare, D Taylor, G Butler, RP de Vries, IE Allijn, J van den Brink, S Ushinsky, R Storms, AJ Powell, IT Paulsen, LDH Elbourne, SE Baker, JK Magnuson, S LaBoissiere, D Martinez, M Wogulis, A Lopez de Leon, M Rey, and A Tsang. 2011. "Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and thielavia terrestris." Nature Biotechnology 29(10):922-927.  doi:10.1038/nbt.1976
  • de Vries RP, I Benoit, G Doehlemann, T Kobayashi, JK Magnuson, EA Panisko, SE Baker, and MH Lebrun. 2011. "Post-genomic approaches to understanding interactions between fungi and their environment." IMA Fungus 2(1):81-86.  doi:10.5598/imafungus.2011.02.01.12
  • Grigoriev IV, D Cullen, SX Goodwin, D Hibbett, TW Jeffries, CP Kubicek, CR Kuske, JK Magnuson, F Martin, JW Spatafora, A Tsang, and SE Baker. 2011. "Fueling the future with fungal genomics." Mycology 2(3):192-209. 
  • Ryu JS, S Shary, CJ Houtman, EA Panisko, P Korripally, FJ St John, C Crooks, M Siika-aho, JK Magnuson, and K Hammel. 2011. "Proteomic and Functional Analysis of the Cellulase System Expressed by Postia placenta during Brown Rot of Solid Wood." Applied and Environmental Microbiology 77(22):7933-7941.  doi:10.1128/AEM.05496-11
  • Zhang F, J Vierock, O Yizhar, LE Fenno, S Tsunoda, A Kianianmomeni, M Prigge, A Berndt, JC Cushman, JE Polle, JK Magnuson, P Hegemann, and K Deisseroth. 2011. "The Microbial Opsin Family of Optogenetic Tools." Cell 147(7):1446-1457.  doi:10.1016/j.cell.2011.12.004


  • Ohm RA, JF de Jong, LG Lugones, A Aerts, E Kothe, JE Stajich, RP de Vries, E Record, A Levasseur, SE Baker, KA Bartholomew, PM Coutinho, S Erdmann, TJ Fowler, AC Gathman, V Lombard, B Henrissat, N Knabe, U Kues, W Lilly, E Lindquist, S Lucas, JK Magnuson, F Piumi, M Raudaskoski, A Salamov, J Schmutz, FW Schwarze, PA vanKuyk, JS Horton, IV Grigoriev, and H Wosten. 2010. "Genome sequence of the model mushroom Schizophyllum commune." Nature Biotechnology 28(9):957-963.  doi:10.1038/nbt.1643
  • Smith DR, RW Lee, JC Cushman, JK Magnuson, D Tran, and JE Polle. 2010. "The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA." BMC Plant Biology 10:Article Number: 83 . 


  • Baker SE, KS Bruno, MG Butcher, JR Collett, DE Culley, Z Dai, JK Magnuson, and EA Panisko. 2009. PNNL Fungal Biotechnology Core DOE-OBP ProjectPNNL-18820, Pacific Northwest National Laboratory, Richland, WA. 
  • Jovanovic I, JK Magnuson, FR Collart, B Robbertse, WS Adney, ME Himmel, and SE Baker. 2009. "Fungal glycoside hydrolases for saccharification of lignocellulose: outlook for new discoveries fueled by genomics and functional studies." Cellulose 16(4):687-697. 
  • Miracle AL, VL Bailey, SE Baker, AL Bunn, JK Magnuson, and BJM Webb-Robertson. 2009. "Integration of 'omics technologies for characterization of complex microbial ecosystems - 8119." In Waste Management Symposium 2008, pp. 832-841.  WM Symposia, Tucson, AZ. 
  • Le Crom S, W Schackwitz, L Pennacchiod, JK Magnuson, DE Culley, JR Collett, JX Martin, IS Druzhinina, H Mathis, F Monot, B Seiboth, B Cherry, M Rey, R Berka, CP Kubicek, SE Baker, and A Margeot. 2009. "Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing." Proceedings of the National Academy of Sciences of the United States of America 106(38):16151-16156. 
  • Martinez D, J Challacombe, I Morgenstern, D Hibbett, M Schmoll, CP Kubicek, P Ferreira, F Ruiz-Duenas, AT Martinez, P Kersten, K Hammel, A Vanden Wymelenberg, J Gaskell, E Lindquist, G Sabat, S Splinter Bondurant, LF Larrondo, P Canessa, R Vicuna, J Yadev, H Doddapaneni, V Subramanian, A Pisabarro, JL Lavin, JA Oguiza, E Master, B Henrissat, PM Coutinho, P Harris, JK Magnuson, SE Baker, KS Bruno, W Kenealy, P Hoegger, U Kues, P Ramaiya, S Lucas, A Salamov, H Shapiro, H Tu, CL Chee, M Misra, G Xie, S Teter, D Yaver, T James, M Mokrejs, M Pospisek, IV Grigoriev, T Brettin, DS Rokhsar, R Berka, and D Cullen. 2009. "Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion." Proceedings of the National Academy of Sciences of the United States of America 106(6):1954-1959.  doi:10.1073/pnas.0809575106


  • Martinez AD, R Berka, B Henrissat, M Saloheimo, M Arvas, SE Baker, J Chapman, O Chertkov, PM Coutinho, D Cullen, EG Danchin, IV Grigoriev, P Harris, M? Jackson, CP kubicek, CF Han, I Ho, LF Larrando, A Lopez de Leon, JK Magnuson, S Merino, M Misra, B Nelson, N Putnam, B Robbertse, A Salamov, M Schmoll, A? Terry, N Thayer, A Westerholm-Parvinen, CL Schoch, J? Yao, R Barbote, MA Nelson, CJ Detter, D Bruce, C Kuske, G Xie, PM Richardson, DS Rokhsar, S Lucas, EM Rubin, N Dunn-Coleman, M? Ward, and T Brettin. 2008. "Genome Sequencing and Analysis of the Biomass-Degrading Fungus Trichoderma reesei (syn. Hypocrea jecorina) ." Nature Biotechnology 26(5):553-560. 
  • Shary S, AN Kapich, EA Panisko, JK Magnuson, D Cullen, and K Hammel. 2008. "Differential Expression in Phanerochaete chrysosporium of Membrane-Associated Proteins Relevant to Lignin Degradation." Applied and Environmental Microbiology 74(23):7252-7257.  doi:10.1128/AEM.01997-08


  • Baker SE, CF Wend, AD Martinez, JK Magnuson, EA Panisko, Z Dai, KS Bruno, KK Anderson, ME Monroe, DS Daly, and LL Lasure. 2007. "Genome and Proteome Analysis of Industrial Fungi." Chapter 1 in Exploitation of Fungi, ed. GD Robson, P van West and G Gadd, pp. 3-9.  Cambridge University Press, New York, NY.  doi:10.1017/CBO9780511902451.002
  • Cuomo CA, U Guldener, JR Xu, F Trail, BG Turgeon, A Di Pietro, JD Walton, LJ Ma, SE Baker, M Rep, G Adam, J Antoniw, T Baldwin, S Calvo, YL Chang, D DeCaprio, LR Gale, S Gnerre, RS Goswami, K Hammond-Kossack, LJ Harris, K Hilburn, JC Kennell, S Kroken, JK Magnuson, G Mannhaupt, E Mauceli, HW Mewes, R Mitterbauer, G Muehlbauer, M Munsterkotter, D Nelson, K O'Donnell, T Ouellet, W Qi, H Quesneville, MI Roncero, KY Seong, IV Tetko, M Urban, C Waalwijk, TJ Ward, J Yao, BW Birren, and HC Kistler. 2007. "The Fusarium Graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization." Science 317(5843):1400-1402.  doi:10.1126/science.1143708


  • Elliott DC, JK Magnuson, and CF Wend. 2006. Feed Processing and Handling DL2 Final Report PNNL-16079, Pacific Northwest National Laboratory, Richland, WA. 
  • Lei C, Y Shin, JK Magnuson, GE Fryxell, LL Lasure, DC Elliott, J Liu, and EJ Ackerman. 2006. "Characterization of Functionalized Nanoporous Supports for Protein Confinement ." Nanotechnology 17(22):5531-5538.  doi:10.1088/0957-4484/17/22/001


  • Magnuson JK, and LL Lasure. 2004. "Organic Acid Production by Filamentous Fungi." Chapter 12 in ADVANCES IN FUNGAL BIOTECHNOLOGY FOR INDUSTRY, AGRICULTURE, AND MEDICINE, ed. Jan S. Tkacz and Lene Lange, pp. 307-340.  Kluwer Academic/Plenum Publishers, New York, NY. 
  • Dai Z, X Mao, JK Magnuson, and LL Lasure. 2004. "Identification of Genes Associated with Morphology in Aspergillus Niger by Using Suppression Subtractive Hybridization ." Applied and Environmental Microbiology 70(4):2474-2485. 
  • Syn CK, JK Magnuson, MT Kingsley, and S Swarup. 2004. "Characterization of Pseudomonas putida Genes Responsive to Nutrient Limitation." Microbiology 150:1661-69 pt.6. 



  • de Henestrosa AR, J Cune, I Erill, JK Magnuson, and J Barbe. 2002. "A Green Nonsulfur Bacterium, Dehalococcoides ethenogenes, with the LexA-binding sequence found in Gram-positive organisms." Journal of Bacteriology 184(21):6073-6080. 


  • Magnuson JK, MF Romine, DR Burris, and MT Kingsley. 2000. "Trichloroethene Reductive Dehalogenase from Dehalococcoides ethenogenes: Sequence of tceA and Substrate Range Characterization." Applied and Environmental Microbiology 66:5141-5147. 

Chemical and Biological Process Development

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