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Fundamental and Computational Sciences Directorate

Staff information

Scott Baker

Science and Technology
Scientist, Team Lead
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-91
Richland, WA 99352

PNNL Publications


  • Pomraning KR, EL Bredeweg, and SE Baker. 2017. "Regulation of nitrogen metabolism by GATA zinc-finger transcription factors in Yarrowia lipolytica." mSphere 2(1):Article No. 00038-17.  doi:10.1128/mSphere.00038-17
  • Boenisch MJ, KL Broz, SO Purvine, WB Chrisler, CD Nicora, L Connolly, M Freitag, SE Baker, and HC Kistler. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7:Article No. 44296.  doi:10.1038/srep44296
  • Bredeweg EL, KR Pomraning, Z Dai, JB Nielsen, EJ Kerkhoven, and SE Baker. 2017. "A Molecular Genetic Toolbox for Yarrowia lipolytica." Biotechnology for Biofuels 10:Article No. 2.  doi:10.1186/s13068-016-0687-7
  • De Vries RP, R Riley, A Wiebenga, G Aguilar-Osorio, S Amillis, CA Uchima, G Anderluh, M Asadollahi, M Askin, KW Barry, E Battaglia, O Bayram, T Benocci, SA Braus-Stromeyer, C Caldana, D Canovas, GC Cerqueira, F Chen, W Chen, C Choi, A Clum, RA Correa Dos Santos, AR De Lima Damasio, G Diallinas, T Emri, E Fekete, M Flipphi, S Freyberg, A Gallo, C Gournas, R Habgood, M Hainaut, ML Harispe, B Henrissat, KS Hilden, R Hope, A Hossain, E Karabika, L Karaffa, Z Karanyi, N Krasevec, A Kuo, H Kusch, KM LaButti, EL Lagendijk, A Lapidus, A Levasseur, E Lindquist, A Lipzen, A Logrieco, A Maccabe, M Mäkelä, I Malavazi, P Melin, V Meyer, N Mielnichuk, M Miskei, AP Molnar, G Mule, CY Ngan, M Orejas, E Orosz, JP Ouedraogo, KM Overkamp, HS Park, G Perrone, F Piumi, PJ Punt, AF Ram, A Ramon, S Rauscher, E Record, DM Riaño-Pachón, V Robert, J Röhrig, R Ruller, A Salamov, NS Salih, RA Samson, E Sandor, M Sanguinetti, T Schutze, K Sepcic, E Shelest, G Sherlock, V Sophianopoulou, FM Squina, H Sun, A Susca, RB Todd, A Tsang, SE Unkles, N Van De Wiele, D Van Rossen-Uffink, J Velasco De Castro Oliveira, TC Vesth, J Visser, JH Yu, M Zhou, MR Andersen, DB Archer, SE Baker, I Benoit, AA Brakhage, G Braus, R Fischer, J Frisvad, GH Goldman, J Houbraken, BR Oakley, I Pocsi, C Scazzocchio, B Seiboth, PA vanKuyk, J Wortman, PS Dyer, and IV Grigoriev. 2017. "Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus." Genome Biology 18:Article No. 28.  doi:10.1186/s13059-017-1151-0
  • Geng T, CR Smallwood, EL Bredeweg, KR Pomraning, AE Plymale, SE Baker, JE Evans, and RT Kelly. 2017. "Multimodal Microfluidic Platform for Controlled Culture and Analysis of Unicellular Organisms." Biomicrofluidics 11(5):054104.  doi:10.1063/1.4986533
  • Geng T, CR Smallwood, Y Zhu, EL Bredeweg, SE Baker, JE Evans, and RT Kelly. 2017. "Multimodal Microchannel and Nanowell-Based Microfluidic Platforms for Bioimaging." In Proceedings of the 10th IEEE International Conference on Nano/Molecular Medicine and Engineering (NANOMED 2016), October 30- November 2, 2016, Macau, China, pp. 155-158.  IEEE, PISCATAWAY, NJ.  doi:10.1109/NANOMED.2016.7883480
  • Haitjema C, SP Gilmore, JK Henske, KV Solomon, RD Groot, A Kuo, SJ Mondo, A Salamov, KM LaButti, ZJ Zhao, J Chiniquy, KW Barry, HM Brewer, SO Purvine, AT Wright, M Hainaut, B Boxma, TA Van Alen, J Hackstein, B Henrissat, SE Baker, IV Grigoriev, and MA O'Malley. 2017. "A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics." Nature Microbiology 2:Article No. 17087.  doi:10.1038/nmicrobiol.2017.87
  • Ivanova C, J Ramoni, T Aouam, A Frischmann, B Seiboth, SE Baker, S Le Crom, S Lemoine, A Margeot, and F Bidard. 2017. "Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction." Biotechnology for Biofuels 10:Article No. 209.  doi:10.1186/s13068-017-0897-7
  • Kerkhoven EJ, YM Kim, S Wei, CD Nicora, TL Fillmore, SO Purvine, BJM Webb-Robertson, RD Smith, SE Baker, TO Metz, and JB Nielsen. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8(3):Article No. e00857-17.  doi:10.1128/mBio.00857-17
  • McCluskey K, and SE Baker. 2017. "Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era." Mycology 8(2):67-83.  doi:10.1080/21501203.2017.1281849


  • Pomraning KR, YM Kim, CD Nicora, RK Chu, EL Bredeweg, SO Purvine, D Hu, TO Metz, and SE Baker. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17(138):1-18.  doi:10.1186/s12864-016-2471-2
  • Goodwin S, CB McCorison, JR Cavaletto, DE Culley, KM LaButti, SE Baker, and IV Grigoriev. 2016. "The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete." Fungal Biology 120(8):961-974.  doi:10.1016/j.funbio.2016.05.003
  • Liu J, M Arentshorst, D Nair, Z Dai, SE Baker, J Frisvad, KF Nielsen, PJ Punt, and AF Ram. 2016. "Identification of a classical mutant in the industrial host Aspergillus niger by systems genetics: LaeA is required for citric acid production and regulates the formation of some secondary metabolites." G3 Genes, Genomes, Genetics 6(1):193-204.  doi:10.1534/g3.115.024067
  • Reilly MC, JM Magnuson, and SE Baker. 2016. "Approaches to understanding protein hypersecretion in fungi." Fungal Biology Reviews 30(4):145-151.  doi:10.1016/j.fbr.2016.06.002
  • Schmoll M, C Dattenbock, N Carreras-Villasenor, A Mendoza-Mendoza, D Tisch, MI Aleman, SE Baker, C Brown, MG Cervantes-Badillo, J Cetz-Chel, GR Cristobal-Mondragon, L Delaye, EU Esquivel-Naranjo, A Frischmann, JJ Gallardo-Negrete, M Garcia-Esquivel, EY Gomez-Rodriguez, DR Greenwood, M Hernndez-Oate, JS Kruszewska, R Lawry, HM Mora-Montes, T Muoz-Centeno, MF Nieto-Jacobo, G Nogueira Lopez, V Olmedo-Monfil, M Osorio-Concepcion, S Pilsyk, KR Pomraning, A Rodriguez-Iglesias, MT Rosales-Saavedra, JA Sanchez-Arreguin, V Seidl-Seiboth, A Stewart, EE Uresti-Rivera, CL Wang, TF Wang, S Zeilinger, S Casas-Flores, and A Herrera-Estrella. 2016. "The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species." Microbiology and Molecular Biology Reviews 80(1):205-327.  doi:10.1128/MMBR.00040-15


  • Baker SE, W Schackwitz, A Lipzen, JX Martin, S Haridas, KM LaButti, IV Grigoriev, BA Simmons, and K McCluskey. 2015. "Draft Genome Sequence of Neurospora crassa Strain FGSC 73." Genome Announcements 3(2):Article No. e00074-15.  doi:10.1128/genomeA.00074-15
  • Pomraning KR, and SE Baker. 2015. "Draft genome sequence of the dimorphic yeast Yarrowia lipolytica, strain W29." Genome Announcements 3(6):Article No. e01211-15.  doi:10.1128/genomeA.01211-15
  • Pomraning KR, S Wei, SA Karagiosis, YM Kim, A Dohnalkova, BW Arey, EL Bredeweg, G Orr, TO Metz, and SE Baker. 2015. "Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis." PLoS One 10(4):e0123188.  doi:10.1371/journal.pone.0123188
  • Emerson JM, BM Bartholomai, C Ringelberg, SE Baker, JJ Loros, and JC Dunlap. 2015. "period-1 encodes an ATP-dependent RNA helicase that in?uences nutritional compensation of the Neurospora circadian clock." Proceedings of the National Academy of Sciences of the United States of America 112(51):15707-15712.  doi:10.1073/pnas.1521918112
  • Geng T, EL Bredeweg, CJ Szymanski, B Liu, SE Baker, G Orr, JE Evans, and RT Kelly. 2015. "Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics." Scientific Reports 5:Article No. 16111.  doi:10.1038/srep16111
  • Lichius A, F Bidard, F Buchholz, S Le Crom, JX Martin, W Schackwitz, T Austerlitz, IV Grigoriev, SE Baker, A Margeot, B Seiboth, and CP Kubicek. 2015. "Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype." BMC Genomics 16(4):Article No. 326.  doi:10.1186/s12864-015-1526-0


  • Qu Y, J Feng, S Deng, L Cao, Q Zhang, R Zhao, Z Zhang, Y Jiang, EM Zink, SE Baker, MS Lipton, L Pasa-Tolic, JZ Hu, and S Wu. 2014. "Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection." Fungal Genetics and Biology : FG & B 72:207-215.  doi:10.1016/j.fgb.2014.08.001
  • Gallo A, BP Knox, KS Bruno, M Solfrizzo, SE Baker, and G Perrone. 2014. "Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius." International Journal of Food Microbiology 179:10-17.  doi:10.1016/j.ijfoodmicro.2014.03.013
  • Takeda I, K Tamano, N Yamane, T Ishii, A Miura, M Umemura, G Terai, SE Baker, H Koike, and M Machida. 2014. "Genome Sequence of the Mucoromycotina Fungus Umbelopsis isabellina, an Effective Producer of Lipids." Genome Announcements 2(1):e00071-14.  doi:10.1128/genomeA.00071-14


  • Baer DR, SE Baker, NM Washton, and BE Linggi. 2013. Status Report on the Development of Research CampaignsPNNL-22924, Pacific Northwest National Laboratory, Richland, WA. 
  • Kim JS, Z Dai, UK Aryal, RJ Moore, DG Camp, II, SE Baker, RD Smith, and W Qian. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85(14):6826-6832.  doi:10.1021/ac401000q
  • 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
  • Tamano K, KS Bruno, SA Karagiosis, DE Culley, S Deng, JR Collett, M Umemura, H Koike, SE Baker, and M Machida. 2013. "Increased Production of Fatty Acids and Triglycerides in Aspergillus oryzae by Enhancing Expressions of Fatty Acid Synthesis-Related Genes." Applied Microbiology and Biotechnology 97(1):269-281.  doi:10.1007/s00253-012-4193-y


  • Beckham GT, Z Dai, JF Mattews, M Momany, CM Payne, WS Adney, SE Baker, and ME Himmel. 2012. "Harnessing glycosylation to improve cellulase activity." Current Opinion in Biotechnology 23(3):338-345.  doi:10.1016/j.copbio.2011.11.030
  • Brown DW, RA Butchko, SE Baker, and RH Proctor. 2012. "Phylogenomic and functional domain analysis of polyketide synthases in Fusarium." Fungal Biology 116(2):318 - 331. 
  • Degenkolb T, RK Aghchehb, R Dieckmann, T Neuhof, SE Baker, IS Druzhinina, CP Kubicek, H Brückner, and H von Dohren. 2012. "The production of Multiple Small Peptaibol Families by Single 14-Module Peptide Synthetases in Trichoderma/Hypocrea." Chemistry and Biodiversity 9(3):499 - 535.  doi:10.1002/cbdv.201100212
  • Gallo A, KS Bruno, M Solfrizzo, G Perrone, G Mule, A Visconti, and SE Baker. 2012. "New insight into the ochratoxin A biosynthetic pathway through deletion of a nonribosomal peptide synthetase gene in Aspergillus carbonarius." Applied and Environmental Microbiology 78(23):8208-8218.  doi:10.1128/AEM.02508-12
  • Schuster A, KS Bruno, JR Collett, SE Baker, B Seiboth, CP Kubicek, and M Schmoll. 2012. "A versatile toolkit for high throughput functional genomics with Trichoderma reesei." Biotechnology for Biofuels 5(1):Article No. 1.  doi:10.1186/1754-6834-5-1
  • Wang L, UK Aryal, Z Dai, AC Mason, ME Monroe, Z Tian, J Zhou, D Su, KK Weitz, T Liu, DG Camp, II, RD Smith, SE Baker, and W Qian. 2012. "Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry." Journal of Proteome Research 11(1):143-56.  doi:10.1021/pr200916k


  • Baker SE, and EA Panisko. 2011. "Proteome Studies of Filamentous Fungi." Chapter 9 in Fungal Genomics: Methods and Protocols. Methods in Molecular Biology, vol. 722, ed. JR Xu and BHH Bluhm, pp. 133-139.  Springer, New York, NY. 
  • 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. 


  • Chiang YM, KM Meyer, M Praseuth , SE Baker, KS Bruno, and CC Wang. 2010. "Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-?-pyrone." Fungal Genetics and Biology : FG & B 48(4):430-437 .  doi:10.1016/j.fgb.2010.12.001
  • Ma LJ, HC van der Does, KA Borkovich, JJ Coleman, MJ Daboussi, A Di Pietro, M Dufresne, M Freitag, M Grabherr, B Henrissat, PM Houterman, S Kang, WB Shim, C Wolochuk, X Xie, JR Xu, J Antoniw, SE Baker, BH Bluhm, A Breakspear, DW Brown, RA Butchko, S Chapman, R Coulson, PM Coutinho, EG Danchin, A Diener, LR Gale, D Gardiner, S Goff, K Hammond-Kossack, K Hilburn, A Hua-Van, W Jonkers, K Kazan, CD Kodira, M Koehrsen, L Kumar, YH Lee, L Li, JM Manners, D Miranda-Saavedra, M Mukherjee, G Park, J Park, SY Park, RH Proctor, A Regev, MC Ruiz-Roldan, D Sain, S Sakthikumar, S Sykes, DC Schwartz, BG Turgeon, I Wapinski, O Yoder, S Young, Q Zeng, S Zhou, J Galagan, CA Cuomo, HC Kistler, and M Rep. 2010. "Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium." Nature 464:367-373.  doi:10.1038/nature08850
  • 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


  • Baker SE. 2009. "Selection to sequence: opportunities in fungal genomics." Environmental Microbiology 11(12):2955-2958. 
  • 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. 
  • 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
  • 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. 
  • Seidl V, L Song, E Lindquist, S Gruber, A Koptchinskiy, S Zeilinger, M Schmoll, P Martinez, J Sun, IV Grigoriev, A Herrera-Estrella, SE Baker, and CP Kubicek. 2009. "Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey." BMC Genomics 10(Article Number: 567):, doi:10.1186/1471-2164-10-567
  • Tsang A, GD Butler, J Powlowski, EA Panisko, and SE Baker. 2009. "Analytical and computational approaches to define the Aspergillus niger secretome." Fungal Genetics and Biology : FG & B 46(1, Suppl. 1):S153-S160.  doi:10.1016/j.fgb.2008.07.014


  • Baker SE, J Thykaer, WS Adney, T Brettin, FJ Brockman, P D'haeseleer, AD Martinez, RM Miller, DS Rokhsar, CW Schadt, T Torok, G Tuskan, JW Bennett, R Berka, S Briggs, J Heitman, J Taylor, BG Turgeon, M Werner-Washburne, and ME Himmel. 2008. "Fungal Genome Sequencing and Bioenergy." Fungal Biology Reviews 22:1-5. 
  • Daly DS, KK Anderson, EA Panisko, SO Purvine, R Fang, ME Monroe, and SE Baker. 2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7(3):1209-1217.  doi:10.1021/pr070441i
  • kubicek CP, SE Baker, C Gamauf, C Kenerley, and IS Druzhinina. 2008. "Purifying Selection and Birth-and-Death Evolution in the Class II Hydrophobin Gene Families of the Ascomycete Trichoderma/Hypocrea." BMC Evolutionary Biology 8(4):, doi:10.1186/1471-2148-8-4
  • 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. 


  • 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
  • Rinker TE, and SE Baker. 2007. "Deletion of a Chitin Synthase Gene in a Citric Acid Producing Strain of Aspergillus niger." Journal of Undergraduate Research 7:138-139. 
  • Rokas A, payne, ND Federova, SE Baker, M Machida, J yu, DR georgianna, RA Dean, D Bhatnagar, TE Cleveland, JR Wortman, R Maiti, V Joardar, P Amedeo, DW Denning, and WC Nierman. 2007. "What can comparative genomics tell us about species concepts in the genus Aspergillus? ." Studies in Mycology 59:11-17. 
  • Turgeon BG, and SE Baker. 2007. "Genetic and Genomic Dissection of the Cochliobolus heterostrophus Tox1 Locus Controlling Biosynthesis of the Polyketide Virulence Factor T-toxin ." In Fungal Genomics, Advances in Genetics, vol. 57, pp. 219-261.  Elsevier Academic Press, San Diego, CA. 


  • Baker SE, S Kroken, P Inderbitzin, T Asvarak, BY Li, L Shi, OC Yoder, and BG Turgeon. 2006. "Two Polyketide Synthase-encoding Genes are Required for Biosynthesis of the Polyketide Virulence Factor, T-toxin, by Cochliobolus heterostrophus ." Molecular Plant-Microbe Interactions, MPMI 19(2):139-49. 
  • Baker SE. 2006. "Aspergillus Niger Genomics: Past, Present and into the Future." In Presented at Advances Against Aspergillosis 2006. Published in Medical Mycology, vol. 44, no. Supplement 1, pp. S17-S21.  Taylor & Francis LTD, Abingdon, United Kingdom.  doi:10.1080/13693780600921037
  • Hixson KK, JN Adkins, SE Baker, RJ Moore, RD Smith, SL McCutchen-Maloney, and MS Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics ." Journal of Proteome Research 5(11):3008-3017. 


  • Annecharico MD, and SE Baker. 2005. "Utilizing the CreA Gene to Better Understand Carbon Flux in Fungi." Journal of Undergraduate Research V(2005):110. 
  • Lev S, R hadar, P Amedeo, SE Baker, O Yoder, and BA Horwitz. 2005. "Activation of an AP1-Like Transcription Factor of the Maize Pathogen Cochliobolus heterostrophus in Response to Oxidative Stress and Plant Signals ." Eukaryotic Cell 4(2):443-454. 

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