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Fundamental and Computational Sciences Directorate

Staff information

Scott Baker

Environmntl Molecular Sci Div
Research Line Manager
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-91
Richland, WA 99352

PNNL Publications


  • Bredeweg E.L., K. Mccluskey, and S.E. Baker. 2022. "Phenotype to genotype in Neurospora crassa: Association of the scumbo phenotype with mutations in the gene encoding ceramide C9-methyltransferase." Current Research in Microbial Sciences 3, no. 2022:Art. No. 100117. PNNL-SA-170486. doi:10.1016/j.crmicr.2022.100117
  • Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and T.L. Lemmon, et al. 2022. "Itaconic acid production is regulated by laeA in Aspergillus pseudoterreus." Metabolic Engineering Communications 15. PNNL-SA-171876. doi:10.1016/j.mec.2022.e00203
  • Tamano K., H. Takayama, S. Yasokawa, M. Sano, and S.E. Baker. 2022. "Major involvement of two laccase genes in conidial pigment biosynthesis in Aspergillus oryzae." Applied Microbiology and Biotechnology 106, no. 1:287-300. PNNL-SA-168546. doi:10.1007/s00253-021-11669-1


  • Chroumpi T., M. Peng, L. Markillie, H.D. Mitchell, C.D. Nicora, C.M. Hutchinson, and V.L. Paurus, et al. 2021. "Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-158642. doi:10.3389/fbioe.2021.644216
  • Ferrara M., A. Gallo, A. Gallo, C. Cervini, L. Gambacorta, M. Solfrizzo, and S.E. Baker, et al. 2021. "Evidence of the Involvement of a Cyclase Gene in the Biosynthesis of Ochratoxin A in Aspergillus carbonarius." Toxins 13, no. 12:Art. No. 892. PNNL-SA-169400. doi:10.3390/toxins13120892
  • Gabriel R., N. Thieme, Q. Liu, F. Li, L.T. Kohler, S. Harth, and M. Jecmencia, et al. 2021. "The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi." Proceedings of the National Academy of Sciences (PNAS) 118, no. 26:Article No. e2025689118. PNNL-SA-163826. doi:10.1073/pnas.2025689118
  • Kim J., S.T. Coradetti, Y. Kim, Y. Gao, J. Yaegashi, J.D. Zucker, and N. Munoz Munoz, et al. 2021. "Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156767. doi:10.3389/fbioe.2020.612832
  • Kim Y., C.J. Petzold, E.J. Kerkhoven, and S.E. Baker. 2021. "Editorial: Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-168498. doi:10.3389/fbioe.2021.818010
  • Ottum E., S.E. Baker, and E.L. Bredeweg. 2021. "Production of Biofuels from Biomass by Fungi." In Encyclopedia of Mycology, edited by O. Zaragoza and A. Casadevall. 555-576. Amsterdam:Elsevier. PNNL-SA-156639. doi:10.1016/B978-0-12-819990-9.00062-7
  • Pomraning K.R., Z. Dai, N. Munoz Munoz, Y. Kim, Y. Gao, S. Deng, and J. Kim, et al. 2021. "Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus." Frontiers in Bioengineering and Biotechnology 9. PNNL-SA-149911. doi:10.3389/fbioe.2021.603832
  • Subedi N.R., P.S. Jung, E.L. Bredeweg, S.H. Nemati, S.E. Baker, D.N. Christodoulides, and A.E. Vasdekis. 2021. "Fusing Quantitative-Phase Imaging with Airy Light- Sheet Microscopy." In Quantitative Phase Imaging VII, March 6-12, 2021. Online. Proceedings of the SPIE, edited by Y. Liu, G. Popescu and Y.K. Park, 11653, Paper No. 116530I. Bellingham, Washington:SPIE. PNNL-SA-160791. doi:10.1117/12.2583926


  • Bredeweg E.L., and S.E. Baker. 2020. "Horizontal gene transfer in Fungi." In Grand Challenges in Fungal Biotechnology, edited by H Nevalainen. 317-332. Cham:Springer International Publishing. PNNL-SA-143450. doi:10.1007/978-3-030-29541-7
  • Daly P., M. Peng, H.D. Mitchell, Y. Kim, C.K. Ansong, H.M. Brewer, and P. De Gijsel, et al. 2020. "Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation." Environmental Microbiology 22, no. 3:1154-1166. PNNL-SA-150305. doi:10.1111/1462-2920.14907
  • Deng S., Z. Dai, M.S. Swita, K.R. Pomraning, B.A. Hofstad, E.A. Panisko, and S.E. Baker, et al. 2020. "Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359." Applied Microbiology and Biotechnology 104, no. 9:3981-3992. PNNL-SA-144713. doi:10.1007/s00253-020-10418-0
  • Ferrara M., A. Gallo, A. Gallo, G. Perrone, G. Perrone, D. Magista, and S.E. Baker. 2020. "Comparative genomic analysis of ochratoxin A biosynthetic cluster in producing fungi: new evidence of a cyclase gene involvement." Frontiers in Microbiology 11. PNNL-SA-158575. doi:10.3389/fmicb.2020.581309
  • Gao Y., T.L. Fillmore, N. Munoz Munoz, G. Bentley, C.W. Johnson, J. Kim, and J. Meadows, et al. 2020. "High-throughput large-scale targeted proteomics assays for quantifying pathway proteins in Pseudomonas putida KT2440." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156111. doi:10.3389/fbioe.2020.603488
  • Haridas S., R. Albert, M. Binder, J. Bloem, K.M. LaButti, A. Salamov, and W.B. Andreopoulos, et al. 2020. "101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens." Studies in Mycology 96. PNNL-SA-150863. doi:10.1016/j.simyco.2020.01.003
  • Kjaerbolling I., T.C. Vesth, J. Frisvad, J. Nybo, S. Theobald, S. Kildgaard, and T.I. Petersen, et al. 2020. "A comparative genomics study of 23 Aspergillus species from section Flavi." Nature Communications 11, no. 1:Article No. 1106. PNNL-SA-146998. doi:10.1038/s41467-019-14051-y
  • Subedi N.R., P.S. Jung, E.L. Bredeweg, S.H. Nemati, S.E. Baker, D.N. Christodoulides, and A.E. Vasdekis. 2020. "Integrative Quantitative-Phase and Airy Light-Sheet Imaging." Scientific Reports 10, no. 1:Article No. 20150. PNNL-SA-153507. doi:10.1038/s41598-020-76730-x


  • Hackstein J., S.E. Baker, J. Van Hellemond, J. Van Hellemond, and A. Tielens. 2019. "Hydrogenosomes of Anaerobic Fungi: an Alternative Way to Adapt to Anaerobic Environments." In Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes, Second Edition. Microbiology Monographs, edited by J Tachezy. 159-175. Cham:Springer. PNNL-SA-146888. doi:10.1007/978-3-030-17941-0_7
  • Leynaud- Kieffer L.M., S.C. Curran, I. Kim, J.K. Magnuson, J.M. Gladden, S.E. Baker, and B.A. Simmons. 2019. "A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable." PLoS One 14, no. 1:Article No. e0210243. PNNL-SA-142504. doi:10.1371/journal.pone.0210243


  • Baker S.E. 2018. "Protein hyperproduction in fungi by design." Applied Microbiology and Biotechnology 102, no. 20:8621-8628. PNNL-SA-137094. doi:10.1007/s00253-018-9265-1
  • Cannon W.R., J.D. Zucker, D.J. Baxter, N. Kumar, S.E. Baker, J. Hurley, and J.C. Dunlap. 2018. "Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa." Processes 6, no. 6:Article No. 63. PNNL-SA-134563. doi:10.3390/pr6060063
  • Daly P., S.C. Lopez, M. Peng, C.S. Lancefield, S.O. Purvine, Y. Kim, and E.M. Zink, et al. 2018. "Dichomitus squalens partially tailors its molecular responses to the composition of solid wood." Environmental Microbiology 20, no. 11:4141-4156. PNNL-SA-135900. doi:10.1111/1462-2920.14416
  • Emri T., K. Antal, R. Riley, Z. Karanyi, M. Miskei, E. Orosz, and S.E. Baker, et al. 2018. "Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance." Studies in Mycology 91. PNNL-SA-139027. doi:10.1016/j.simyco.2018.10.003
  • Hurley J.M., M.S. Jankowski, H. De Los Santos, A.M. Crowell, S. Fordyce, J.D. Zucker, and N. Kumar, et al. 2018. "Circadian proteomic analysis uncovers mechanisms of post-transcriptional regulation in metabolic pathways." Cell Systems 7, no. 6:613-626. PNNL-SA-138421. doi:10.1016/j.cels.2018.10.014
  • Khosravi C., E. Battaglia, R.S. Kun, S. Dalhuijsen, J. Visser, M.V. Aguilar-Pontes, and M. Zhou, et al. 2018. "Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans." BMC Genomics 19, no. 1:Article No. 214. PNNL-SA-132841. doi:10.1186/s12864-018-4609-x
  • Kjaerbolling I., T.C. Vesth, J.C. Frisvad, J. Nybo, S. Theobald, A. Kuo, and A. Kuo, et al. 2018. "Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species." Proceedings of the National Academy of Sciences (PNAS) 115, no. 4:E753-E761. PNNL-SA-131168. doi:10.1073/pnas.1715954115
  • Pomraning K.R., E.L. Bredeweg, E.J. Kerkhoven, K.W. Barry, S. Haridas, H. Hundley, and K.M. LaButti, et al. 2018. "Regulation of yeast-to-hyphae transition in Yarrowia lipolytica." mSphere 3, no. 6:Article No. e00541-18. PNNL-SA-131456. doi:10.1128/mSphere.00541-18
  • Reilly M.C., J. Kim, J.J. Lynn, B.A. Simmons, J.M. Gladden, J.K. Magnuson, and S.E. Baker. 2018. "Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger." Applied Microbiology and Biotechnology 102, no. 4:1797-1807. PNNL-SA-132880. doi:10.1007/s00253-017-8717-3
  • Reilly M.C., S.A. Campen, B.A. Simmons, S.E. Baker, J.M. Gladden, and J.K. Magnuson. 2018. "Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger." In Cellulases: Methods and Protocols. Methods in Molecular Biology, edited by M Lubeck. 123-133. New York, New York:Humana Press. PNNL-SA-135995. doi:10.1007/978-1-4939-7877-9_10
  • Vesth T.C., J. Nybo, S. Theobald, J. Frisvad, T.O. Larsen, K.F. Nielsen, and J.B. Hoof, et al. 2018. "Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri." Nature Genetics 50, no. 12:1688-1695. PNNL-SA-133567. doi:10.1038/s41588-018-0246-1


  • Boenisch M.J., K.L. Broz, S.O. Purvine, W.B. Chrisler, C.D. Nicora, L. Connolly, and M. Freitag, et al. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7. PNNL-SA-125650. doi:10.1038/srep44296
  • Bredeweg E.L., K.R. Pomraning, Z. Dai, J.B. Nielsen, E.J. Kerkhoven, and S.E. Baker. 2017. "A Molecular Genetic Toolbox for Yarrowia lipolytica." Biotechnology for Biofuels 10. PNNL-SA-118953. doi:10.1186/s13068-016-0687-7
  • Brown D.W., and S.E. Baker. 2017. "Mycotoxins: A Fungal Genomics Perspective." In Mycotoxigenic Fungi. Methods in Molecular Biology, edited by A Moretti and A Susca. 367-379. New York, New York:Humana Press. PNNL-SA-129681. doi:10.1007/978-1-4939-6707-0_24
  • Campen S.A., J.J. Lynn, S. Sibert, S. Srikrishnan, P.A. Phatale, T. Feldman, and J. Guenther, et al. 2017. "Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger." PLoS One 12, no. 12:Article No. e0189604. PNNL-SA-132873. doi:10.1371/journal.pone.0189604
  • Cannon W.R., and S.E. Baker. 2017. "Non-Steady State Mass Action Dynamics Without Rate Constants: Dynamics of Coupled Reactions using Chemical Potentials." Physical Biology 14, no. 5:Article No. 055003. PNNL-SA-114146. doi:10.1088/1478-3975/aa7d80
  • De Vries R.P., R. Riley, A. Wiebenga, G. Aguilar-Osorio, S. Amillis, C. Uchima, and G. Anderluh, et al. 2017. "Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus." Genome Biology 18. PNNL-SA-124113. doi:10.1186/s13059-017-1151-0
  • Geng T., C.R. Smallwood, E.L. Bredeweg, K.R. Pomraning, A.E. Plymale, S.E. Baker, and J.E. Evans, et al. 2017. "Multimodal Microfluidic Platform for Controlled Culture and Analysis of Unicellular Organisms." Biomicrofluidics 11, no. 5:054104. PNNL-SA-129125. doi:10.1063/1.4986533
  • Geng T., C.R. Smallwood, Y. Zhu, E.L. Bredeweg, S.E. Baker, J.E. Evans, and R.T. 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, 155-158. Piscataway, New Jersey:IEEE. PNNL-SA-124699. doi:10.1109/NANOMED.2016.7883480
  • Haitjema C., S.P. Gilmore, J.K. Henske, K.V. Solomon, R.D. Groot, A. Kuo, and S.J. Mondo, et al. 2017. "A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics." Nature Microbiology 2. PNNL-SA-120227. doi:10.1038/nmicrobiol.2017.87
  • Ivanova C., J. Ramoni, T. Aouam, A. Frischmann, B. Seiboth, S.E. Baker, and S. Le Crom, et al. 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. PNNL-SA-129680. doi:10.1186/s13068-017-0897-7
  • Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
  • Kowalczyk J.E., C. Khosravi, S.O. Purvine, A. Dohnalkova, W.B. Chrisler, G. Orr, and E.W. Robinson, et al. 2017. "High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger." Environmental Microbiology 19, no. 11:4587-4598. PNNL-SA-134692. doi:10.1111/1462-2920.13923
  • McCluskey K., and S.E. Baker. 2017. "Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era." Mycology 8, no. 2:67-83. PNNL-SA-129553. doi:10.1080/21501203.2017.1281849
  • Pomraning K.R., E.L. Bredeweg, and S.E. Baker. 2017. "Regulation of nitrogen metabolism by GATA zinc-finger transcription factors in Yarrowia lipolytica." mSphere 2, no. 1:Article No. 00038-17. PNNL-SA-122638. doi:10.1128/mSphere.00038-17
  • Tisch D., K.R. Pomraning, J.R. Collett, M. Freitag, S.E. Baker, C. Chen, and P.W. Hsu, et al. 2017. "Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels." Applied and Environmental Microbiology 83, no. 22:e01578-17. PNNL-SA-129552. doi:10.1128/AEM.01578-17


  • Corrochano L., A. Kuo, M. Marcet-Houben, S. Polaino, A. Salamov, J.M. Villalobos-Escobedo, and J. Grimwood, et al. 2016. "Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication." Current Biology 26, no. 12:1577-1584. PNNL-SA-118345. doi:10.1016/j.cub.2016.04.038
  • Goodwin S., C.B. McCorison, J.R. Cavaletto, D.E. Culley, K.M. LaButti, S.E. Baker, and I.V. Grigoriev. 2016. "The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete." Fungal Biology 120, no. 8:961-974. PNNL-SA-118347. doi:10.1016/j.funbio.2016.05.003
  • Kerkhoven E., K.R. Pomraning, S.E. Baker, and J.B. Nielsen. 2016. "Regulation of amino acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica." npj Systems Biology and Applications 2. PNNL-SA-111282. doi:10.1038/npjsba.2016.5
  • Niu J., M. Arentshorst, D. Nair, Z. Dai, S.E. Baker, J. Frisvad, and K.F. Nielsen, et al. 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, no. 1:193-204. PNNL-SA-114553. doi:10.1534/g3.115.024067
  • Pomraning K.R., Y. Kim, C.D. Nicora, R.K. Chu, E.L. Bredeweg, S.O. Purvine, and D. Hu, et al. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17, no. 138:1-18. PNNL-SA-112784. doi:10.1186/s12864-016-2471-2
  • Reilly M.C., J.M. Magnuson, and S.E. Baker. 2016. "Approaches to understanding protein hypersecretion in fungi." Fungal Biology Reviews 30, no. 4:145-151. PNNL-SA-123941. doi:10.1016/j.fbr.2016.06.002
  • Schmoll M., C. Dattenbock, N. Carreras-Villasenor, A. Mendoza-Mendoza, D. Tisch, M.I. Aleman, and S.E. Baker, et al. 2016. "The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species." Microbiology and Molecular Biology Reviews 80, no. 1:205-327. PNNL-SA-118679. doi:10.1128/MMBR.00040-15


  • Baker S.E., W. Schackwitz, A. Lipzen, J.X. Martin, S. Haridas, K.M. LaButti, and I.V. Grigoriev, et al. 2015. "Draft Genome Sequence of Neurospora crassa Strain FGSC 73." Genome Announcements 3, no. 2:Article No. e00074-15. PNNL-SA-108092. doi:10.1128/genomeA.00074-15
  • Emerson J.M., B.M. Bartholomai, C. Ringelberg, S.E. Baker, J.J. Loros, and J.C. Dunlap. 2015. "period-1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of the Neurospora circadian clock." Proceedings of the National Academy of Sciences (PNAS) 112, no. 51:15707-15712. PNNL-SA-114898. doi:10.1073/pnas.1521918112
  • Geng T., E.L. Bredeweg, C.J. Szymanski, B. Liu, S.E. Baker, G. Orr, and J.E. Evans, et al. 2015. "Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics." Scientific Reports 5. PNNL-SA-109268. doi:10.1038/srep16111
  • Lichius A., F. Bidard, F. Buchholz, S. Le Crom, J.X. Martin, W. Schackwitz, and T. Austerlitz, et al. 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, no. 4:Article No. 326. PNNL-SA-110701. doi:10.1186/s12864-015-1526-0
  • Pomraning K.R., and S.E. Baker. 2015. "Draft genome sequence of the dimorphic yeast Yarrowia lipolytica, strain W29." Genome Announcements 3, no. 6:Article No. e01211-15. PNNL-SA-112964. doi:10.1128/genomeA.01211-15
  • Pomraning K.R., S. Wei, S.A. Karagiosis, Y. Kim, A. Dohnalkova, B.W. Arey, and E.L. Bredeweg, et al. 2015. "Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis." PLoS One 10, no. 4:e0123188. PNNL-SA-105704. doi:10.1371/journal.pone.0123188
  • Tamano K., K.S. Bruno, H. Koike, T. Ishii, A. Miura, M. Umemura, and D.E. Culley, et al. 2015. "Increased Production of Free Fatty Acids in Aspergillus oryzae by Disruption of a Predicted Acyl-CoA Synthetase Gene." Applied Microbiology and Biotechnology 99, no. 7:3103-3113. PNNL-SA-104678. doi:10.1007/s00253-014-6336-9


  • Gallo A., B.P. Knox, K.S. Bruno, M. Solfrizzo, S.E. 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. PNNL-SA-101669. doi:10.1016/j.ijfoodmicro.2014.03.013
  • Qu Y., J. Feng, S. Deng, L. Cao, Q. Zhang, R. Zhao, and Z. Zhang, et al. 2014. "Structural Analysis of N- and O-glycans Using ZIC-HILIC/Dialysis Coupled to NMR Detection." Fungal Genetics and Biology : FG & B 72. PNNL-SA-101957. doi:10.1016/j.fgb.2014.08.001
  • Riley R., A. Salamov, D.W. Brown, L.G. Nagy, D. Floudas, B.W. Held, and A. Levasseur, et al. 2014. "Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi." Proceedings of the National Academy of Sciences (PNAS) 111, no. 27:9923-9928. PNNL-SA-103485. doi:10.1073/pnas.1400592111
  • Takeda I., K. Tamano, N. Yamane, T. Ishii, A. Miura, M. Umemura, and G. Terai, et al. 2014. "Genome Sequence of the Mucoromycotina Fungus Umbelopsis isabellina, an Effective Producer of Lipids." Genome Announcements 2, no. 1:e00071-14. PNNL-SA-101763. doi:10.1128/genomeA.00071-14


  • Atanasova L., B.P. Knox, C.P. Kubicek, I. Druzhinina, and S.E. Baker. 2013. "The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance." Eukaryotic Cell 12, no. 11:1499-1508. PNNL-SA-100641. doi:10.1128/EC.00103-13
  • Baer D.R., S.E. Baker, N.M. Washton, and B.E. Linggi. 2013. Status Report on the Development of Research Campaigns. PNNL-22924. Richland, WA: Pacific Northwest National Laboratory. Status Report on the Development of Research Campaigns
  • Baker S.E. 2013. "Fungi and Industrial Biotechnology - A special issue for an amazing kingdom." Industrial Biotechnology 9, no. 3:105-107. PNNL-SA-96018. doi:10.1089/ind.2013.1576
  • Condon B., Y. Leng, D. Wu, K.E. Bushey, R.A. Ohm, R.P. Otillar, and J.X. Martin, et al. 2013. "Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens." PLoS Genetics 9, no. 1:Article No. e1003233. PNNL-SA-94188. doi:10.1371/journal.pgen.1003233
  • Dai Z., U.K. Aryal, A.K. Shukla, W. Qian, R.D. Smith, J.K. Magnuson, and W.S. Adney, et al. 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. PNNL-SA-93855. doi:10.1016/j.fgb.2013.09.004
  • Geiser D., T. Aoki, C.W. Bacon, S.E. Baker, M. Bhattacharyya, M. Brandt, and D.W. Brown, et al. 2013. "One Fungus, One Name: Defining the genus Fusarium in a scientifically robust way that preserves longstanding use." Phytopathology 103, no. 5:400-408. PNNL-SA-94193. doi:10.1094/PHYTO-07-12-0150-LE
  • Karimi-Aghcheh R., J.W. Bok, P.A. Phatale, K.M. Smith, S.E. Baker, A. Lichius, and M. Omann, et al. 2013. "Functional Analyses of Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator." G3 Genes, Genomes, Genetics 3, no. 2:369-378. PNNL-SA-94192. doi:10.1534/g3.112.005140
  • Kim J., Z. Dai, U.K. Aryal, R.J. Moore, D.G. Camp, S.E. Baker, and R.D. Smith, et al. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85, no. 14:6826-6832. PNNL-SA-92785. doi:10.1021/ac401000q
  • Koike H., A. Aerts, K.M. LaButti, I.V. Grigoriev, and S.E. Baker. 2013. "Comparative genomics analysis of Trichoderma reesei strains." Industrial Biotechnology 9, no. 6:352-367. PNNL-SA-99523. doi:10.1089/ind.2013.0015
  • Tamano K., K.S. Bruno, S.A. Karagiosis, D.E. Culley, S. Deng, J.R. Collett, and M. Umemura, et al. 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, no. 1:269-281. PNNL-SA-86701. doi:10.1007/s00253-012-4193-y


  • Baker S.E., G. Perrone, N.M. Richardson, A. Gallo, and C.P. Kubicek. 2012. "Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma." Microbiology 158, no. 1:147-154. PNNL-SA-84089. doi:10.1099/mic.0.053462-0
  • Beckham G.T., Z. Dai, J.F. Mattews, M. Momany, C.M. Payne, W.S. Adney, and S.E. Baker, et al. 2012. "Harnessing glycosylation to improve cellulase activity." Current Opinion in Biotechnology 23, no. 3:338-345. PNNL-SA-83208. doi:10.1016/j.copbio.2011.11.030
  • Brown D.W., R.A. Butchko, S.E. Baker, and R.H. Proctor. 2012. "Phylogenomic and functional domain analysis of polyketide synthases in Fusarium." Fungal Biology 116, no. 2:318 - 331. PNNL-SA-84807.
  • Degenkolb T., R. Aghchehb, R. Dieckmann, T. Neuhof, S.E. Baker, I.S. Druzhinina, and I.S. Druzhinina, et al. 2012. "The production of Multiple Small Peptaibol Families by Single 14-Module Peptide Synthetases in Trichoderma/Hypocrea." Chemistry and Biodiversity 9, no. 3:499 - 535. PNNL-SA-84088. doi:10.1002/cbdv.201100212
  • Gallo A., K.S. Bruno, M. Solfrizzo, G. Perrone, G. Mule, A. Visconti, and S.E. 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, no. 23:8208-8218. PNNL-SA-87351. doi:10.1128/AEM.02508-12
  • Schuster A., K.S. Bruno, J.R. Collett, S.E. Baker, B. Seiboth, C.P. Kubicek, and M. Schmoll. 2012. "A versatile toolkit for high throughput functional genomics with Trichoderma reesei." Biotechnology for Biofuels 5, no. 1:Article No. 1. PNNL-SA-85701. doi:10.1186/1754-6834-5-1
  • Wang L., U.K. Aryal, Z. Dai, A.C. Mason, M.E. Monroe, Z. Tian, and J. Zhou, et al. 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, no. 1:143-56. PNNL-SA-82556. doi:10.1021/pr200916k


  • Andersen M.R., M. Salazar, P. Schaap, P. van de Vondervoort, D.E. Culley, J. Thykaer, and J.C. Frisvad, et al. 2011. "Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88." Genome Research 21, no. 6:885-897. PNNL-SA-78790. doi:10.1101/gr.112169.110
  • Baker S.E., and E.A. Panisko. 2011. "Proteome Studies of Filamentous Fungi." In Fungal Genomics: Methods and Protocols. Methods in Molecular Biology, edited by JR Xu and BHH Bluhm. 133-139. New York, New York:Springer. PNNL-SA-78038.
  • Berka R., I.V. Grigoriev, R.P. Otillar, A. Salamov, J. Grimwood, I. Reid, and N. Ishmael, et al. 2011. "Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and thielavia terrestris." Nature Biotechnology 29, no. 10:922-927. PNNL-SA-83457. doi:10.1038/nbt.1976
  • de Vries R.P., I. Benoit, G. Doehlemann, T. Kobayashi, J.K. Magnuson, E.A. Panisko, and S.E. Baker, et al. 2011. "Post-genomic approaches to understanding interactions between fungi and their environment." IMA Fungus 2, no. 1:81-86. PNNL-SA-80280. doi:10.5598/imafungus.2011.02.01.12
  • Eastwood D.C., D. Floudas, M. Binder, A. Majcherczyk, P. Schneider, A. Aerts, and F.O. Asiegbu, et al. 2011. "The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi." Science 333, no. 6043:762-765. PNNL-SA-90657. doi:10.1126/science.1205411
  • Grigoriev I.V., D. Cullen, S.X. Goodwin, D. Hibbett, T.W. Jeffries, C.P. Kubicek, and C.R. Kuske, et al. 2011. "Fueling the future with fungal genomics." Mycology 2, no. 3:192-209. PNNL-SA-80132.
  • Seidl-Seiboth V., S. Gruber, U. Sezerman, T. Schwecke, A. Albayrak, T. Neuhof, and H. von Dohren, et al. 2011. "Novel hydrophobins from Trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation and processing." Journal of Molecular Evolution 72, no. 4:339-351. PNNL-SA-80050. doi:10.1007/s00239-011-9438-3


  • Chiang Y.M., K.M. Meyer, M. Praseuth, S.E. Baker, K.S. Bruno, and C.C. 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, no. 4:430-437. PNNL-SA-74396. doi:10.1016/j.fgb.2010.12.001
  • Griffith G.W., S.E. Baker, K. Fliegerova, A. Liggenstoffer, M. van der Giezen, K. Voigt, and G. Beakes. 2010. "Anaerobic fungi: Neocallimastigomycota." IMA Fungus 1, no. 2:181-185. PNNL-SA-76641.
  • Ma L.J., H.C. van der Does, K.A. Borkovich, J.J. Coleman, M. Daboussi, A. Di Pietro, and A. Di Pietro, et al. 2010. "Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium." Nature 464. PNNL-SA-70493. doi:10.1038/nature08850
  • Ohm R.A., J.F. de Jong, L.G. Lugones, A. Aerts, E. Kothe, J.E. Stajich, and R.P. de Vries, et al. 2010. "Genome sequence of the model mushroom Schizophyllum commune." Nature Biotechnology 28, no. 9:957-963. PNNL-SA-75499. doi:10.1038/nbt.1643


  • Baker S.E. 2009. "Selection to sequence: opportunities in fungal genomics." Environmental Microbiology 11, no. 12:2955-2958. PNNL-SA-69812.
  • Baker S.E., K.S. Bruno, M.G. Butcher, J.R. Collett, D.E. Culley, Z. Dai, and J.K. Magnuson, et al. 2009. PNNL Fungal Biotechnology Core DOE-OBP Project. PNNL-18820. Richland, WA: Pacific Northwest National Laboratory. PNNL Fungal Biotechnology Core DOE-OBP Project
  • Jovanovic I., J.K. Magnuson, F.R. Collart, B. Robbertse, W.S. Adney, M.E. Himmel, and S.E. Baker. 2009. "Fungal glycoside hydrolases for saccharification of lignocellulose: outlook for new discoveries fueled by genomics and functional studies." Cellulose 16, no. 4:687-697. PNNL-SA-66360.
  • Le Crom S., W. Schackwitz, L. Pennacchiod, J.K. Magnuson, D.E. Culley, J.R. Collett, and J.X. Martin, et al. 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, no. 38:16151-16156. PNNL-SA-67636.
  • Martinez D., J. Challacombe, I. Morgenstern, D. Hibbett, M. Schmoll, C.P. Kubicek, and P. Ferreira, et al. 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, no. 6:1954-1959. PNNL-SA-64450. doi:10.1073/pnas.0809575106
  • Miracle A.L., V.L. Bailey, S.E. Baker, A.L. Bunn, J.K. Magnuson, and B.M. Webb-Robertson. 2009. "Integration of ‘omics technologies for characterization of complex microbial ecosystems - 8119." In Waste Management Symposium 2008, 832-841. Tucson, Arizona:WM Symposia. PNNL-SA-58003.
  • Seidl V., L. Song, E. Lindquist, S. Gruber, A. Koptchinskiy, S. Zeilinger, and M. Schmoll, et al. 2009. "Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey." BMC Genomics 10, no. Article Number: 567. PNNL-SA-70039. doi:10.1186/1471-2164-10-567
  • Thykaer J., M.R. Andersen, and S.E. Baker. 2009. "Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus." Medical Mycology 47, no. Sup 1:S80-S87. PNNL-SA-62804. doi:10.1080/13693780802455305
  • Tsang A., G.D. Butler, G.D. Butler, J. Powlowski, E.A. Panisko, and S.E. Baker. 2009. "Analytical and computational approaches to define the Aspergillus niger secretome." Fungal Genetics and Biology : FG & B 46, no. 1, Suppl. 1:S153-S160. PNNL-SA-65695. doi:10.1016/j.fgb.2008.07.014
  • Wright J.C., D. Sugden, S. Francis-McIntyre, I. Riba-Garcia, S.J. Gaskell, I.V. Grigoriev, and S.E. Baker, et al. 2009. "Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger." BMC Genomics 10. PNNL-SA-65830. doi:10.1186/1471-2164-10-61


  • Baker S.E., J. Thykaer, W.S. Adney, T. Brettin, F.J. Brockman, P. D'haeseleer, and A.D. Martinez, et al. 2008. "Fungal Genome Sequencing and Bioenergy." Fungal Biology Reviews 22. PNNL-SA-60119.
  • Daly D.S., K.K. Anderson, E.A. Panisko, S.O. Purvine, R. Fang, M.E. Monroe, and S.E. Baker. 2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7, no. 3:1209-1217. PNNL-SA-57824. doi:10.1021/pr070441i
  • kubicek C.P., S.E. Baker, C. Gamauf, C. Kenerley, I.S. Druzhinina, and I.S. 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, no. 4. PNNL-SA-56508. doi:10.1186/1471-2148-8-4
  • Martinez A.D., R. Berka, B. Henrissat, B. Henrissat, M. Saloheimo, M. Arvas, and S.E. Baker, et al. 2008. "Genome Sequencing and Analysis of the Biomass-Degrading Fungus Trichoderma reesei (syn. Hypocrea jecorina)." Nature Biotechnology 26, no. 5:553-560. PNNL-SA-60199.


  • Baker S.E., C.F. Wend, A.D. Martinez, J.K. Magnuson, E.A. Panisko, Z. Dai, and K.S. Bruno, et al. 2007. "Genome and Proteome Analysis of Industrial Fungi." In Exploitation of Fungi, edited by GD Robson, P van West and G Gadd. 3-9. New York, New York:Cambridge University Press. PNNL-SA-51617. doi:10.1017/CBO9780511902451.002
  • Cuomo C.A., U. Guldener, J.R. Xu, F. Trail, B.G. Turgeon, A. Di Pietro, and A. Di Pietro, et al. 2007. "The Fusarium Graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization." Science 317, no. 5843:1400-1402. PNNL-SA-57387. doi:10.1126/science.1143708
  • Rinker T.E., and S.E. Baker. 2007. "Deletion of a Chitin Synthase Gene in a Citric Acid Producing Strain of Aspergillus niger." Journal of Undergraduate Research 7. PNNL-SA-51517.
  • Rokas A., g. payne, N.D. Federova, S.E. Baker, M. Machida, J. yu, and D.R. georgianna, et al. 2007. "What can comparative genomics tell us about species concepts in the genus Aspergillus?." Studies in Mycology 59. PNNL-SA-58814.
  • Turgeon B.G., and S.E. 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. 219-261. San Diego, California:Elsevier Academic Press. PNNL-SA-55067.


  • Baker S.E. 2006. "Aspergillus Niger Genomics: Past, Present and into the Future." Medical Mycology 44, no. Supplement 1:S17-S21. PNNL-SA-51518. doi:10.1080/13693780600921037
  • Baker S.E., S. Kroken, P. Inderbitzin, T. Asvarak, B. Li, L. Shi, and O.C. Yoder, et al. 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, no. 2:139-49. PNNL-SA-46869.
  • Hixson K.K., J.N. Adkins, S.E. Baker, R.J. Moore, R.D. Smith, S.L. McCutchen-Maloney, and M.S. Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics." Journal of Proteome Research 5, no. 11:3008-3017. PNNL-SA-49565.


  • Annecharico M.D., and S.E. Baker. 2005. "Utilizing the CreA Gene to Better Understand Carbon Flux in Fungi." Journal of Undergraduate Research V, no. 2005:110. PNNL-SA-42496.
  • Lev S., R. hadar, P. Amedeo, S.E. Baker, O. Yoder, and B.A. 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, no. 2:443-454. PNNL-SA-44883.

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