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Scott Baker
Microbial Molecular Phenotyping Capability Leader

Scott E. Baker is the Microbial Molecular Phenotyping Capability Leader at the Environmental Molecular Sciences Laboratory. His research interests include biotechnology, genomics, and genetics, especially as they relate to fungal metabolite production, enzyme secretion, and cell morphology. Baker has a joint appointment as a fungal biotechnology scientist with the U.S. Department of Energy (DOE) Joint BioEnergy Institute (JBEI) located in Emeryville, California. At JBEI, his research is focused on heterologous production of lignin active enzymes by fungi.

For more than a decade he has led and contributed to fungal genome projects, from single genomes, to resequencing of classical genetic mutant strains, to whole fungal genus sequencing efforts. In 2009 and 2010, with DOE Joint Genome Institute (JGI) staff members, he co-led the development and launch of the JGI Fungal Genomics Program.

Baker has served on the Board of Directors of Society for Industrial Microbiology and Biotechnology (SIMB) as both a Director and President, and is a recent SIMB Fellow. He has contributed to nine journals as a reviewer, has been on the editorial board for the Industrial Biotechnology journal since 2011, and guest edited numerous special edition journals.

Research Interests

  • Biotechnology
  • Biofuels and chemicals
  • Microbiology
  • Mycology


  • PhD in Cell and Molecular Biology, Northwestern University, 1996
  • BS in Biology, Oregon State University, 1992

Awards and Recognition

  • Short-Term Mission (Visiting Scientist) Award, Institute of Sciences of Food Production, Italian National Research Council (2020, 2008)
  • Elected Fellow, Society for Industrial Microbiology and Biotechnology (2019)
  • Service Award Postdoctoral Fellowship, National Institues of Health National Research, University of Arizona (1997 – 2000)

Affiliations and Professional Service

  • Past President, Society for Industrial Microbiology and Biotechnology (2016 – 2017)
  • President, Society for Industrial Microbiology and Biotechnology (2015 – 2016)
  • President Elect, Society for Industrial Microbiology and Biotechnology (2014 – 2015)
  • Director, Society for Industrial Microbiology and Biotechnology (2010 – 2013)
  • American Society for Microbiology
  • Mycological Society of America
  • American Association for the Advancement of Science
  • Genetics Society of America


  • Dai, Z. and Baker, S.E. “Enhanced itaconic acid production in Aspergillus with increased LaeA expression.” US Patent 9,909,152.
  • Dai, Z. and Baker, S.E. “Enhanced citric acid production in Aspergillus with inactivated asparagine-linked glycosylation protein 3 (Alg3), and/or increased LaeA expression.” US Patent 9,023,637.
  • Dai, Z. and Baker, S.E. “Enhanced citric acid production in Aspergillus with inactivated asparagine-linked glycosylation protein 3 (Alg3), and/or increased LaeA expression.” US Patent 9,206,450.



Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S.E., Barry, K., Bills, G., Bluhm, B.H., Cannon, C., Castanera, R., Culley, D.E., Daum, C., Ezra, D., González, J.B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S.J., Nolan, M., Ohm, R.A., Pangilinan, J., Park, H.J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L.H., Turgeon, B.G., Goodwin, S.B., Spatafora, J.W., Crous, P.W., Grigoriev, I.V. 2020. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud Mycol., 96:141-153. doi: 10.1016/j.simyco.2020.01.003

Deng, S., Dai, Z., Swita, M., Pomraning, K.R., Hofstad, B., Panisko, E., Baker, S.E., Magnuson, J.K. 2020. Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359. Applied Microbiology and Biotechnology, pp.1-12.

Daly, P., Peng, M., Mitchell, H.D., Kim, Y.M., Ansong, C., Brewer, H., de Gijsel, P., Lipton, M..S, Markillie, L.M., Nicora, C.D., Orr, G., Wiebenga, A., Hildén, K.S., Kabel, M.A., Baker, S.E., Mäkelä, M.R., de Vries, R.P. 2020. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. Environ Microbiol. 2020 Mar;22(3):1154-1166. doi: 10.1111/1462-2920.14907

Kjærbølling, I., Vesth, T., Frisvad, J.C., Nybo, J.L., Theobald, S., Kildgaard, S., Petersen, T.I., Kuo, A., Sato, A., Lyhne, E.K., Kogle, M.E., Wiebenga, A., Kun, R.S., Lubbers, R.J.M., Mäkelä, M.R., Barry, K., Chovatia, M., Clum, A., Daum, C., Haridas, S., He, G., LaButti, K., Lipzen, A., Mondo, S, Pangilinan, J., Riley, R., Salamov, A., Simmons, B.A., Magnuson, J.K., Henrissat, B., Mortensen, U.H., Larsen, T.O., de Vries, R.P., Grigoriev, I.V., Machida, M., Baker S.E., Andersen, M.R. 2020. A comparative genomics study of 23 Aspergillus species from section Flavi. Nature Com., 11(1), pp.1-12.

Balasubramanian, V.K., Jansson, C., Baker, S.E., Ahkami, A.H. 2020. “Molecular Mechanisms of Plant–Microbe Interactions in the Rhizosphere as Targets for Improving Plant Productivity”. In Rhizosphere Biology: Interactions Between Microbes and Plants, pp. 295-338. Springer, Singapore.

Bredeweg, E.L., Baker, S.E. 2020. “Horizontal Gene Transfer in Fungi”. In Grand Challenges in Fungal Biotechnology, pp. 317-332. Springer, Cham.

Hackstein, J.H.P., Baker, S.E., van Hellemond, J.J., Tielens, A.G.M. 2020. "Hydrogenosomes of anaerobic fungi: an alternative way to adapt to anaerobic environments." In Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes, pp. 159-175. Springer, Cham.


Leynaud-Kieffer, L.M.C., Curran, S.C., Kim, I., Magnuson, J.K., Gladden, J. M., Baker, S.E., Simmons, B.A. 2019. A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable. PLoS One. 14(1):e0210243.


Hurley, J.M., Jankowski, M.S., De los Santos, H., Crowell, A.M., Fordyce, S.B.,  Zucker, J.D., Kumar, N.,  Purvine, S.O., Robinson, E.W., Shukla, A., Zink, E., Cannon, W.R., Baker, S.E., Loros, J.L., Dunlap, J.C., 2018. Circadian proteomic analysis uncovers mechanisms of post-transcriptional regulation in metabolic pathways. Cell Systems. 7(6):613-626.

Pomraning, K.R., Bredeweg, E.L., Kerkhoven, E.J., Barry, K., Haridas, S., Hundley, H., LaButti, K., Lipzen, A., Yan, M., Magnuson J.K., Simmons, B.A., Grigoriev, I.V., Nielsen, J., Baker, S.E. 2018. Regulation of yeast-to-hyphae transition in Yarrowia lipolytica. mSphere 3:e00541-18

Emri, T., Antal, K., Riley, R., Karányi, Z., Miskei, M., Orosz, E., Baker, S.E., Wiebenga, A., de Vries, R.P., Pócsi, I. 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. Stud. Mycol. doi: 10.1016/j.simyco.2018.10.003.

Vesth, T.C., Nybo, J.L., Theobald, S., Frisvad, J.C., Larsen, T.O., Nielsen, K.F., Hoof, J.,B., Brandl, J., Salamov, A., Riley, R., Gladden, J.M., Phatale, P., Nielsen, MT., Lyhne, E.K., Kogle, M.E., Kimchi Strasser, K., McDonnell, E., Barry, K., Clum, A., Chen, C.,  Nolan, M., Sandor, L., Kuo, A., Lipzen, A., Hainaut, M., Drula, E., Tsang, A., Magnuson, J.K., Henrissat, B., Wiebenga, A., Simmons, B.A., Mäkelä, M.R., de Vries, R.P.,  Grigoriev, I.V., Mortensen, U.H., Baker, S.E., Andersen, M.R. 2018. Section-level genome sequencing of Aspergillus section Nigri to investigate inter- and intra-species variation. Nature Genetics. doi: 10.1038/s41588-018-0246-1.

Daly P, Casado López S, Peng M, Lancefield CS, Purvine SO, Kim YM, Zink EM, Dohnalkova A, Singan VR, Lipzen A, Dilworth D, Wang M, Ng V, Robinson E, Orr G, Baker SE, Bruijnincx PCA, Hilden KS, Grigoriev IV, Mäkelä MR, de Vries RP. 2018. Dichomitus squalens partially tailors its molecular responses to the composition of solid wood. Environ Microbiol. doi: 10.1111/1462-2920.

Baker, S.E. 2018. Protein hyperproduction in fungi by design. Appl Microbiol Biotechnol.

Cannon, W.R., Zucker, J.D., Baxter, D.J., Kumar, N., Baker, S.E., Hurley, J.M., Dunlap, J.C. 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(6):63.

Reilly, M.C., Campen, S.A., Simmons, B.A., Baker, S.E., Gladden, J.M., Magnuson, J.K. 2018. Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger. Methods Mol Biol. 1796:123-133.

Khosravi, C., Battaglia, E., Kun, R.S., Dalhuijsen, S., Visser, J., Aguilar-Pontes, M.V., Zhou, M., Heyman, H.M., Kim, Y.M., Baker, S.E., de Vries, R.P. 2018. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans. BMC Genomics. 122;19(1):214.

Kjærbølling, I., Vesth,T.C., Frisvad, J.C., Nybo, J.L., Theobald, S., Kuo, A., Bowyer, P., Matsuda, Y., Mondo, S., Lyhne, E.K., Kogle, M.E., Clum, A., Lipzen, A., Salamov, A., Ngan, C.Y., Daum, C., Chiniquy, J., Barry, K., LaButti, K., Haridas, S., Simmons, B.A., Magnuson, J.K., Mortensen, U.H., Larsen,T.O., Grigoriev, I.V., Baker, S.E., Andersen, M.R. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E753-E761.

Reilly, M.C., Kim, J., Lynn, J., Simmons, B.A., Gladden, J.M., Magnuson, J.K., Baker, S.E. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Appl Microbiol Biotechnol. 2018 Feb;102(4):1797-1807.


Amaike Campen, S., Lynn, J., Sibert, S.J., Srikrishnan, S., Phatale, P., Feldman, T., Guenther, J.M., Hiras, J., Tran, Y.T.A., Singer, S.W., Adams, P.D., Sale, K.L., Simmons, B.A., Baker, S.E., Magnuson, J.K., Gladden, J.M. Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One. 2017 Dec 27;12(12):e0189604.

Geng, T., Smallwood, C.R., Bredeweg, E.L., Pomraning, K.R., Plymale, A.E., Baker, S.E., Evans, J.E., Kelly, R.T. 2017. Multimodal microfluidic platform for controlled culture and analysis of unicellular organisms. Biomicrofluidics. 11(5).

Tisch, D., Pomraning, K.R., Collett, J.R., Freitag, M., Baker, S.E., Chen, C.L., Hsu, P.W., Chuang, Y.C., Schuster, A., Dattenböck, C., Stappler, E., Sulyok, M., Böhmdorfer, S., Oberlerchner, J., Wang, T.F., Schmoll, M. Omics analyses of Trichoderma reesei CBS999.97 and QM6a indicate a relevance of female fertility for CAZyme and transporter levels. Appl Environ Microbiol. pii: AEM.01578-17.

Ivanova, C., Ramoni, J., Aouam, T., Frischmann, A., Seiboth, B., Baker, S.E., Le Crom, S., Lemoine, S., Margeot, A., Bidard, F. 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. Biotechnol Biofuels.: 10:209.

Cannon, W.R., Baker, S.E. 2017. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials. Phys Biol. 16;14(5):055003.

Kerkhoven, E.J., Kim, Y.M., Wei, S., Nicora, C.D., Fillmore, T.L., Purvine, S.O., Webb-Robertson, B.J., Smith, R.D., Baker, S.E., Metz, T.O., Nielsen, J. 2017. Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica. MBio, 8(3).

Haitjema, C.H., Gilmore, S.P., Henske, J.K., Solomon, K.V., de Groot, R., Kuo, A., Mondo. S.J., Salamov, A.A., LaButti, K., Zhao, Z., Chiniquy, J., Barry, K., Brewer, H.M., Purvine, S.O., Wright, A.T., Hainaut, M., Boxma, B., van Alen, T., Hackstein, J.H.P., Henrissat, B., Baker, S.E., Grigoriev, I.V., O'Malley, M.A. 2017. A parts list for fungal cellulosomes revealed by comparative genomics. Nat. Microbiol., 2:17087.

Boenisch, M.J., Broz, K.L., Purvine, S.O., Chrisler, W.B., Nicora, C.D., Connolly, L.R., Freitag, M., Baker, S.E., Kistler, H.C. 2017. Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis. Sci Rep., 13;7:44296.

Pomraning, K.R., Bredeweg, E.L., Baker, S.E. 2017. Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica. mSphere, 2(1).

McCluskey, K., Baker, S.E. 2017. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era. Mycology, 8(2), 67-83.

Brown, D.W., Baker, S.E. 2017. Mycotoxins: A Fungal Genomics Perspective. 2017. Methods Mol Biol., 1542:367-379.

Bredeweg,E.L., Pomraning, K.R.,  Dai, Z., Nielsen, J.,  Kerkhoven, E.J., Baker, S.E. 2017. A molecular genetic toolbox for Yarrowia lipolytica. Biotechnology for Biofuels 10(1), 2.

Mäkelä, M.R., Bredeweg, E.L., Magnuson, J.K., Baker, S.E., de Vries, R.P., Hildén, K. 2016. Fungal Ligninolytic Enzymes and Their Applications. Microbiology Spectrum, 4 (6),

de Vries, R.P., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Uchima C.A., Anderluh, G., Asadollahi, M., Askin, M., Barry, K., Battaglia, E., Bayram, Ö., Benocci, T., Braus-Stromeyer, S.A., Caldana, C., Cánovas, D., Cerqueira, G.C., Chen, F., Chen, W., Choi, C., Clum, A., Dos Santos, R.A., Damásio, A.R., Diallinas, G., Emri, T., Fekete, E., Flipphi, M., Freyberg, S., Gallo, A., Gournas, C., Habgood, R., Hainaut, M., Harispe, M.L., Henrissat, B., Hildén, K.S., Hope, R., Hossain, A., Karabika, E., Karaffa, L., Karányi, Z., Kraševec, N., Kuo, A., Kusch, H., LaButti, K., Lagendijk, E.L., Lapidus, A., Levasseur, A., Lindquist, E., Lipzen, A., Logrieco, A.F., MacCabe, A., Mäkelä, M.R., Malavazi, I., Melin, P., Meyer, V., Mielnichuk, N., Miskei, M., Molnár, Á.P., Mulé, G., Ngan, C.Y., Orejas, M., Orosz, E., Ouedraogo, J.P., Overkamp, K.M., Park, H.S., Perrone, G., Piumi, F., Punt, P.J., Ram, A.F., Ramón, A., Rauscher, S., Record, E., Riaño-Pachón, D.M., Robert, V., Röhrig, J., Ruller, R., Salamov, A., Salih, N.S., Samson, R.A., Sándor, E., Sanguinetti, M., Schütze, T., Sepčić, K., Shelest, E., Sherlock, G., Sophianopoulou, V., Squina, F.M., Sun, H., Susca, A., Todd, R.B., Tsang, A., Unkles, S.E., van de Wiele, N., van Rossen-Uffink, D., Oliveira, J.V., Vesth, T.C., Visser, J., Yu, J.H., Zhou, M., Andersen, M.R., Archer, D.B., Baker, S.E., Benoit, I., Brakhage, A.A., Braus, G.H., Fischer, R., Frisvad, J.C., Goldman, G.H., Houbraken, J., Oakley, B., Pócsi, I., Scazzocchio, C., Seiboth, B., vanKuyk, P.A., Wortman, J., Dyer, P.S., Grigoriev, I.V. 2017. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology, 18:28.

Reilly, M.C., Magnuson, J.K., Baker, S.E. 2017. Approaches to understanding protein hypersecretion in fungi. Fungal Biology Reviews 30 (4), 145-151.


Corrochano, L.M., Kuo, A., Marcet-Houben, M., Polaino, S., Salamov, A., Villalobos-Escobedo, J.M., Grimwood, J., Álvarez, M.I., Avalos, J., Bauer, D., Benito, E.P., Benoit, I., Burger, G., Camino, L.P., Cánovas, D., Cerdá-Olmedo, E., Cheng, J.F., Domínguez, A., Eliáš, M., Eslava, A.P., Glaser, F., Gutiérrez, G., Heitman, J., Henrissat B., Iturriaga, E.A., Lang, B.F., Lavín, J.L., Lee, S.C., Li, W., Lindquist, E., López-García, S., Luque, E.M., Marcos, A.T., Martin, J., McCluskey, K., Medina, H.R., Miralles-Durán, A., Miyazaki, A., Muñoz-Torres, E., Oguiza, J.A., Ohm, R.A., Olmedo, M., Orejas, M., Ortiz-Castellanos, L., Pisabarro, A.G., Rodríguez-Romero, J., Ruiz-Herrera, J., Ruiz-Vázquez, R., Sanz, C., Schackwitz, W., Shahriari, M., Shelest, E., Silva-Franco, F., Soanes, D., Syed, K., Tagua, V.G., Talbot, N.J., Thon, M.R., Tice, H., de Vries, R.P., Wiebenga, A., Yadav, J.S., Braun, E.L., Baker, S.E., Garre, V., Schmutz, J., Horwitz, B.A., Torres-Martínez, S., Idnurm, A., Herrera-Estrella, A., Gabaldón, T., Grigoriev, I.V. 2016. Expansion of signal transduction pathways in fungi by extensive genome duplication. Current Biology, 26 (12), 1577-1584.

Nguyen, H.D.T., McMullin, D.R., Ponomareva, E., Riley, R., Pomraning, K.R., Baker, S.E., Seifert, K.A. 2016. Ochratoxin A production by Penicillium thymicola. Fungal Biology. 120 (8), 1041-1049.

Schuerg, T., Gabriel, R., Baecker, N., Baker, S.E., Singer, S.W. 2016. Thermoascus aurantiacus: an Intriguing Thermophilic Fungus for Cellulase Production. Current Biotech., 5(3).

Goodwin, S.B., McCorison, C.B., Cavaletto, J.R., Culley, D.E., LaButti, K., Baker, S.E., Grigoriev, I.V. 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.

Pomraning, K.R., Kim, Y.-M., Nicora, C.D., Chu, R.K., Bredeweg, E.L., Purvine, S.O., Hu, D., Metz, T.O., Baker, S.E. 2016. Multi-omics analyses reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. BMC Genomics.17:138.

Kerkhoven, E. Pomraning, K.R., Baker, S.E., Nielsen, J. 2016. Regulation of amino acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. npj Systems Biology and Applications. 2:16005.

Schmoll, M., Dattenböck, C., Carreras-Villaseñor, N., Mendoza-Mendoza, A., Tisch, D., Aleman, M.I., Baker, S.E., Brown, C., Cervantes-Badillo, M.G., Cetz-Chel, J., Cristobal-Mondragon, G.R., Delaye, L., Esquivel-Naranjo, E.U., Frischmann, A., Gallardo-Negrete, J.d.J., Garacia-Esquival, M., Gomez-Rodriguez, E.Y., Greenwood, D.R., Hernández-Oñate, M.A., Kruszewska, J.S., Lawry, R., Mora-Montes, H.M., Munoz-Centeno, T., Nieto-Jacobo, F., Nogueira-Lopez, G., Olmedo-Monfil, V., Osorio-Concepcion, M., Pilsyk, S., Pomraning, K., Rodriguez-Iglesias, A., Rosales-Saavedra, M.T., Sánchez-Arreguin, A., Seidl-Seiboth, V., Alison Stewart, A., Uresti-Rivera, E.E., Wang, C.-L., Wang, T.F., Zeilinger, S., Casas-Flores, S., Herrera-Estrella, A.H. 2016. The genomes of three uneven siblings – footprints of the lifestyle of three Trichoderma species. Microbiol. Mol. Biol. Rev. 80 (1), 205-327.

Niu, J., Arentshorst, M., Nair, P.D.S., Dai, Z., Baker, S.E., Frisvad, J.C., Nielsen, K.F., Punt, P.J. Ram, A.F.J. 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. 6(1):193-204.

Emerson, J.M., Bartholomai, B.M., Ringelberg, C.S., Baker, S.E., Loros, J.J., Dunlap, J.C. 2015. period-1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of the Neurospora circadian clock. Proc Natl Acad Sci U S A. 112(51):15707-12.

Bredeweg, E.L., Baker, S.E. 2016. Comparative genomics, resequencing and fast forward genetics in Aspergillus and Penicillium. In “Aspergillus and Penicillium in the post-genomic era”. Eds R.P. de Vries, I. Benoit and M.R. Andersen.


Pomraning, K.R., Baker, S.E. 2015. Draft genome sequence of the dimorphic yeast Yarrowia lipolytica strain W29. Genome Announc. 3(6). pii: e01211-15.

Geng, T., Bredeweg, E.L., Szymanski, C.J., Liu, B., Baker, S.E., Orr, G., Evans, J.E., Kelly, R.T. 2015. Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics. Sci. Rep. 5:16111.

McCluskey, K., Baker, S.E. 2015. A brief history of fungal genomics from linkage maps to sequences. In “Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi”. Eds R.R.M. Paterson and N. Lima.

Yang, D., Pomraning, K., Kopchinskiy, A., Karimi-Aghcheh, R., Atanasova, L., Chenthamara, K., Baker, S.E., Zhang, R., Shen, Q., Freitag, M., Kubicek, C., Druzhinina., I. 2015. Genome Sequence and Annotation of Trichoderma parareesei, the ancestor of the cellulase producer Trichoderma reesei. Genome Announc. 3(4): pii: e00885-15.

Lichius, A., Bidard, F., Buchholz, F., Le Crom, S., Martin, J., Schackwitz, W., Austerlitz, T., Grigoriev, I.V., Baker, S.E., Margeot, A., Seiboth, B., Kubicek, C.P. 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(1):326.

Pomraning, K.R., Wei, S., Karagiosis, S.A., Kim, Y.M., Dohnalkova, A.C., Arey, B.W., Bredeweg, E.L., Orr, G., Metz, T.O., Baker, S.E. 2015. Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis. PLoS One. 10(4):e0123188.

Baker, S.E., Schackwitz, W., Lipzen, A., Martin, J., Haridas, S., LaButti, K., Grigoriev, I.V., Simmons, B.A., McCluskey, K. 2015. Draft genome sequence of Neurospora crassa strain FGSC 73. 3(2). Genome Announc. 3(2): pii:e00074-15.

Tamano, K., Bruno, K.S., Koike, H., Ishii, T., Miura, A., Umemura, M., Culley, D.E., Baker, S.E., Machida, M. 2015. Increased production of free fatty acids in Aspergillus oryzae by disruption of a predicted acyl-CoA synthetase gene. Appl Microbiol Biotechnol. 99(7): 3103-13.


Qu, Y., Feng, J., Deng, S., Cao, L., Zhang, Q., Zhao, R., Zhang, Z., Jiang, Y., Zink, E.M., Baker, S.E., Lipton, M.S., Paša-Tolić, L., Hu, J.Z., Wu, S. 2014. Structural analysis of N- and O-glycans using ZIC-HILIC/dialysis coupled to NMR detection. Fungal Genet Biol. 72:207-15.

Riley, R., Salamov, A.A., Brown, D.W., Nagy, L.G., Floudas, D., Held, B.W., Levasseur, A., Lombard, V., Morin, E., Otillar, R., Lindquist, E.A., Sun, H., LaButti, K.M., Schmutz, J., Jabbour, D., Luo, H., Baker, S.E., Pisabarro, A.G., Walton, J.D., Blanchette, R.A., Henrissat, B., Martin, F., Cullen, D., Hibbett, D.S., Grigoriev, I.V. 2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A. 111 (27), 9923-8.

Gallo, A., Knox, B.P., Bruno, K.S., Solfrizzo, M., Baker, S.E., Perrone, G. 2014. Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius. Int J Food Microbiol. 179:10-7.

Takeda I, Tamano K, Yamane N, Ishii T, Miura A, Umemura M, Terai G, Baker SE, Koike H, Machida M. 2014. Genome sequence of the Mucoromycotina fungus Umbelopsis isabellina, an effective producer of lipids. Genome Announc. 2(1).


Koike H., Aerts, A., LaButti, K., Grigoriev, I.V., Baker, S.E. 2013. Comparative genomics analysis of Trichoderma reesei strains. Indust. Biotech. 9(6): 352-367.

Baker, S.E. 2013. Return of the Fungi. Indust. Biotech. 9(6). 328-330.

Dai, Z., Aryal, U.K., Shukla, A., Qian, W.J., Smith, R.D., Magnuson, J.K., Adney, W.S., Beckham, G.T., Brunecky, R., Himmel, M.E., Decker, S.R., Ju, X., Zhang, X., Baker, S.E. 2013. Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger. Fungal Genet Biol. 61:120-132.

Atanasova, L., Knox, B.P., Kubicek, C.P., Druzhinina, I.S., Baker, S.E. 2013. The polyketide synthase gene PKS4 of Trichoderma reesei provides pigmentation and stress resistance. Eukaryot Cell. 12(11):1499-1508.

Karagiosis, S., Baker, S.E. 2013. Trichoderma and the biorefinery: From plant health to enzymes to biofuel production. In “Trichoderma: Genetics and Applications”. Ed. Prasun K. Mukherjee ,  B. A. Horwitz, U.S. Singh ,  M. Mukherjee and M. Schmoll.

Benoit, I., Malavazi, I., Goldman, G.H., Baker, S.E.,  de Vries, R.P. Aspergillus - Genomics of a cosmopolitan fungus. 2013. In “Genomics of Soil- and Plant-Associated Fungi”. Ed. B.A. Horowitz, et al.

Benoit, I., de Vries, R.P., Baker, S.E., Karagiosis, S.A. Aspergilli and biomass-degrading fungi. In “Ecological Genomics of the Fungi”. Ed. F. Martin.

Kim, J.S., Dai, Z., Aryal, U.K., Moore, R.J., Camp, D.G., Baker, S.E., Smith, R.D, Qian, W.J. 2013. Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing. Anal. Chem. 85(14):6826–6832.

Baker, S.E. 2013. Fungi and Industrial Biotechnology – A Special Issue for an Amazing Kingdom. Indust. Biotech. 9(3):105-107.

Geiser, D.M., Aoki, T., Bacon, C.W., Baker, S.E., Bhattacharyya, M.K., Brandt, M.E., Brown, D.W., Burgess, L.W., Chulze, S.N., Coleman, J.J., Correll, J.C., Covert, S., Crous, P.W., Cuomo, C.A., de Hoog, G.S., Di Pietro, A., Elmer, W.H., Epstein, L., Frandsen, R.J., Freeman, S., Gagkaeva, T., Glenn, A.E., Gordon, T., Gregory, N.F., Hammond-Kosack, K., Hanson, L., Jimenez-Gasco, M.D., Kang, S., Kistler, H.C., Kuldau, G.A., Leslie, J.H., Logrieco, A., Lü ,G., Lysøe, E., Ma, L.J., McCormick, S., Migheli, Q., Moretti, A., Munaut, F., O'Donnell, K., Pfenning, L.H., Ploetz, R., Proctor, R., Rehner, S.A., Robert, V.A., Rooney, A.P., Salleh, B., Scandiani, M.M., Scauflaire, J., Short, D.P., Steenkamp, E., Suga, H., Summerell, B.A., Sutton, D.A., Thrane, U., Trail, F., van Diepeningen, A., Vanetten, H., Viljoen, A., Waalwijk, C., Ward, T., Wingfield, M.J., Xu, J.R., Yang, X.B., Yli-Matilla, T., Zhang, N. 2013. One Fungus, One Name: Defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology. 103(5):400-408.

Karimi-Aghcheh, R., Bok, J.W., Phatale, P.A., Smith, K.M., Baker, S.E., Lichius, A., Omann, M., Zeilinger, S., Seiboth, B., Rhee, C., Keller, N.P., Freitag, M., Kubicek, C.P. 2013. Functional Analyses of Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator. G3. 3(2):369-78.

Tamano, K., Bruno, K.S., Karagiosis, S.A., Culley, D.E., Deng, S., Collett, J.R., Umemura, M., Koike, H., Baker, S.E., Machida, M. 2013. Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes. Appl Microbiol Biotechnol. 97(1):269-81.

Condon, B.J., Leng, Y., Wu, D., Bushley, K.E., Ohm, R.A., Otillar, R., Martin, J., Schackwitz, W., Grimwood, J., Mohdzainudin, N., Xue, C., Wang, R., Manning, V.A., Dhillon, B., Tu, Z.J., Steffenson, B.J., Salamov, A., Sun, H., Lowry, S., Labutti, K., Han, J., Copeland, A., Lindquist, E., Barry, K., Schmutz, J., Baker, S.E., Ciuffetti, L.M., Grigoriev, I.V., Zhong, S., Turgeon, B.G. 2013. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens. PLOS Genetics. 9(1):e1003233.

Weist, A., Baker, S.E., McCluskey, K. 2013. Neurospora gene and genome analysis: Past through future. In “Neurospora genomics and molecular biology”. D.P. Kasbekar and K. McCluskey, Eds. Caister Academic Press, Norfolk, UK.


Gallo, A., Bruno, K.S., Solfrizzo, M., Perrone, G., Mulè, G., Visconti, A., Baker, S.E. 2012. New insight in the ochratoxin A biosynthetic pathway by deletion of an nrps gene in Aspergillus carbonarius. Appl Environ Microbiol. 78(23):8208-18.

Seiboth, B., Karimi, R.A., Phatale, P.A., Linke, R., Hartl, L., Sauer, D.G., Smith, K.M., Baker, S.E., Freitag, M., Kubicek, C.P. 2012. The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei. Mol Microbiol. 84(6):1150-1164.

Beckham, G.T., Dai Z., Matthews, J.F., Momany, M., Payne, C.M., Adney, W.S., Baker, S.E., Himmel, M.E. 2012. Harnessing glycosylation to improve cellulase activity. Curr Opin Biotechnol. 23(3):338-45.

Degenkolba, T., Aghchehb, R.K.,Dieckmann, R., Neuhof, T., Baker, S.E., Druzhinina, I.S., Kubicek, C.P.,  Brückner, H.,  von Döhren, H. 2011. The production of multiple small peptaibol families by single 14-module peptide synthetases in Trichoderma/Hypocrea. Chem Biodivers. 9:499-535.

Karagiosis, S.A., Baker, S.E. Fungal Cell Factories. 2012. In “Food and Industrial Bioproducts and Bioprocessing” Ed. N.T. Dunford and H.B. Dunford. Wiley-Blackwell.

Brown, D.W., Butchko, R.A.E., Baker, S.E., Proctor, R.H. 2012. Phylogenomic and functional domain analysis of polyketide synthases in Fusarium. Fung. Biol. 116:318-331.

Schuster, A., Bruno, K.S., Collett, J.R., Baker, S.E., Seiboth, B., Kubicek, C.P., Schmoll, M. 2012. A versatile toolkit for high throughput functional genomics with Trichoderma reesei. Biotechnol Biofuels. 5(1):1.

Baker, S.E., Perrone, G., Richardson, N.M., Gallo, A., Kubicek, C.P. 2012. Phylogenomic analysis of polyketide synthase encoding genes in Trichoderma. Microbiol. 158(1):147-54.


Wang, L. Aryal, U.K, Dai, Z., Mason, A.C., Monroe, M.E., Tian, Z-X., Zhou, J-Y., Su, D., Weitz, K.K., Liu, T., Camp, D.G., Smith, R.D., Baker, S.E., Wei-Jun Qian, W-J. 2011. Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry. J. Prot. Res. 11(1):143-56.

Berka, R.M., Grigoriev, I.V., Otillar, R., Salamov, A., Grimwood, J., Reid, I., Ishmael, N., John, T., Darmond, C., Moisan, M.-C., Henrissat, B., Coutinho, P.M., Lombard, V., Natvig, D., Lindquist, E., Schmutz,  J., Lucas, S., Harris, P., Powlowski, J., Bellemare, A., Taylor, D., Butler, G., de Vries, R.P., Allijn, I.E., van den Brink, J., Ushinsky, S., Storms, R., Powell, A.J., Paulsen, I.T., Elbourne, L.D.H., Baker, S.E., Magnuson, J.K., LaBoissiere,S., Clutterbuck, A.J., Martinez, D., Wogulis, M., Lopez de Leon, A., Rey, M.W., Tsang, A. 2011. Comparative Genomic Analysis of the Thermophilic Biomass-Degrading Fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol. 29(10):922-7.

Grigoriev, I.V., Cullen, D., Hibbett, D., Goodwin, S.B., Jeffries, T.W., Kubicek, C.P., Kuske, C., Magnuson, J., Martin, F., Spatafora, J.W., Baker, S.E. 2011. Fueling the future with fungal genomics. Mycology, 2(3):192-209.

McCluskey, K., Wiest, A.E., Grigoriev, I.V., Lipzen, A., Martin, M.,  Schackwitz, W., Baker, S.E. 2011. Rediscovery by whole genome sequencing: Classical mutations and genome polymorphisms in Neurospora crassa. G3, 1:303-316.

Eastwood, D.C, Floudas, D., Binder, M.,  Majcherczyk, A., Schneider, P., Aerts, A.,  Asiegbu, F.O., Baker, S.E., Barry, K., Bendiksby, M., Blumentritt, M., Coutinho, P.M., Cullen, D., de Vries, R.P., Gathman, A., Goodell, B., Henrissat, B., Ihrmark, K., Kauserud, H., Kohler, A., LaButti, K., Lapidus, A., Lavin, J.L., Lee, Y.-H., Lindquist, E., Lilly, W., Lucas, S., Morin, E., Murat, C., Oguiza, J.A., Park, J.,  Pisabarro, A.G., Riley, R., Rosling, A., Salamov, A., Schmidt, O., Schmutz, J.,  Skrede, I., Stenlid, J., Wiebenga, A., Xie, X., Kües, U., Hibbett, D.S., Hoffmeister, D., Högberg, N., Martin, F., Grigoriev, I.V., Watkinson, S.C. 2011. The plant cell wall decomposing machinery underlies the functional diversity of forest fungi. Science. 333: 762-765.

de Vries, R.P., Benoit, I., Doehlemann, G., Kobayashi, T., Magnuson, J.K., Panisko, E.A, Baker, S.E., Lebrun, M.-H. Post-genomic approaches to understanding interactions between fungi and their environment. IMA Fungus. 2(1):81-86.

Andersen, M.R., Salazar, M.P., Schaap, P.J., van de Vondervoort, P.J., Culley, D., Thykaer, J., Frisvad, J.C., Nielsen, K.F., Albang, R., Albermann, K., Berka, R.M., Braus, G.H., Braus-Stromeyer, S.A., Corrochano, L.M., Dai Z., van Dijck, P.W., Hofmann, G., Lasure, L.L., Magnuson, J.K., Menke, H., Meijer, M., Meijer, S.L., Nielsen, J.B., Nielsen, M.L., van Ooyen, A.J., Pel, H.J., Poulsen, L., Samson, R.A., Stam, H., Tsang, A., van den Brink, J.M., Atkins, A., Aerts, A., Shapiro, H., Pangilinan, J., Salamov, A., Lou, Y., Lindquist, E., Lucas, S., Grimwood, J., Grigoriev, I.V., Kubicek, C.P., Martinez, D., van Peij, N.N., Roubos, J.A., Nielsen, J., Baker, S.E. 2011. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. 21(6):885-97.

Kubicek, C.P., Herrera-Estrella, A., Seidl-Seiboth, V., Martinez, D.A., Druzhinina, I.S., Thon, M., Zeilinger, S., Casas-Flores, S., Horwitz, B.A., Mukherjee, P.K., Mukherjee, M., Kredics, L., Alcaraz, L.D., Aerts, A., Antal, Z., Atanasova, L., Cervantes-Badillo, M.G., Challacombe, J., Chertkov, O., McCluskey, K., Coulpier, F., Deshpande, N., von Doehren, H., Ebbole, D.J., Esquivel-Naranjo, E.U., Fekete, E., Flipphi, M., Glaser, F., Gomez-Rodriguez, E.Y., Gruber, S., Han, C., Henrissat, B., Hermosa, R., Hernandez-Onate, M., Karaffa, L., Kosti, I., Le Crom, S., Lindquist, E., Lucas, S., Lubeck, M., Lubeck, P.S., Margeot, A., Metz, B., Misra, M., Nevalainen, H., Omann, M., Packer, N., Perrone, G., Uresti-Rivera, E.E., Salamov, A., Schmoll, M., Seiboth, B., Shapiro, H., Sukno, S., Tamayo-Ramos, J.A., Tisch, D., Wiest, A., Wilkinson, H.H., Zhang, M., Coutinho, P.M., Kenerley, C.M., Monte, E., Baker, S.E., Grigoriev, I.V. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 12(4):R40.

Seidl-Seiboth, V., Gruber, S., Sezerman, U., Schwecke, T., Albayrak, A., Neuhof, T., von Döhren, H., Baker, S.E., Kubicek, C.P. 2011. Novel Hydrophobins from Trichoderma Define a New Hydrophobin Subclass: Protein Properties, Evolution, Regulation and Processing. J Mol Evol. 72(4):339-51.

Baker, S.E, Panisko, E.A. Proteome Studies of Filamentous Fungi. 2011. In Fungal Genomics, Methods in Molecular Biology, Vol. 722. Ed. J.R. Xu and B. H. Bluhm, Springer.

Martin, F., Cullen, D., Hibbett, D., Pisabarro, A., Spatafora, J.W., Baker, S.E., Grigoriev, I.V. 2011. Sequencing the Fungal Tree of Life. New Phytologist. 190(4):818-821.

Chiang, Y.M., Meyer, K.M., Praseuth, M., Baker, S.E., Bruno, K.S., Wang, C.C.C. Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone. 2011. Fungal Genet Biol. 48: 430-7.


Griffith, G.W., Baker, S.E., Fliegerova, K., Liggenstoffer, A., Giezen, M., Voigt, K., Beakes, G. 2010. Anaerobic fungi: Neocallimastigomycota. IMA Fungus. 1(2): 181–185.

Ohm R.A., de Jong J.F., Lugones L.G., Aerts A., Kothe E., Stajich J.E., de Vries R.P., Record E., Levasseur A., Baker S.E., Bartholomew K.A., Coutinho P.M., Erdmann S., Fowler T.J., Gathman A.C., Lombard V., Henrissat B., Knabe N., Kües U, Lilly W.W., Lindquist E., Lucas S., Magnuson J.K., Piumi F., Raudaskoski M., Salamov A., Schmutz J., Schwarze F.W., vanKuyk P.A., Horton JS, Grigoriev I.V., Wösten H.A. 2010. Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnol. 28(9):957-63.

Ma L.J., van der Does H.C., Borkovich K.A., Coleman J.J., Daboussi M.J., Di Pietro A., Dufresne M., Freitag M., Grabherr M., Henrissat B., Houterman P.M., Kang S., Shim W.B.,Woloshuk C., Xie X., Xu J.R., Antoniw J, Baker S.E., Bluhm B.H., Breakspear A., Brown D.W., Butchko R.A., Chapman S., Coulson R., Coutinho P.M., Danchin E.G., Diener A., Gale L.R., Gardiner D.M., Goff S., Hammond-Kosack K.E., Hilburn K., Hua-Van A., Jonkers W., Kazan K., Kodira C.D., Koehrsen M., Kumar L., Lee Y.H., Li L., Manners J.M., Miranda-Saavedra D., Mukherjee M., Park G., Park J., Park S.Y., Proctor R.H., Regev A., Ruiz-Roldan M.C., Sain D., Sakthikumar S., Sykes S., Schwartz D.C., Turgeon B.G., Wapinski I., Yoder O., Young S., Zeng Q., Zhou S., Galagan J., Cuomo C.A., Kistler H.C., Rep M. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 464(7287):367-73.


Baker S.E. 2009. Selection to sequence: opportunities in fungal genomics. Environ Microbiol. 11(12):2955-8.

Seidl V., Song L., Lindquist E., Gruber S., Koptchinskiy A., Zeilinger S., Schmoll M., Martínez P., Sun J., Grigoriev I.V., Herrera-Estrella A., Baker S.E., Kubicek C.P.. 2009. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics. 10:567.

Jovanovic I., Magnuson J.K., Collart F., Robbertse B., Adney W.S., Himmel M.E., Baker S.E. 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., Schackwitz W., Pennacchio L., Magnuson J.K., Culley D.E., Collett J.R., Martin J., Druzhinina I.S., Mathis H., Monot F.., Seiboth B., Cherry B, Rey M., Berka R., Kubicek C.P., Baker S.E., Margeot A. 2009. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 106(38):16151-6.

Tsang A., Butler G., Powlowski J., Panisko E.A., Baker S.E. 2009. Analytical and computational approaches to define the Aspergillus niger secretome. Fungal Genet Biol. 46 Suppl 1:S153-S160.

Martinez D., Challacombe J., Morgenstern I., Hibbett D., Schmoll M., Kubicek C.P., Ferreira P., Ruiz-Duenas F.J., Martinez A.T., Kersten P., Hammel K.E., Vanden Wymelenberg A., Gaskell J., Lindquist E., Sabat G., Bondurant S.S., Larrondo L.F., Canessa P., Vicuna R., Yadav J., Doddapaneni H., Subramanian V., Pisabarro A.G., Lavín J.L., Oguiza J.A., Master E., Henrissat B., Coutinho P.M., Harris P, Magnuson J.K., Baker S.E., Bruno K., Kenealy W., Hoegger P.J., Kües U., Ramaiya P., Lucas S., Salamov A., Shapiro H., Tu H., Chee C.L., Misra M., Xie G., Teter S., Yaver D., James T., Mokrejs M., Pospisek M., Grigoriev I.V., Brettin T., Rokhsar D., Berka R., Cullen D.. 2009. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A. 106(6):1954-9.

Thykaer J., Andersen M.R., Baker S.E. 2009. Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus. Med Mycol. 47 Suppl 1:S80-7.

Panisko, E.A., Grigoriev, I., Daly, D.S., Webb-Robertson, B-J, Baker, S.E. 2009. Genomes to Proteomes. In “Automation in Genomics and Proteomics: An Engineering Case-Based Approach” Eds: G. Alterovitz, M. Ramoni, R.M. Benson. Wiley.

Wright, J.C., Sugden, D., Francis-McIntyre, S., Riba-Garcia, I., Gaskell, S.J., Grigoriev. I.V., Baker. S.E., Beynon, R.J., Hubbard, S.J. 2009. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics. 10(1):61.


Zhou K., Panisko E.A., Magnuson J.K., Baker S.E., Grigoriev I. Proteomics for validation of automated gene model predictions. 2008. In “Mass Spectrometry of Proteins and Peptides” Eds: M Lipton, L Paša-Tolić. Humana Press.

Baker, S.E., Thykaer, J., Adney, W.S., Brettin, T., Brockman, F., D’haeseleer, P., Martinez, A. D., Miller, R.M., Rokhsar, D., Schadt, C.W., Torok, T., Tuskan, G., Bennett, J.W., Berka, R., Briggs, S. Heitman, J., Taylor, J.,  Turgeon, B.G., Werner-Washburne, M., Himmel, M.E. 2008. Fungal genome sequencing and bioenergy. Fungal Biology Reviews. 22:1-5.

Martinez, D., Berka, R.M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S.E., Chapman, J., Chertkov, O., Coutinho, P.M., Cullen, D., Danchin, E.G.J., Grigoriev, I.V., Harris, P., Jackson, M., Kubicek, C.P., Han, C.S., Ho, I., Larrondo, L.F., de Leon, A.L., Magnuson, J.K., Merino, S., Misra, M., Nelson, B., Putnam, N., Robbertse, B., Salamov, A., Schmoll, M., Terry, A., Thayer, N., Westerholm-Parvinen, A., Schoch, C.L., Yao, J., Barbote, R., Nelson, M.A., Detter, C., Bruce, D., Kuske, C.R., Xie, G., Richardson, P., Rokhsar, D.S., Lucas, S.M., Rubin, E.M., Dunn-Coleman, N., Ward M., Brettin T. S. 2008. Genome Sequence Analysis of the Biomass-Degrading Fungus Trichoderma reesei (syn. Hypocrea jecorina) Reveals a Surprisingly Limited Inventory of Carbohydrate Active Enzymes. 2008. Nat. Biotech. 26:553-560.

Hackstein, J.H.P, Baker, S.E., van Hellemond, J.J., Tielens, A.J.M. 2008.Hydrogenosomes of anaerobic chytrids: An alternative way to adapt to anaerobic environments. In “Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes.” Ed. J. Tachezy. Microbiol. Monogr. 9:147-162.

Daly D.S., Anderson, K.K., Panisko, E.A., Purvine, S.O., Monroe M.E., Baker S.E. 2008. A mixed effects statistical model for comparative LC-MS proteomics studies. J Proteomics Res. 7:1209-17.

Kubicek, C.P., Baker, S.E., Christian Gamauf, C., Kenerley, C.M., Druzhinina, I.S. 2008. Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea. BMC Evol. Biol. 8:4.

Bidartondo, M.I., Bruns, T.D., Blackwell, M., Ivan Edwards, I., Taylor, A.F.S., Horton, T., Zhang, N., Kõljalg, U., May,G., Kuyper, T.W., Bever, J.D., Gilbert, G., Taylor, J.W., DeSantis, T.Z., Pringle, A., Borneman, J., Thorn, G., Berbee, M., Mueller, G.M., Andersen, G.L., Villinga, E.C., Branco, S., Anderson, I., Dickie, I.A., Avis, P., Timonen, S., Kjöller, R., Lodge, D.J., Bateman, R.M., Purvis, A., Crous, P.W., Hawkes, C., Barraclough, T., Burt, A., Henrik Nilsson, R., Larsson, K-H, Alexander, I., Moncalvo, J.M., Berube, J., Spatafora, J., Lumbsch, H.T., Blair, J.E., Suh, S-O., Pfister, D.H., Binder, M., Boehm, E.W., Kohn, I., Mata, J.L., Dyer, P., Sung, G-H., Dentinger, B., Simmons, E.G., Baird, R.E., Volk, T.J., Perry, B.A., Kerrigan, R.W., Campbell, J., Rajesh, J., Reynolds, D.R., Geiser, D., Humber, R.A., Hausmann, N., Szaro, T., Stajich, J., Gathman, A., Peay, K.G., Henkel, T., Robinson, C.H., Pukkila, P.J., Nguyen, N.H., Villata, C., Kennedy, P., Bergemann, S., Aime, M.C., Kauff, F., Porras-Alfaro, A., Gueidan, C., Beck, A., Andersen, B., Marek, S., Crouch, J.A., Kerrigan, J., Ristaino, J.B., Hodge, K.T., Kuldau, G., Samuels, G.J., Raja, H.J., Voglmayr, H., Gardes, M., Janos, D.P., Rogers, J.D., Cannon, P., Woolfolk, S.W., Kistler, H.C., Castellano, M.A., Maldonado-Ramírez, S.L., Kirk, P.M., Farrar, J.J., Osmundson, T., Currah, R.S., Vujanovic, V., Chen, W., Korf, R.P., Atallah, Z.K., Harrison, K.J., Guarro, J., Bates, S.T., Bonello, P., Bridge, P., Schell, W., Rossi, W., Stenlid, J., Frisvad, J.C., Miller, R.M., Baker, S.E., Hallen, H.E., Janso, J.E., Wilson, A.W., Conway, K.E., Egerton-Warburton, L., Wang, Z., Eastburn, D., Ho, W.W.H., Kroken, S., Stadler, M., Turgeon, G., Lichtwardt, R.W., Stewart, E.L., Wedin, M., Li, D-W., Uchida, J.Y., Jumpponen, A., Deckert, J., Beker, H.J., Rogers, S.O., Xu, J., Johnston, P., Shoemaker, R.A.,  Liu, M., Marques, G., Summerell, B., Sokolski, S., Thrane, U., Widden, P., Bruhn, J.N., Bianchinotti, V., Tuthill, D., Baroni, T.J., Barron, G., Hosaka, K. Preserving accuracy in GenBank. 2008. Science. 319: 1616.

Baker, S.E. and Bennett, J.W. An overview of the genus Aspergillus. 2008. In “The Aspergilli: Genomics, Medicine, Biotechnology and Research Methods.” Ed. G.H. Goldman and S. Osmani. CRC Press, Taylor and Francis, Boca Raton, Florida.

Baker, S.E. 2008. Aspergillus genomics and DHN-melanin conidial pigmentation. In “Aspergillus in the Genomics Era.” Eds. J. Varga and R. Samson. Wageningen Academic Publishers, Wageningen, The Netherlands.


Rokas, A., Payne, G., Fedorova, N.D., Baker, S.E., Machida, M., Yu, J., Georgianna, D.R., Dean, R.A., Bhatnagar, D., Cleveland, T.E., Wortman, J.R., Maiti, R.,  Joardar, V., Amedeo, P., Denning, D.W., Nierman, W.C. 2007. What can comparative genomics tell us about species concepts in the genus Aspergillus? Studies in Mycology. 59: 11-17.

Cuomo C.A., Güldener U., Xu J.R., Trail F., Turgeon B.G., Di Pietro A., Walton J.D., Ma L.J., Baker S.E., Rep M., Adam G., Antoniw J., Baldwin T., Calvo S., Chang Y.L., Decaprio D., Gale L.R., Gnerre S., Goswami R.S., Hammond-Kosack K., Harris L.J., Hilburn K., Kennell J.C., Kroken S., Magnuson J.K., Mannhaupt G., Mauceli E., Mewes H.W., Mitterbauer R., Muehlbauer G., Münsterkötter M., Nelson D., O'donnell K., Ouellet T., Qi W., Quesneville H., Roncero M.I., Seong K.Y., Tetko I.V., Urban M., Waalwijk C., Ward T.J., Yao J., Birren B.W., Kistler H.C. 2007. The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization. Science. 317: 1400-1402. 

Baker, S.E., Wend CF,  Martinez, D, Magnuson, JK, Panisko, EA, Dai, Z, Bruno, KS, Anderson, KK, Monroe, ME, Daly, DS, Lasure, LL. 2007. Genome and Proteome Analysis of Industrial Fungi. In "Exploitation of Fungi." Ed. G.D. Robson, P. van West, G.M. Gadd. Cambridge press, pgs 3-9.

Turgeon, B.G. and Baker, S.E. 2007.Genetic and genomic dissection of the Cochliobolus heterostrophus Tox1 locus controlling biosynthesis of the polyketide virulence factor T-toxin. Adv Genet. 57:219-61.


Hixson, K.K., Adkins, J.N., Baker, S.E., Moore, R.J., Chromy, B.A., Smith, R.D., McCutchen-Maloney, S.L., Lipton, M.S. 2006. Biomarker candidate identification in Yersinia pestis using organism wide semi-quantitative proteomics. Journal of Proteome Research. 5:3008-17.

Baker, SE. 2006. Aspergillus niger genomics: Past, present and into the future. Medical Mycology.  44:S17-21.

Baker, S.E., Kroken, S. Asvarak, T. Inderbitzin, P., Shi, L. Li, B.Y., Wang, X., Yoder, O.C., Turgeon, B.G. 2006. Two polyketide synthases are required for biosynthesis of the polyketide virulence factor, T-toxin, by Cochliobolus heterostrophus. MPMI, 19(2):139-49.


Lev S., Hadar R., Amedeo P., Baker S.E., Yoder O.C., Horwitz B.A. 2005. Activation of an AP1-like transcription factor of the maize pathogen Cochliobolus heterostrophus in response to oxidative stress and plant signals. Eukaryot. Cell. 4:443-54.


Baker, S.E., Lorenzen, J.A., Miller, S.W., Bunch, T.A., Jannuzi, A.L., Ginsberg, M., Perkins, L.A., Brower, D.L. 2002. Genetic interaction between integrins and moleskin, a gene encoding a Drosophila homologue of Importin-7. Genetics. 162:285-296.


Lorenzen, J.A., Baker, S.E., Denhez, F., Melnick, M.B., Brower, D.L., Perkins, L.A. 2001. Nuclear import of activated D-ERK by DIM-7, an importin family member encoded by the gene moleskin. Development. 128:1403-14.


Gonzales, M., Haan, K., Baker, S.E., Fitchmun, M.I., Todorov, I., Weitzman, S. and Jones, J.C.R. 1999. A cell signal pathway involving laminin-5, α3β1 integrin and MAP kinase can regulate epithelial cell proliferation. Mol. Biol. Cell, 10:259-270.


Brabant, M.C., Fristrom, D., Bunch, T.A., Baker, S.E. and Brower, D.L. 1998. The PS integrins are required for a regulatory event during Drosophila wing morphogenesis. Ann. New York Acad. Sci. 857:99-109.

Jones, J.C.R., Skalli, O., Goldman, R.D. and Baker, S.E. 1998. What links laminin-5 to the keratin cytoskeleton in epithelial cells? Biol. Bull. 194:371-3.

Baker, S.E. and Jones, J.C.R. 1998. Identification of a functional domain in laminin-5. Biol. Bull. 194:400-401.

Baker, S.E., Skalli, O., Goldman, R.D. and Jones, J.C.R. 1998. Laminin-5 and modulation of keratin cytoskeleton arrangement in epithelial cells: IFAP300 involvement and evidence for laminin-5 induced dephosphorylation of α6 integrin. Cell Mot. Cytoskel. 37:271-286.


Baker, S.E., DiPasquale, A., Stock, E.L., Plopper, G., Quaranta, V., Fitchmun, M., Jones, J.C.R. 1996. Morphogenetic effects and utility in organ culture of a soluble laminin variant, laminin-5R. Exp. Cell Res. 228:262-270.

Baker, S.E., DiPasquale, A., Stock, E.L., Plopper, G., Quaranta, V., Fitchmun, M. and Jones, J.C.R. 1996. Laminin-5 and hemidesmosomes: role of α3 chain subunit in hemidesmosome assembly. J. Cell Sci. 109:2509-2520.


Hopkinson, S.B., Baker, S.E. and Jones, J.C.R. 1995. Molecular genetic studies of a human epidermal autoantigen (the 180kD Bullous Pemphigoid antigen/BP180): identification of functionally important sequences within the BP180 molecule and evidence for an interaction between BP180 and alpha 6 integrin. J. Cell. Biol. 130:117-126.


Langhofer, M., Baker, S.E., Hopkinson, S.B., Jones, J.C.R. 1994. "Hemidesmosome: form, function and assembly" in Molecular Biology of Desmosomes and Hemidesmosomes. Collins, J.E. and Garrod, D.R., eds. R.G. Landes Co., Austin, pp. 69-86.

Jones, J.C.R., Asmuth, J., Baker, S.E., Langhofer, M., Roth, S.I. and Hopkinson, S.B. 1994. Hemidesmosomes: extracellular matrix/intermediate filament connectors. Exp. Cell Res. 213:1-11.