Castrillo J, Zeef L, Hoyle D, Zhang N, Hayes A, Gardner D, Cornell M, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn W, Broadhurst D, O'Donoghue K, Hester S, Dunkley T, Hart S, Swainston N, Li P, Gaskell S, Paton N, Lilley K, Kell D, Oliver S: Growth control of the eukaryote cell: a systems biology study in yeast. Journal of Biology. 2007, 6 (2): 4-10.1186/jbiol54.
Article
PubMed
PubMed Central
Google Scholar
Gutteridge A, Pir P, Castrillo J, Charles P, Lilley K, Oliver S: Nutrient control of eukaryote cell growth: a systems biology study in yeast. BMC biology. 2010, 8: 68-10.1186/1741-7007-8-68.
Article
PubMed
PubMed Central
CAS
Google Scholar
Goffeau A, Barrell B, Bussey H, Davis R, Dujon B, Feldmann H, Galibert F, Hoheisel J, Jacq C, Johnston M, Louis E, Mewes H, Murakami Y, Philippsen P, Tettelin H, Oliver S: Life with 6000 genes. Science. 1996, 274 (5287): 546-10.1126/science.274.5287.546.
Article
CAS
PubMed
Google Scholar
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, et al: Genome evolution in yeasts. Nature. 2004, 430 (6995): 35-44. 10.1038/nature02579.
Article
PubMed
Google Scholar
Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttilä M, Oliver S: Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC genomics. 2007, 8: 325-10.1186/1471-2164-8-325.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zaman S, Lippman S, Zhao X, Broach J: How Saccharomyces responds to nutrients. Annual review of genetics. 2008, 42: 27-81. 10.1146/annurev.genet.41.110306.130206.
Article
CAS
PubMed
Google Scholar
Usaite R, Jewett M, Oliveira A, Yates J, Olsson L, Nielsen J: Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Molecular Systems Biology. 2009, 5:
Google Scholar
Pokholok D, Harbison C, Levine S, Cole M, Hannett N, Lee T, Bell G, Walker K, Rolfe P, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford D, Young R: Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 2005, 122 (4): 517-527. 10.1016/j.cell.2005.06.026.
Article
CAS
PubMed
Google Scholar
Biddick R, Law G, Chin K, Young E: The transcriptional coactivators SAGA, SWI/SNF, and mediator make distinct contributions to activation of glucose-repressed genes. Journal of Biological Chemistry. 2008, 283 (48): 33101-10.1074/jbc.M805258200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rep M, Kistler H: The genomic organization of plant pathogenicity in Fusarium species. Current opinion in plant biology. 2010
Google Scholar
Coleman J, Rounsley S, Rodriguez-Carres M, Kuo A, Wasmann C, Grimwood J, Schmutz J, Taga M, White G, Zhou S, et al: The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet. 2009, 5 (8): e1000618-10.1371/journal.pgen.1000618.
Article
PubMed
PubMed Central
CAS
Google Scholar
Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, et al: Genome sequencing and analysis of Aspergillus oryzae. Nature. 2005, 438 (7071): 1157-1161. 10.1038/nature04300.
Article
PubMed
Google Scholar
Kämper J, Kahmann R, Bölker M, Ma L, Brefort T, Saville B, Banuett F, Kronstad J, Gold S, Müller O, et al: Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature. 2006, 444 (7115): 97-101. 10.1038/nature05248.
Article
PubMed
CAS
Google Scholar
Martinez D, Berka R, Henrissat B, Saloheimo M, Arvas M, Baker S, Chapman J, Chertkov O, Coutinho P, Cullen D, et al: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology. 2008, 26: 553-560. 10.1038/nbt1403.
Article
CAS
PubMed
Google Scholar
Fedorova N, Khaldi N, Joardar V, Maiti R, Amedeo P, Anderson M, Crabtree J, Silva J, Badger J, Albarraq A, et al: Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genetics. 2008, 4 (4): e1000046-10.1371/journal.pgen.1000046.
Article
PubMed
PubMed Central
CAS
Google Scholar
Stajich J, Wilke S, Ahrén D, Au C, Birren B, Borodovsky M, Burns C, Canbäck B, Casselton L, Cheng C, et al: Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences. 2010, 107 (26): 11889-10.1073/pnas.1003391107.
Article
CAS
Google Scholar
Rehmeyer C, Li W, Kusaba M, Kim YS, Brown D, Staben C, Dean R, Farman M: Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucl Acids Res. 2006, 34 (17): 4685-4701. 10.1093/nar/gkl588.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barton A, Pekosz M, Kurvathi R, Kaback D: Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae. Genetics. 2008, 179 (3): 1221-10.1534/genetics.107.083493.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kasuga T, Mannhaupt G, Glass N: Relationship between phylogenetic distribution and genomic features in Neurospora crassa. PLoS One. 2009, 4 (4): 5286-10.1371/journal.pone.0005286.
Article
CAS
Google Scholar
Tamano K, Sano M, Yamane N, Terabayashi Y, Toda T, Sunagawa M, Koike H, Hatamoto O, Umitsuki G, Takahashi T, Koyama Y, Asai R, Abe K, Machida M: Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation. Fungal Genetics and Biology. 2008, 45 (2): 139-151. 10.1016/j.fgb.2007.09.005.
Article
CAS
PubMed
Google Scholar
McDonagh A, Fedorova N, Crabtree J, Yu Y, Kim S, Chen D, Loss O, Cairns T, Goldman G, Armstrong-James D, Haynes K, Haas H, Schrettl M, May G, Nierman W, Bignell E: Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog. 2008, 4 (9): e1000154-10.1371/journal.ppat.1000154.
Article
PubMed
PubMed Central
CAS
Google Scholar
MacPherson S, Larochelle M, Turcotte B: A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiology and Molecular Biology Reviews. 2006, 70 (3): 583-10.1128/MMBR.00015-06.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keller N, Turner G, Bennett J: Fungal secondary metabolism - from biochemistry to genomics. Nature Reviews Microbiology. 2005, 3 (12): 937-947. 10.1038/nrmicro1286.
Article
CAS
PubMed
Google Scholar
Bok J, Chiang Y, Szewczyk E, Reyes-Dominguez Y, Davidson A, Sanchez J, Lo H, Watanabe K, Strauss J, Oakley B, Wang C, Keller N: Chromatin-level regulation of biosynthetic gene clusters. Nature chemical biology. 2009, 5 (7): 462-464. 10.1038/nchembio.177.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shwab E, Bok J, Tribus M, Galehr J, Graessle S, Keller N: Histone deacetylase activity regulates chemical diversity in Aspergillus. Eukaryotic Cell. 2007
Google Scholar
Bergmann S, Schumann J, Scherlach K, Lange C, Brakhage A, Hertweck C: Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nature chemical biology. 2007, 3 (4): 213-217.
Article
CAS
PubMed
Google Scholar
Roze L, Arthur A, Hong S, Chanda A, Linz J: The initiation and pattern of spread of histone H4 acetylation parallel the order of transcriptional activation of genes in the aflatoxin cluster. Molecular microbiology. 2007, 66 (3): 713-726. 10.1111/j.1365-2958.2007.05952.x.
Article
CAS
PubMed
Google Scholar
Cherry J, Fidantsef A: Directed evolution of industrial enzymes: an update. Current Opinion in Biotechnology. 2003, 14 (4): 438-443. 10.1016/S0958-1669(03)00099-5.
Article
CAS
PubMed
Google Scholar
Castillo F, Blanch H, Wilke C: Lactase production in continuous culture by Trichoderma reesei Rut-C30. Biotechnology letters. 1984, 6 (9): 593-596. 10.1007/BF00135688.
Article
CAS
Google Scholar
Chaudhuri B, Sahai V: Comparison of growth and maintenance parameters for cellulase biosynthesis by Trichoderma reesei-C5 with some published data. Enzyme and microbial technology. 1994, 16 (12): 1079-1083. 10.1016/0141-0229(94)90146-5.
Article
CAS
Google Scholar
Schafner D, Toledo R: Cellulase production in continuous culture by Trichoderma reesei on xylose-based media. Biotechnology and bioengineering. 1992, 39 (8): 865-869. 10.1002/bit.260390808.
Article
CAS
PubMed
Google Scholar
Pakula T, Salonen K, Uusitalo J, Penttilä M: The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei. Microbiology. 2005, 151: 135-143. 10.1099/mic.0.27458-0.
Article
CAS
PubMed
Google Scholar
Wiebe M, Robson G, Shuster J, Trinci A: Growth-rate-independent production of recombinant glucoamylase by Fusarium venenatum JeRS 325. Biotechnology and bioengineering. 2000, 68 (3): 245-251. 10.1002/(SICI)1097-0290(20000505)68:3<245::AID-BIT2>3.0.CO;2-F.
Article
CAS
PubMed
Google Scholar
Spohr A, Carlsen M, Nielsen J, Villadsen J: [alpha]-Amylase production in recombinant Aspergillus oryzae during fed-batch and continuous cultivations. Journal of Fermentation and Bioengineering. 1998, 86: 49-56. 10.1016/S0922-338X(98)80033-0.
Article
CAS
Google Scholar
Pedersen H, Beyer M, Nielsen J: Glucoamylase production in batch, chemostat and fed-batch cultivations by an industrial strain of Aspergillus niger. Applied microbiology and biotechnology. 2000, 53 (3): 272-277. 10.1007/s002530050020.
Article
CAS
PubMed
Google Scholar
Strauss J, Mach R, Zeilinger S, Hartler G, Stöffer G, Wolschek M, Kubicek C: Crel, the carbon catabolite repressor protein from Trichoderma reesei. FEBS letters. 1995, 376 (1-2): 103-107. 10.1016/0014-5793(95)01255-5.
Article
CAS
PubMed
Google Scholar
Seiboth B, Pakdaman B, Hartl L, Kubicek C: Lactose metabolism in filamentous fungi: how to deal with an unknown substrate. Fungal Biology Reviews. 2007, 21: 42-48. 10.1016/j.fbr.2007.02.006.
Article
Google Scholar
Kubicek C, Mikus M, Schuster A, Schmoll M, Seiboth B: Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina. Biotechnology for Biofuels. 2009, 2: 19-10.1186/1754-6834-2-19.
Article
PubMed
PubMed Central
CAS
Google Scholar
Daran-Lapujade P, Jansen M, Daran J, van Gulik W, de Winde J, Pronk J: Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. Journal of Biological Chemistry. 2004, 279 (10): 9125-10.1074/jbc.M309578200.
Article
CAS
PubMed
Google Scholar
Knijnenburg T, Daran J, Van Den Broek M, Daran-Lapujade P, De Winde J, Pronk J, Reinders M, Wessels L: Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data. BMC genomics. 2009, 10: 53-10.1186/1471-2164-10-53.
Article
PubMed
PubMed Central
CAS
Google Scholar
Saloheimo M, Valkonen M, M P: Activation mechanisms of the HAC1-mediated unfolded protein response in filamentous fungi. Mol Microbiol. 2003, 47 (4): 1149-61. 10.1046/j.1365-2958.2003.03363.x.
Article
CAS
PubMed
Google Scholar
Rautio JJ, Kataja K, Satokari R, Penttilä M, Soderlund H, Saloheimo M: Rapid and multiplexed transcript analysis of microbial cultures using capillary electophoresis-detectable oligonucleotide probe pools. Journal of microbiological methods. 2006, 65 (3): 404-416. 10.1016/j.mimet.2005.08.010.
Article
CAS
PubMed
Google Scholar
Anderson R, Bitterman K, Wood J, Medvedik O, Sinclair D: Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae. Nature. 2003, 423 (6936): 181-185. 10.1038/nature01578.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zembek P, Perlińska-Lenart U, Rawa K, Górka-Nieć W, Palamarczyk G, Kruszewska J: Cloning and functional analysis of the dpm2 and dpm3 genes from Trichoderma reesei expressed in a Saccharomyces cerevisiae dpm1Δ mutant strain. Biological Chemistry. 2011, 392 (6): 517-527. 10.1515/BC.2011.058.
Article
CAS
PubMed
Google Scholar
Saloheimo M, Lund M, Penttilä M: The protein disulphide isomerase gene of the fungus Trichoderma reesei is induced by endoplasmic reticulum stress and regulated by the carbon source. Molecular and General Genetics MGG. 1999, 262: 35-45. 10.1007/s004380051057.
Article
CAS
PubMed
Google Scholar
Patil K, Nielsen J: Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (8): 2685-10.1073/pnas.0406811102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lindfors E, Gopalacharyulu P, Halperin E, Orešič : Detection of Molecular Paths Associated with Insulitis and Type 1 Diabetes in Non-Obese Diabetic Mouse. PloS one. 2009, 4 (10): 7323-10.1371/journal.pone.0007323.
Article
CAS
Google Scholar
Andersen M, Nielsen M, Nielsen J: Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Molecular Systems Biology. 2008, 4:
Google Scholar
Ward T, Bielawski J, Kistler H, Sullivan E, O'Donnell K: Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium. Proceedings of the National Academy of Sciences of the United States of America. 2002, 99 (14): 9278-10.1073/pnas.142307199.
Article
CAS
PubMed
PubMed Central
Google Scholar
Torronen A, Mach R, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek C: The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Nature Biotechnology. 1992, 10 (11): 1461-1465. 10.1038/nbt1192-1461.
Article
CAS
Google Scholar
Moran-Diez E, Hermosa R, Ambrosino P, Cardoza R, Gutiérrez S, Lorito M, Monte E: The ThPG1 endopolygalacturonase is required for the Trichoderma harzianum-plant beneficial interaction. Molecular Plant-Microbe Interactions. 2009, 22 (8): 1021-1031. 10.1094/MPMI-22-8-1021.
Article
CAS
PubMed
Google Scholar
Ramos A, Chambergo F, Bonaccorsi E, Ferreira A, Cella N, Gombert A, Tonso A, El-Dorry H: Oxygen-and Glucose-Dependent Expression of Trhxt1, a Putative Glucose Transporter Gene of Trichoderma reesei. Biochemistry. 2006, 45 (26): 8184-8192. 10.1021/bi052553y.
Article
CAS
PubMed
Google Scholar
Shoemaker S, Schweickart V, Ladner M, Gelfand D, Kwok S, Myambo K, Innis M: Molecular Cloning of Exo-Cellobiohydrolase I Derived from Trichoderma Reesei Strain L27. Nature Biotechnology. 1983, 1 (8): 691-696. 10.1038/nbt1083-691.
Article
CAS
Google Scholar
Asp E, Sunnerhagen P: Mkp1 and Mkp2, two MAPKAP-kinase homologues in Schizosaccharomyces pombe, interact with the MAP kinase Sty1. Molecular Genetics and Genomics. 2003, 268 (5): 585-597.
CAS
PubMed
Google Scholar
Martin-Cuadrado A, Dueñas E, Sipiczki M, Vázquez A, Del Rey F: The endo-beta-1, 3-glucanase eng1p is required for dissolution of the primary septum during cell separation in Schizosaccharomyces pombe. Journal of cell science. 2003, 116 (Pt 9): 1689-
Article
CAS
PubMed
Google Scholar
Hong S, Horiuchi H, Ohta A: Molecular cloning of a phospholipase D gene from Aspergillus nidulans and characterization of its deletion mutants. FEMS microbiology letters. 2003, 224 (2): 231-237. 10.1016/S0378-1097(03)00440-3.
Article
CAS
PubMed
Google Scholar
Lee B, Han S, Choi H, Kim J, Han K, Han D: Screening of growth-or development-related genes by using genomic library with inducible promoter in Aspergillus nidulans. Journal of microbiology (Seoul, Korea). 2005, 43 (6): 523-
CAS
Google Scholar
Ohi M, Link A, Ren L, Jennings J, McDonald W, Gould K: Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Molecular and cellular biology. 2002, 22 (7): 2011-10.1128/MCB.22.7.2011-2024.2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arvas M, Haiminen N, Smit B, Rautio J, Vitikainen M, Wiebe M, Martinez D, Chee C, Kunkel J: Detecting novel genes with sparse arrays. Gene. 2010, 467: 41-51. 10.1016/j.gene.2010.07.009.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peterbauer C, Litscher D, Kubicek C: The Trichoderma atroviride seb1 (stress response element binding) gene encodes an AGGGG-binding protein which is involved in the response to high osmolarity stress. Molecular Genetics and Genomics. 2002, 268 (2): 223-231. 10.1007/s00438-002-0732-z.
Article
CAS
PubMed
Google Scholar
Seidl V, Seiboth B, Karaffa L, Kubicek C: The fungal STRE-element-binding protein Seb1 is involved but not essential for glycerol dehydrogenase (gld1) gene expression and glycerol accumulation in Trichoderma atroviride during osmotic stress. Fungal genetics and biology. 2004, 41 (12): 1132-1140. 10.1016/j.fgb.2004.09.002.
Article
CAS
PubMed
Google Scholar
Schmoll M: The information highways of a biotechnological workhorse - signal transduction in Hypocrea jecorina. BMC genomics. 2008, 9: 430-10.1186/1471-2164-9-430.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ruijter G, Bax M, Patel H, Flitter S, van de Vondervoort P, de Vries R, vanKuyk P, Visser J: Mannitol is required for stress tolerance in Aspergillus niger conidiospores. Eukaryotic Cell. 2003, 2 (4): 690-10.1128/EC.2.4.690-698.2003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kuorelahti S, Kalkkinen N, Penttilä M, Londesborough J, Richard P: Identification in the Mold Hypocrea jecorina of the First Fungal d-Galacturonic Acid Reductase. Biochemistry. 2005, 44 (33): 11234-11240. 10.1021/bi050792f.
Article
CAS
PubMed
Google Scholar
Hartl L, Seiboth B: Sequential gene deletions in Hypocrea jecorina using a single blaster cassette. Current genetics. 2005, 48 (3): 204-211. 10.1007/s00294-005-0011-8.
Article
CAS
PubMed
Google Scholar
Rautio J, Bailey M, Kivioja T, Soderlund H, Penttilä M, Saloheimo M: Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis. BMC biotechnology. 2007, 7: 28-10.1186/1472-6750-7-28.
Article
PubMed
PubMed Central
CAS
Google Scholar
Le Crom S, Schackwitz W, Pennacchio L, Magnuson J, Culley D, Collett J, Martin J, Druzhinina I, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek C, Baker S, Margeot A: Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proceedings of the National Academy of Sciences. 2009, 106 (38): 16151-10.1073/pnas.0905848106.
Article
CAS
Google Scholar
Vitikainen M, Arvas M, Pakula T, Oja M, Penttilä M, Saloheimo M: Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties. BMC genomics. 2010, 11: 441-10.1186/1471-2164-11-441.
Article
PubMed
PubMed Central
CAS
Google Scholar
Geysens S, Pakula T, Uusitalo J, Dewerte I, Penttila M, Contreras R: Cloning and characterization of the glucosidase II alpha subunit gene of Trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain Rut-C30. Applied and environmental microbiology. 2005, 71 (6): 2910-10.1128/AEM.71.6.2910-2924.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ilmen M, Thrane C, Penttilä M: The glucose repressor gene cre1 of Trichoderma: Isolation and expression of a full-length and a truncated mutant form. Molecular and General Genetics MGG. 1996, 251 (4): 451-460.
CAS
PubMed
Google Scholar
Pakula T, Laxell M, Huuskonen A, Uusitalo J, Saloheimo M, Penttilä M: The effects of drugs inhibiting protein secretion in the filamentous fungus Trichoderma reesei. Journal of Biological Chemistry. 2003, 278 (45): 45011-10.1074/jbc.M302372200.
Article
CAS
PubMed
Google Scholar
Patil C, Li H, Walter P: Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response. PLoS biology. 2004, 2: 1208-1223.
Article
CAS
Google Scholar
Arvas M, Pakula T, Lanthaler K, Saloheimo M, Valkonen M, Suortti T, Robson G, Penttilä M: Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC genomics. 2006, 7: 32-10.1186/1471-2164-7-32.
Article
PubMed
PubMed Central
CAS
Google Scholar
Collén A, Saloheimo M, Bailey M, Penttilä M, Pakula T: Protein production and induction of the unfolded protein response in Trichoderma reesei strain Rut-C30 and its transformant expressing endoglucanase I with a hydrophobic tag. Biotechnology and bioengineering. 2005, 89 (3): 335-344. 10.1002/bit.20350.
Article
PubMed
CAS
Google Scholar
Griffin T, Gygi S, Ideker T, Rist B, Eng J, Hood L, Aebersold R: Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics. 2002, 1 (4): 323-10.1074/mcp.M200001-MCP200.
Article
CAS
Google Scholar
Van De Peppel J, Kemmeren P, Van Bakel H, Radonjic M, Van Leenen D, Holstege F: Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO reports. 2003, 4 (4): 387-393. 10.1038/sj.embor.embor798.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mittal N, Scherrer T, Gerber A, Janga S: Interplay between post-transcriptional and post-translational interactions of RNA-binding proteins. Journal of Molecular Biology. 2011
Google Scholar
Castelli L, Lui J, Campbell S, Rowe W, Zeef L, Holmes L, Hoyle N, Bone J, Selley J, Sims P, Ashe M: Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated. Molecular Biology of the Cell. 2011, 22 (18): 3379-3393. 10.1091/mbc.E11-02-0153.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brockmann R, Beyer A, Heinisch J, Wilhelm T: Posttranscriptional expression regulation: what determines translation rates. PLoS Comput Biol. 2007, 3 (3): e57-10.1371/journal.pcbi.0030057.
Article
PubMed
PubMed Central
CAS
Google Scholar
Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R: Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology. 2011, 7:
Google Scholar
Cziferszky A, Seiboth B, Kubicek C: The Snf1 kinase of the filamentous fungus Hypocrea jecorina phosphorylates regulation-relevant serine residues in the yeast carbon catabolite repressor Mig1 but not in the filamentous fungal counterpart Cre1. Fungal Genetics and Biology. 2003, 40 (2): 166-175. 10.1016/S1087-1845(03)00082-3.
Article
CAS
PubMed
Google Scholar
Yu J, Chang P, Ehrlich K, Cary J, Bhatnagar D, Cleveland T, Payne G, Linz J, Woloshuk C, Bennett J: Clustered pathway genes in aflatoxin biosynthesis. Applied and Environmental Microbiology. 2004, 70 (3): 1253-10.1128/AEM.70.3.1253-1262.2004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colijn C, Brandes A, Zucker J, Lun D, Weiner B, Farhat M, Cheng T, Moody D, Murray M, Galagan J: Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS computational biology. 2009, 5 (8): e1000489-10.1371/journal.pcbi.1000489.
Article
PubMed
PubMed Central
CAS
Google Scholar
Alam M, Merlo M, Consortium S, Hodgson D, Wellington E, Takano E, Breitling R: Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC genomics. 2010, 11: 202-10.1186/1471-2164-11-202.
Article
PubMed
PubMed Central
CAS
Google Scholar
Plata G, Hsiao T, Olszewski K, Llinás M, Vitkup D: Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Molecular systems biology. 2010, 6:
Google Scholar
Sorokina O, Corellou F, Dauvillée D, Sorokin A, Goryanin I, Ball S, Bouget F, Millar A: Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. BMC Systems Biology. 2011, 5: 36-10.1186/1752-0509-5-36.
Article
PubMed
PubMed Central
Google Scholar
Chambergo F, Bonaccorsi E, Ferreira A, Ramos A, Ferreira J, Abrahaõ-Neto J, Farah J, El-Dorry H: Elucidation of the Metabolic Fate of Glucose in the Filamentous Fungus Trichoderma reesei Using Expressed Sequence Tag (EST) Analysis and cDNA Microarrays. Journal of Biological Chemistry. 2002, 277 (16): 13983-13988. 10.1074/jbc.M107651200.
Article
CAS
PubMed
Google Scholar
Maeda H, Sano M, Maruyama Y, Tanno T, Akao T, Totsuka Y, Endo M, Sakurada R, Yamagata Y, Machida M, Akita O, Hasegawa F, Abe K, Gomi K, Nakajima T: Transcriptional analysis of genes for energy catabolism and hydrolytic enzymes in the filamentous fungus Aspergillus oryzae using cDNA microarrays and expressed sequence tags. Applied microbiology and biotechnology. 2004, 65: 74-83.
Article
CAS
PubMed
Google Scholar
Xie X, Wilkinson H, Correa A, Lewis Z, Bell-Pedersen D, Ebbole D: Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genetics and Biology. 2004, 41 (12): 1104-1119. 10.1016/j.fgb.2004.08.009.
Article
CAS
PubMed
Google Scholar
Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch T: More than just orphans: are taxonomically-restricted genes important in evolution?. Trends in Genetics. 2009, 25 (9): 404-413. 10.1016/j.tig.2009.07.006.
Article
CAS
PubMed
Google Scholar
Kotte O, Zaugg J, Heinemann M: Bacterial adaptation through distributed sensing of metabolic fluxes. Molecular systems biology. 2010, 6:
Google Scholar
Wellen K, Hatzivassiliou G, Sachdeva U, Bui T, Cross J, Thompson C: ATP-citrate lyase links cellular metabolism to histone acetylation. Science. 2009, 324 (5930): 1076-10.1126/science.1164097.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nowrousian M, Kuck U, Loser K, Weltring K: The fungal acl1 and acl2 genes encode two polypeptides with homology to the N-and C-terminal parts of the animal ATP citrate lyase polypeptide. Current Genetics. 2000, 37 (3): 189-193. 10.1007/s002940050518.
Article
CAS
PubMed
Google Scholar
Hynes M, Murray S: ATP-Citrate Lyase Is Required for Production of Cytosolic Acetyl Coenzyme A and Development in Aspergillus nidulans. Eukaryotic Cell. 2010, 9 (7): 1039-10.1128/EC.00080-10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takahashi H, McCaffery J, Irizarry R, Boeke J: Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Molecular cell. 2006, 23 (2): 207-217. 10.1016/j.molcel.2006.05.040.
Article
CAS
PubMed
Google Scholar
Son H, Lee J, Park A, Lee Y: ATP citrate lyase is required for normal sexual and asexual development in Gibberella zeae. Fungal Genetics and Biology. 2011
Google Scholar
Abrahao Neto J, Rossini C, El-Gogary S, Henrique-Silva F, Crivellaro O, El-Dorry H: Mitochondrial functions mediate cellulase gene expression in Trichoderma reesei. Biochemistry. 1995, 34 (33): 10456-10462. 10.1021/bi00033a018.
Article
CAS
PubMed
Google Scholar
Reverberi M, Ricelli A, Zjalic S, Fabbri A, Fanelli C: Natural functions of mycotoxins and control of their biosynthesis in fungi. Applied microbiology and biotechnology. 2010, 87 (3): 899-911. 10.1007/s00253-010-2657-5.
Article
CAS
PubMed
Google Scholar
Roze L, Chanda A, Linz J: Compartmentalization and molecular traffic in secondary metabolism: A new understanding of established cellular processes. Fungal Genetics and Biology. 2010, 48: 35-48.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roze L, Chanda A, Laivenieks M, Beaudry R, Artymovich K, Koptina A, Awad D, Valeeva D, Jones A, Linz J: Volatile profiling reveals intracellular metabolic changes in Aspergillus parasiticus: veA regulates branched chain amino acid and ethanol metabolism. BMC biochemistry. 2010, 11: 33-10.1186/1471-2091-11-33.
Article
PubMed
PubMed Central
CAS
Google Scholar
Deckert J, Struhl K: Histone acetylation at promoters is differentially affected by specific activators and repressors. Molecular and Cellular Biology. 2001, 21 (8): 2726-10.1128/MCB.21.8.2726-2735.2001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Montenecourt BS, Eveleigh DE: Selective screening methods for the isolation of high yielding cellulase mutants of Trichoderma reesei. Advances in Chemistry Series. 1979, 181: 289-301.
Article
Google Scholar
Rautio J, Smit B, Wiebe M, Penttilä M, Saloheimo M: Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei. BMC Genomics. 2006, 7: 247-10.1186/1471-2164-7-247.
Article
PubMed
PubMed Central
CAS
Google Scholar
T. reesei genome sequence version 1.2 Database. [http://genome.jgi-psf.org/trire1/trire1.home.html]
T. reesei genome sequence version 2 Database. [http://genome.jgi-psf.org/Trire2/Trire2.home.html]
Poutanen M, Salusjärvi L, Ruohonen L, Penttilä M, Kalkkinen N: Use of matrix-assisted laser desorption/ionization time-of-flight mass mapping and nanospray liquid chromatography/electrospray ionization tandem mass spectrometry sequence tag analysis for high sensitivity identification of yeast proteins separated by two-dimensional gel electrophoresis. Rapid Communications in Mass Spectrometry. 2001, 15 (18): 1685-1692. 10.1002/rcm.424.
Article
CAS
PubMed
Google Scholar
Moulder R, Filén J, Salmi J, Katajamaa M, Nevalainen O, Oresic M, Aittokallio T, Lahesmaa R, Nyman T: A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics. 2005, 5 (11): 2748-2760. 10.1002/pmic.200401187.
Article
CAS
PubMed
Google Scholar
Pinheiro J, Bates D, DebRoy S, Sarkar D, Team RDC: nlme: Linear and Nonlinear Mixed Effects Models. 2010, [R package version 3.1-97]
Google Scholar
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R: InterProScan: protein domains identifier. Nucleic Acids Res. 2005, W116-20. 33 Web Server
Jensen L, Gupta R, Staerfeldt H, Brunak S: Prediction of human protein function according to Gene Ontology categories. Bioinformatics. 2003, 19 (5): 635-10.1093/bioinformatics/btg036.
Article
CAS
PubMed
Google Scholar
Emanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nature protocols. 2007, 2 (4): 953-971. 10.1038/nprot.2007.131.
Article
CAS
PubMed
Google Scholar
Gasparetti C, Faccio G, Arvas M, Buchert J, Saloheimo M, Kruus K: Discovery of a new tyrosinase-like enzyme family lacking a C-terminally processed domain: production and characterization of an Aspergillus oryzae catechol oxidase. Applied microbiology and biotechnology. 2010, 86: 213-226. 10.1007/s00253-009-2258-3.
Article
CAS
PubMed
Google Scholar
Saccharomyces Genome Database. [http://www.yeastgenome.org/]
Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes H: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research. 2004, 32 (18): 5539-10.1093/nar/gkh894.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goloboff P: Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics. 1999, 15 (4): 415-428. 10.1111/j.1096-0031.1999.tb00278.x.
Article
Google Scholar
Carbohydrate Active enZYmes Database. [http://www.cazy.org/]
Cantarel B, Coutinho P, Rancurel C, Bernard T, Lombard V, Henrissat B: The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic acids research. 2009, D233-37 Database
Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.
Article
CAS
PubMed
PubMed Central
Google Scholar
Geysens S, Whyteside G, Archer D: Genomics of protein folding in the endoplasmic reticulum, secretion stress and glycosylation in the aspergilli. Fungal Genetics and Biology. 2009, 46: S121-S140. 10.1016/j.fgb.2008.07.016.
Article
CAS
Google Scholar
R Development Core Team: R A Language and Environment for Statistical Computing. 2008, R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], [http://www.R-project.org]
Google Scholar
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J: Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
Article
PubMed
PubMed Central
Google Scholar
Irizarry R, Bolstad B, Collin F, Cope L, Hobbs B, Speed T: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research. 2003, 31 (4): e15-10.1093/nar/gng015.
Article
PubMed
PubMed Central
CAS
Google Scholar
Smyth G: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology. 2004, 3: 1027-
Article
Google Scholar
Storey J, Taylor J, Siegmund D: Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. Journal of the Royal Statistical Society Series B (Statistical Methodology). 2004, 66: 187-205. 10.1111/j.1467-9868.2004.00439.x.
Article
Google Scholar
Alon N, Yuster R, Zwick U: Color-coding. Journal of the ACM (JACM). 1995, 42 (4): 844-856. 10.1145/210332.210337.
Article
Google Scholar
Metz B, de Vries R, Polak S, Seidl V, Seiboth B: The Hypocrea jecorina (syn. Trichoderma reesei) lxr1 gene encodes a D-mannitol dehydrogenase and is not involved in L-arabinose catabolism. FEBS letters. 2009, 583 (8): 1309-1313. 10.1016/j.febslet.2009.03.027.
Article
CAS
PubMed
Google Scholar
Seiboth B, Hartl L, Pail M, Kubicek C: D-Xylose metabolism in Hypocrea jecorina: Loss of the xylitol dehydrogenase step can be partially compensated for by lad1-encoded L-arabinitol-4-dehydrogenase. Eukaryotic Cell. 2003, 2 (5): 867-10.1128/EC.2.5.867-875.2003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seiboth B, Gamauf C, Pail M, Hartl L, Kubicek C: The d-xylose reductase of Hypocrea jecorina is the major aldose reductase in pentose and d-galactose catabolism and necessary for β-galactosidase and cellulase induction by lactose. Molecular microbiology. 2007, 66 (4): 890-900. 10.1111/j.1365-2958.2007.05953.x.
Article
CAS
PubMed
Google Scholar
Richard P, Londesborough J, Putkonen M, Kalkkinen N, Penttilä M: Cloning and expression of a fungal L-arabinitol 4-dehydrogenase gene. Journal of Biological Chemistry. 2001, 276 (44): 40631-10.1074/jbc.M104022200.
Article
CAS
PubMed
Google Scholar
Seiboth B, Karaffa L, Sándor E, Kubicek C: The Hypocrea jecorina gal10 (uridine 5'-diphosphate-glucose 4-epimerase-encoding) gene differs from yeast homologues in structure, genomic organization and expression. Gene. 2002, 295: 143-149. 10.1016/S0378-1119(02)00834-X.
Article
CAS
PubMed
Google Scholar