-
1
-
-
84862229138
-
Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation
-
Adav S.S., Chao L.T., Sze S.K. Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Mol. Cell. Proteomics 2012, 11(M111):012419.
-
(2012)
Mol. Cell. Proteomics
, vol.11
, Issue.M111
, pp. 012419
-
-
Adav, S.S.1
Chao, L.T.2
Sze, S.K.3
-
2
-
-
84891930378
-
A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations
-
Benz J.P., Chau B.H., Zheng D., Bauer S., Glass N.L., Somerville C.R. A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations. Mol. Microbiol. 2014, 91:275-299.
-
(2014)
Mol. Microbiol.
, vol.91
, pp. 275-299
-
-
Benz, J.P.1
Chau, B.H.2
Zheng, D.3
Bauer, S.4
Glass, N.L.5
Somerville, C.R.6
-
3
-
-
84897671128
-
Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes
-
Benz J.P., Protzko R.J., Andrich J.M.S., Bauer S., Dueber J.E., Somerville C.R. Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes. Biotechnol. Biofuels 2014, 7:20.
-
(2014)
Biotechnol. Biofuels
, vol.7
, pp. 20
-
-
Benz, J.P.1
Protzko, R.J.2
Andrich, J.M.S.3
Bauer, S.4
Dueber, J.E.5
Somerville, C.R.6
-
4
-
-
36048974163
-
Xyr1 regulates xylanase but not cellulase formation in the head blight fungus Fusarium graminearum
-
Brunner K., Lichtenauer A.M., Kratochwill K., Delic M., Mach R.L. Xyr1 regulates xylanase but not cellulase formation in the head blight fungus Fusarium graminearum. Curr. Genet. 2007, 52:213-220.
-
(2007)
Curr. Genet.
, vol.52
, pp. 213-220
-
-
Brunner, K.1
Lichtenauer, A.M.2
Kratochwill, K.3
Delic, M.4
Mach, R.L.5
-
5
-
-
80053927149
-
Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures
-
Chundawat S.P., Lipton M.S., Purvine S.O., Uppugundla N., Gao D., Balan V., Dale B.E. Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures. J. Proteome Res. 2011, 10:4365-4372.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 4365-4372
-
-
Chundawat, S.P.1
Lipton, M.S.2
Purvine, S.O.3
Uppugundla, N.4
Gao, D.5
Balan, V.6
Dale, B.E.7
-
6
-
-
0034383949
-
The regulation of protein function by multisite phosphorylation - a 25 year update
-
Cohen P. The regulation of protein function by multisite phosphorylation - a 25 year update. Trends Biochem. Sci. 2000, 25:596-601.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 596-601
-
-
Cohen, P.1
-
7
-
-
84860805742
-
Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi
-
Coradetti S.T., Craig J.P., Xiong Y., Shock T., Tian C., Glass N.L. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proc. Natl. Acad. Sci. USA 2012, 109:7397-7402.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 7397-7402
-
-
Coradetti, S.T.1
Craig, J.P.2
Xiong, Y.3
Shock, T.4
Tian, C.5
Glass, N.L.6
-
8
-
-
84893450996
-
Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa
-
Coradetti S.T., Xiong Y., Glass N.L. Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa. Microbiologyopen 2013, 2:595-609.
-
(2013)
Microbiologyopen
, vol.2
, pp. 595-609
-
-
Coradetti, S.T.1
Xiong, Y.2
Glass, N.L.3
-
9
-
-
0037177862
-
Phosphorylation positively regulates DNA binding of the carbon catabolite repressor Cre1 of Hypocrea jecorina (Trichoderma reesei)
-
Cziferszky A., Mach R.L., Kubicek C.P. Phosphorylation positively regulates DNA binding of the carbon catabolite repressor Cre1 of Hypocrea jecorina (Trichoderma reesei). J. Biol. Chem. 2002, 277:14688-14694.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 14688-14694
-
-
Cziferszky, A.1
Mach, R.L.2
Kubicek, C.P.3
-
10
-
-
0038187312
-
Genetic evidence for the heterodimeric structure of glucosidase II. The effect of disrupting the subunit-encoding genes on glycoprotein folding
-
D'Alessio C., Fernandez F., Trombetta E.S., Parodi A.J. Genetic evidence for the heterodimeric structure of glucosidase II. The effect of disrupting the subunit-encoding genes on glycoprotein folding. J. Biol. Chem. 1999, 274:25899-25905.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 25899-25905
-
-
D'Alessio, C.1
Fernandez, F.2
Trombetta, E.S.3
Parodi, A.J.4
-
11
-
-
55249096894
-
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
-
de Godoy L.M., Olsen J.V., Cox J., Nielsen M.L., Hubner N.C., Frohlich F., Walther T.C., Mann M. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455:1251-1254.
-
(2008)
Nature
, vol.455
, pp. 1251-1254
-
-
de Godoy, L.M.1
Olsen, J.V.2
Cox, J.3
Nielsen, M.L.4
Hubner, N.C.5
Frohlich, F.6
Walther, T.C.7
Mann, M.8
-
12
-
-
79959214917
-
Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose
-
de Oliveira J.M., van Passel M.W., Schaap P.J., de Graaff L.H. Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose. PLoS ONE 2011, 6:e20865.
-
(2011)
PLoS ONE
, vol.6
, pp. e20865
-
-
de Oliveira, J.M.1
van Passel, M.W.2
Schaap, P.J.3
de Graaff, L.H.4
-
13
-
-
84866145069
-
Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing
-
Delmas S., Pullan S.T., Gaddipati S., Kokolski M., Malla S., Blythe M.J., Ibbett R., Campbell M., Liddell S., Aboobaker A., Tucker G.A., Archer D.B. Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet. 2012, 8:e1002875.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002875
-
-
Delmas, S.1
Pullan, S.T.2
Gaddipati, S.3
Kokolski, M.4
Malla, S.5
Blythe, M.J.6
Ibbett, R.7
Campbell, M.8
Liddell, S.9
Aboobaker, A.10
Tucker, G.A.11
Archer, D.B.12
-
14
-
-
84876886672
-
Mutation of the Xylanase regulator 1 causes a glucose blind hydrolase expressing phenotype in industrially used Trichoderma strains
-
Derntl C., Gudynaite-Savitch L., Calixte S., White T., Mach R.L., Mach-Aigner A.R. Mutation of the Xylanase regulator 1 causes a glucose blind hydrolase expressing phenotype in industrially used Trichoderma strains. Biotechnol. Biofuels 2013, 6:62.
-
(2013)
Biotechnol. Biofuels
, vol.6
, pp. 62
-
-
Derntl, C.1
Gudynaite-Savitch, L.2
Calixte, S.3
White, T.4
Mach, R.L.5
Mach-Aigner, A.R.6
-
15
-
-
84865534061
-
Secretome analysis of the fungus Trichoderma harzianum grown on cellulose
-
Do Vale L.H., Gomez-Mendoza D.P., Kim M.S., Pandey A., Ricart C.A., Ximenes F.F.E., Sousa M.V. Secretome analysis of the fungus Trichoderma harzianum grown on cellulose. Proteomics 2012, 12:2716-2728.
-
(2012)
Proteomics
, vol.12
, pp. 2716-2728
-
-
Do Vale, L.H.1
Gomez-Mendoza, D.P.2
Kim, M.S.3
Pandey, A.4
Ricart, C.A.5
Ximenes, F.F.E.6
Sousa, M.V.7
-
16
-
-
0031742219
-
Carbon catabolite repression of gene expression and conidiation in Neurospora crassa
-
Ebbole D.J. Carbon catabolite repression of gene expression and conidiation in Neurospora crassa. Fungal Genet. Biol. 1998, 25:15-21.
-
(1998)
Fungal Genet. Biol.
, vol.25
, pp. 15-21
-
-
Ebbole, D.J.1
-
17
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng J.K., McCormack A.L., Yates J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
-
(1994)
J. Am. Soc. Mass Spectrom.
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates, J.R.3
-
18
-
-
48849113878
-
Comparative protein structure modeling using MODELLER
-
Chapter 2, Unit 2 9
-
Eswar N., Webb B., Marti-Renom M.A., Madhusudhan M.S., Eramian D., Shen M.Y., Pieper U., Sali A. Comparative protein structure modeling using MODELLER. Curr. Protoc. Protein Sci. 2007, Chapter 2, Unit 2 9.
-
(2007)
Curr. Protoc. Protein Sci.
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.Y.6
Pieper, U.7
Sali, A.8
-
19
-
-
33846268455
-
The Saccharomyces cerevisiae YFR041C/ERJ5 gene encoding a type I membrane protein with a J domain is required to preserve the folding capacity of the endoplasmic reticulum
-
Fama M.C., Raden D., Zacchi N., Lemos D.R., Robinson A.S., Silberstein S. The Saccharomyces cerevisiae YFR041C/ERJ5 gene encoding a type I membrane protein with a J domain is required to preserve the folding capacity of the endoplasmic reticulum. Mol. Cell Res. 2007, 1773:232-242.
-
(2007)
Mol. Cell Res.
, vol.1773
, pp. 232-242
-
-
Fama, M.C.1
Raden, D.2
Zacchi, N.3
Lemos, D.R.4
Robinson, A.S.5
Silberstein, S.6
-
20
-
-
84863636068
-
Principles of carbon catabolite repression in the rice blast fungus: Tps1, Nmr1-3, and a MATE-family pump regulate glucose metabolism during infection
-
Fernandez J., Wright J.D., Hartline D., Quispe C.F., Madayiputhiya N., Wilson R.A. Principles of carbon catabolite repression in the rice blast fungus: Tps1, Nmr1-3, and a MATE-family pump regulate glucose metabolism during infection. PLoS Genet. 2012, 8:e1002673.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002673
-
-
Fernandez, J.1
Wright, J.D.2
Hartline, D.3
Quispe, C.F.4
Madayiputhiya, N.5
Wilson, R.A.6
-
21
-
-
66349093926
-
Magnetic bead processor for rapid evaluation and optimization of parameters for phosphopeptide enrichment
-
Ficarro S.B., Adelmant G., Tomar M.N., Zhang Y., Cheng V.J., Marto J.A. Magnetic bead processor for rapid evaluation and optimization of parameters for phosphopeptide enrichment. Anal. Chem. 2009, 81:4566-4575.
-
(2009)
Anal. Chem.
, vol.81
, pp. 4566-4575
-
-
Ficarro, S.B.1
Adelmant, G.2
Tomar, M.N.3
Zhang, Y.4
Cheng, V.J.5
Marto, J.A.6
-
22
-
-
76649110552
-
Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin
-
Fournier M.L., Paulson A., Pavelka N., Mosley A.L., Gaudenz K., Bradford W.D., Glynn E., Li H., Sardiu M.E., Fleharty B., Seidel C., Florens L., Washburn M.P. Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol. Cell. Proteomics 2010, 9:271-284.
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 271-284
-
-
Fournier, M.L.1
Paulson, A.2
Pavelka, N.3
Mosley, A.L.4
Gaudenz, K.5
Bradford, W.D.6
Glynn, E.7
Li, H.8
Sardiu, M.E.9
Fleharty, B.10
Seidel, C.11
Florens, L.12
Washburn, M.P.13
-
23
-
-
77957347059
-
Cellodextrin transport in yeast for improved biofuel production
-
Galazka J.M., Tian C., Beeson W.T., Martinez B., Glass N.L., Cate J.H. Cellodextrin transport in yeast for improved biofuel production. Science 2010, 330:84-86.
-
(2010)
Science
, vol.330
, pp. 84-86
-
-
Galazka, J.M.1
Tian, C.2
Beeson, W.T.3
Martinez, B.4
Glass, N.L.5
Cate, J.H.6
-
24
-
-
60649098811
-
Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains
-
Herpoel-Gimbert I., Margeot A., Dolla A., Jan G., Molle D., Lignon S., Mathis H., Sigoillot J.C., Monot F., Asther M. Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains. Biotechnol. Biofuels 2008, 1:18.
-
(2008)
Biotechnol. Biofuels
, vol.1
, pp. 18
-
-
Herpoel-Gimbert, I.1
Margeot, A.2
Dolla, A.3
Jan, G.4
Molle, D.5
Lignon, S.6
Mathis, H.7
Sigoillot, J.C.8
Monot, F.9
Asther, M.10
-
25
-
-
14844363721
-
Signaling by target of rapamycin proteins in cell growth control
-
Inoki K., Ouyang H., Li Y., Guan K.L. Signaling by target of rapamycin proteins in cell growth control. Microbiol. Mol. Biol. Rev. 2005, 69:79-100.
-
(2005)
Microbiol. Mol. Biol. Rev.
, vol.69
, pp. 79-100
-
-
Inoki, K.1
Ouyang, H.2
Li, Y.3
Guan, K.L.4
-
26
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001, 305:567-580.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.4
-
27
-
-
84865561632
-
Microbial cellulases and their industrial applications
-
Kuhad R.C., Gupta R., Singh A. Microbial cellulases and their industrial applications. Enzyme Res. 2011, 2011:280696.
-
(2011)
Enzyme Res.
, vol.2011
, pp. 280696
-
-
Kuhad, R.C.1
Gupta, R.2
Singh, A.3
-
28
-
-
0028675509
-
Molecular taxonomy of the yeasts
-
Kurtzman C.P. Molecular taxonomy of the yeasts. Yeast 1994, 10:1727-1740.
-
(1994)
Yeast
, vol.10
, pp. 1727-1740
-
-
Kurtzman, C.P.1
-
29
-
-
70349482673
-
Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing
-
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. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc. Natl. Acad. Sci. USA 2009, 106:16151-16156.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 16151-16156
-
-
Le Crom, S.1
Schackwitz, W.2
Pennacchio, L.3
Magnuson, J.K.4
Culley, D.E.5
Collett, J.R.6
Martin, J.7
Druzhinina, I.S.8
Mathis, H.9
Monot, F.10
Seiboth, B.11
Cherry, B.12
Rey, M.13
Berka, R.14
Kubicek, C.P.15
Baker, S.E.16
Margeot, A.17
-
30
-
-
79960581086
-
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
-
Lee M.V., Topper S.E., Hubler S.L., Hose J., Wenger C.D., Coon J.J., Gasch A.P. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol. Syst. Biol. 2011, 7:514.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 514
-
-
Lee, M.V.1
Topper, S.E.2
Hubler, S.L.3
Hose, J.4
Wenger, C.D.5
Coon, J.J.6
Gasch, A.P.7
-
31
-
-
84885436956
-
Secretome diversity and quantitative analysis of cellulolytic Aspergillus fumigatus Z5 in the presence of different carbon sources
-
Liu D., Li J., Zhao S., Zhang R., Wang M., Miao Y., Shen Y., Shen Q. Secretome diversity and quantitative analysis of cellulolytic Aspergillus fumigatus Z5 in the presence of different carbon sources. Biotechnol. Biofuels 2013, 6:149.
-
(2013)
Biotechnol. Biofuels
, vol.6
, pp. 149
-
-
Liu, D.1
Li, J.2
Zhao, S.3
Zhang, R.4
Wang, M.5
Miao, Y.6
Shen, Y.7
Shen, Q.8
-
32
-
-
84875769164
-
Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes
-
Liu G., Zhang L., Qin Y., Zou G., Li Z., Yan X., Wei X., Chen M., Chen L., Zheng K., Zhang J., Ma L., Li J., Liu R., Xu H., Bao X., Fang X., Wang L., Zhong Y., Liu W., Zheng H., Wang S., Wang C., Xun L., Zhao G.P., Wang T., Zhou Z., Qu Y. Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes. Sci. Rep. 2013, 3:1569.
-
(2013)
Sci. Rep.
, vol.3
, pp. 1569
-
-
Liu, G.1
Zhang, L.2
Qin, Y.3
Zou, G.4
Li, Z.5
Yan, X.6
Wei, X.7
Chen, M.8
Chen, L.9
Zheng, K.10
Zhang, J.11
Ma, L.12
Li, J.13
Liu, R.14
Xu, H.15
Bao, X.16
Fang, X.17
Wang, L.18
Zhong, Y.19
Liu, W.20
Zheng, H.21
Wang, S.22
Wang, C.23
Xun, L.24
Zhao, G.P.25
Wang, T.26
Zhou, Z.27
Qu, Y.28
more..
-
33
-
-
0036753494
-
Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control
-
Loewith R., Jacinto E., Wullschleger S., Lorberg A., Crespo J.L., Bonenfant D., Oppliger W., Jenoe P., Hall M.N. Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol. Cell 2002, 10:457-468.
-
(2002)
Mol. Cell
, vol.10
, pp. 457-468
-
-
Loewith, R.1
Jacinto, E.2
Wullschleger, S.3
Lorberg, A.4
Crespo, J.L.5
Bonenfant, D.6
Oppliger, W.7
Jenoe, P.8
Hall, M.N.9
-
34
-
-
78650642557
-
Defining the transcriptome and proteome in three functionally different human cell lines
-
Lundberg E., Fagerberg L., Klevebring D., Matic I., Geiger T., Cox J., Algenas C., Lundeberg J., Mann M., Uhlen M. Defining the transcriptome and proteome in three functionally different human cell lines. Mol. Syst. Biol. 2010, 6:450.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 450
-
-
Lundberg, E.1
Fagerberg, L.2
Klevebring, D.3
Matic, I.4
Geiger, T.5
Cox, J.6
Algenas, C.7
Lundeberg, J.8
Mann, M.9
Uhlen, M.10
-
35
-
-
55049124006
-
Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina
-
Mach-Aigner A.R., Pucher M.E., Steiger M.G., Bauer G.E., Preis S.J., Mach R.L. Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Appl. Environ. Microbiol. 2008, 74:6554-6562.
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 6554-6562
-
-
Mach-Aigner, A.R.1
Pucher, M.E.2
Steiger, M.G.3
Bauer, G.E.4
Preis, S.J.5
Mach, R.L.6
-
36
-
-
71149108056
-
Correlation of mRNA and protein in complex biological samples
-
Maier T., Guell M., Serrano L. Correlation of mRNA and protein in complex biological samples. FEBS Lett. 2009, 583:3966-3973.
-
(2009)
FEBS Lett.
, vol.583
, pp. 3966-3973
-
-
Maier, T.1
Guell, M.2
Serrano, L.3
-
37
-
-
0037032835
-
The protein kinase complement of the human genome
-
Manning G., Whyte D.B., Martinez R., Hunter T., Sudarsanam S. The protein kinase complement of the human genome. Science 2002, 298:1912-1934.
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
38
-
-
0002934149
-
Improved plasmids for gene targeting at the his-3 locus of Neurospora crassa by electroporation
-
Margolin B.S., Freitag M., Selker E.U. Improved plasmids for gene targeting at the his-3 locus of Neurospora crassa by electroporation. Fungal Genet. Newslett. 1997, 44:34-36.
-
(1997)
Fungal Genet. Newslett.
, vol.44
, pp. 34-36
-
-
Margolin, B.S.1
Freitag, M.2
Selker, E.U.3
-
39
-
-
0024271454
-
Isolation and characterization of a Neurospora glucose-repressible gene
-
McNally M.T., Free S.J. Isolation and characterization of a Neurospora glucose-repressible gene. Curr. Genet. 1988, 14:545-551.
-
(1988)
Curr. Genet.
, vol.14
, pp. 545-551
-
-
McNally, M.T.1
Free, S.J.2
-
40
-
-
43249087428
-
MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features
-
Monroe M.E., Shaw J.L., Daly D.S., Adkins J.N., Smith R.D. MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Comput. Biol. Chem. 2008, 32:215-217.
-
(2008)
Comput. Biol. Chem.
, vol.32
, pp. 215-217
-
-
Monroe, M.E.1
Shaw, J.L.2
Daly, D.S.3
Adkins, J.N.4
Smith, R.D.5
-
41
-
-
84869206637
-
Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum
-
Nguyen T.H., Brechenmacher L., Aldrich J.T., Clauss T.R., Gritsenko M.A., Hixson K.K., Libault M., Tanaka K., Yang F., Yao Q., Pasa-Tolic L., Xu D., Nguyen H.T., Stacey G. Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum. Mol. Cell. Proteomics 2012, 11:1140-1155.
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1140-1155
-
-
Nguyen, T.H.1
Brechenmacher, L.2
Aldrich, J.T.3
Clauss, T.R.4
Gritsenko, M.A.5
Hixson, K.K.6
Libault, M.7
Tanaka, K.8
Yang, F.9
Yao, Q.10
Pasa-Tolic, L.11
Xu, D.12
Nguyen, H.T.13
Stacey, G.14
-
42
-
-
79957857260
-
Xylose triggers reversible phosphorylation of XlnR, the fungal transcriptional activator of xylanolytic and cellulolytic genes in Aspergillus oryzae
-
Noguchi Y., Tanaka H., Kanamaru K., Kato M., Kobayashi T. Xylose triggers reversible phosphorylation of XlnR, the fungal transcriptional activator of xylanolytic and cellulolytic genes in Aspergillus oryzae. Biosci. Biotechnol. Biochem. 2011, 75:953-959.
-
(2011)
Biosci. Biotechnol. Biochem.
, vol.75
, pp. 953-959
-
-
Noguchi, Y.1
Tanaka, H.2
Kanamaru, K.3
Kato, M.4
Kobayashi, T.5
-
43
-
-
84875439343
-
ManR, a transcriptional regulator of the beta-mannan utilization system, controls the cellulose utilization system in Aspergillus oryzae
-
Ogawa M., Kobayashi T., Koyama Y. ManR, a transcriptional regulator of the beta-mannan utilization system, controls the cellulose utilization system in Aspergillus oryzae. Biosci. Biotechnol. Biochem. 2013, 77:426-429.
-
(2013)
Biosci. Biotechnol. Biochem.
, vol.77
, pp. 426-429
-
-
Ogawa, M.1
Kobayashi, T.2
Koyama, Y.3
-
44
-
-
0032572527
-
A functional GTPase domain, but not its transmembrane domain, is required for function of the SRP receptor beta-subunit
-
Ogg S.C., Barz W.P., Walter P. A functional GTPase domain, but not its transmembrane domain, is required for function of the SRP receptor beta-subunit. J. Cell Biol. 1998, 142:341-354.
-
(1998)
J. Cell Biol.
, vol.142
, pp. 341-354
-
-
Ogg, S.C.1
Barz, W.P.2
Walter, P.3
-
45
-
-
80052450370
-
Quantitative proteomic approach for cellulose degradation by Neurospora crassa
-
Phillips C.M., Iavarone A.T., Marletta M.A. Quantitative proteomic approach for cellulose degradation by Neurospora crassa. J. Proteome Res. 2011, 10:4177-4185.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 4177-4185
-
-
Phillips, C.M.1
Iavarone, A.T.2
Marletta, M.A.3
-
46
-
-
84876377014
-
Single nucleotide polymorphism analysis of a Trichoderma reesei hyper-cellulolytic mutant developed in Japan
-
Porciuncula Jde O., Furukawa T., Mori K., Shida Y., Hirakawa H., Tashiro K., Kuhara S., Nakagawa S., Morikawa Y., Ogasawara W. Single nucleotide polymorphism analysis of a Trichoderma reesei hyper-cellulolytic mutant developed in Japan. Biosci. Biotechnol. Biochem. 2013, 77:534-543.
-
(2013)
Biosci. Biotechnol. Biochem.
, vol.77
, pp. 534-543
-
-
Porciuncula Jde, O.1
Furukawa, T.2
Mori, K.3
Shida, Y.4
Hirakawa, H.5
Tashiro, K.6
Kuhara, S.7
Nakagawa, S.8
Morikawa, Y.9
Ogasawara, W.10
-
47
-
-
36749001066
-
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes
-
Rapoport T.A. Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 2007, 450:663-669.
-
(2007)
Nature
, vol.450
, pp. 663-669
-
-
Rapoport, T.A.1
-
48
-
-
84881161294
-
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger
-
Ries L., Pullan S., Delmas S., Malla S., Blythe M., Archer D.B. Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. BMC Genomics 2013, 14:541.
-
(2013)
BMC Genomics
, vol.14
, pp. 541
-
-
Ries, L.1
Pullan, S.2
Delmas, S.3
Malla, S.4
Blythe, M.5
Archer, D.B.6
-
49
-
-
9144257282
-
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
-
Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., Tetko I., Guldener U., Mannhaupt G., Munsterkotter M., Mewes H.W. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004, 32:5539-5545.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5539-5545
-
-
Ruepp, A.1
Zollner, A.2
Maier, D.3
Albermann, K.4
Hani, J.5
Mokrejs, M.6
Tetko, I.7
Guldener, U.8
Mannhaupt, G.9
Munsterkotter, M.10
Mewes, H.W.11
-
50
-
-
0025790341
-
GAL4 is phosphorylated as a consequence of transcriptional activation
-
Sadowski I., Niedbala D., Wood K., Ptashne M. GAL4 is phosphorylated as a consequence of transcriptional activation. Proc. Natl. Acad. Sci. USA 1991, 88:10510-10514.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 10510-10514
-
-
Sadowski, I.1
Niedbala, D.2
Wood, K.3
Ptashne, M.4
-
51
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhausser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., Chen W., Selbach M. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhausser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
Wolf, J.6
Chen, W.7
Selbach, M.8
-
52
-
-
84892563850
-
Human-like eukaryotic translation initiation factor 3 from Neurospora crassa
-
Smith M.D., Gu Y., Querol-Audi J., Vogan J.M., Nitido A., Cate J.H. Human-like eukaryotic translation initiation factor 3 from Neurospora crassa. PLoS ONE 2013, 8:e78715.
-
(2013)
PLoS ONE
, vol.8
, pp. e78715
-
-
Smith, M.D.1
Gu, Y.2
Querol-Audi, J.3
Vogan, J.M.4
Nitido, A.5
Cate, J.H.6
-
53
-
-
0035660414
-
Effects of calnexin deletion in Saccharomyces cerevisiae on the secretion of glycosylated lysozymes
-
Song Y., Sata J., Saito A., Usui M., Azakami H., Kato A. Effects of calnexin deletion in Saccharomyces cerevisiae on the secretion of glycosylated lysozymes. J. Biochem. 2001, 130:757-764.
-
(2001)
J. Biochem.
, vol.130
, pp. 757-764
-
-
Song, Y.1
Sata, J.2
Saito, A.3
Usui, M.4
Azakami, H.5
Kato, A.6
-
54
-
-
38649100624
-
Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei)
-
Stricker A.R., Mach R.L., de Graaff L.H. Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Appl. Microbiol. Biotechnol. 2008, 78:211-220.
-
(2008)
Appl. Microbiol. Biotechnol.
, vol.78
, pp. 211-220
-
-
Stricker, A.R.1
Mach, R.L.2
de Graaff, L.H.3
-
55
-
-
84859143948
-
Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa
-
Sun J., Tian C., Diamond S., Glass N.L. Deciphering transcriptional regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa. Eukaryot. Cell 2012, 11:482-493.
-
(2012)
Eukaryot. Cell
, vol.11
, pp. 482-493
-
-
Sun, J.1
Tian, C.2
Diamond, S.3
Glass, N.L.4
-
56
-
-
84867657593
-
Crystal structure of a bacterial homologue of glucose transporters GLUT1-4
-
Sun L., Zeng X., Yan C., Sun X., Gong X., Rao Y., Yan N. Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature 2012, 490:361-366.
-
(2012)
Nature
, vol.490
, pp. 361-366
-
-
Sun, L.1
Zeng, X.2
Yan, C.3
Sun, X.4
Gong, X.5
Rao, Y.6
Yan, N.7
-
57
-
-
84901625675
-
Complex regulation of hydrolytic enzyme genes for cellulosic biomass degradation in filamentous fungi
-
Tani S., Kawaguchi T., Kobayashi T. Complex regulation of hydrolytic enzyme genes for cellulosic biomass degradation in filamentous fungi. Appl. Microbiol. Biotechnol. 2014, 10.1007/s00253-014-5707-6.
-
(2014)
Appl. Microbiol. Biotechnol.
-
-
Tani, S.1
Kawaguchi, T.2
Kobayashi, T.3
-
58
-
-
77955102352
-
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y., Choi P.J., Li G.W., Chen H., Babu M., Hearn J., Emili A., Xie X.S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-538.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.W.3
Chen, H.4
Babu, M.5
Hearn, J.6
Emili, A.7
Xie, X.S.8
-
59
-
-
0031660773
-
The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger
-
van Peij N.N., Gielkens M.M., de Vries R.P., Visser J., de Graaff L.H. The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger. Appl. Environ. Microbiol. 1998, 64:3615-3619.
-
(1998)
Appl. Environ. Microbiol.
, vol.64
, pp. 3615-3619
-
-
van Peij, N.N.1
Gielkens, M.M.2
de Vries, R.P.3
Visser, J.4
de Graaff, L.H.5
-
60
-
-
77956261738
-
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
-
Vogel C., Abreu Rde S., Ko D., Le S.Y., Shapiro B.A., Burns S.C., Sandhu D., Boutz D.R., Marcotte E.M., Penalva L.O. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol. Syst. Biol. 2010, 6:400.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 400
-
-
Vogel, C.1
Abreu Rde, S.2
Ko, D.3
Le, S.Y.4
Shapiro, B.A.5
Burns, S.C.6
Sandhu, D.7
Boutz, D.R.8
Marcotte, E.M.9
Penalva, L.O.10
-
61
-
-
84858439862
-
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
-
Vogel C., Marcotte E.M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 2012, 13:227-232.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 227-232
-
-
Vogel, C.1
Marcotte, E.M.2
-
62
-
-
83055163866
-
Protein expression regulation under oxidative stress
-
Vogel C., Silva G.M., Marcotte E.M. Protein expression regulation under oxidative stress. Mol. Cell. Proteomics 2011, 10(M111):009217.
-
(2011)
Mol. Cell. Proteomics
, vol.10
, Issue.M111
, pp. 009217
-
-
Vogel, C.1
Silva, G.M.2
Marcotte, E.M.3
-
63
-
-
0001963674
-
A convenient growth medium for Neurospora (medium N)
-
Vogel H. A convenient growth medium for Neurospora (medium N). Microb. Genet Bull. 1956, 13:2-43.
-
(1956)
Microb. Genet Bull.
, vol.13
, pp. 2-43
-
-
Vogel, H.1
-
64
-
-
82255173966
-
The unfolded protein response: from stress pathway to homeostatic regulation
-
Walter P., Ron D. The unfolded protein response: from stress pathway to homeostatic regulation. Science 2011, 334:1081-1086.
-
(2011)
Science
, vol.334
, pp. 1081-1086
-
-
Walter, P.1
Ron, D.2
-
65
-
-
79955752894
-
Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells
-
Wang Y., Yang F., Gritsenko M.A., Clauss T., Liu T., Shen Y., Monroe M.E., Lopez-Ferrer D., Reno T., Moore R.J., Klemke R.L., Camp D.G., Smith R.D. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 2011, 11:2019-2026.
-
(2011)
Proteomics
, vol.11
, pp. 2019-2026
-
-
Wang, Y.1
Yang, F.2
Gritsenko, M.A.3
Clauss, T.4
Liu, T.5
Shen, Y.6
Monroe, M.E.7
Lopez-Ferrer, D.8
Reno, T.9
Moore, R.J.10
Klemke, R.L.11
Camp, D.G.12
Smith, R.D.13
-
66
-
-
8644278216
-
Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa
-
Xie X., Wilkinson H.H., Correa A., Lewis Z.A., Bell-Pedersen D., Ebbole D.J. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genet. Biol. 2004, 41:1104-1119.
-
(2004)
Fungal Genet. Biol.
, vol.41
, pp. 1104-1119
-
-
Xie, X.1
Wilkinson, H.H.2
Correa, A.3
Lewis, Z.A.4
Bell-Pedersen, D.5
Ebbole, D.J.6
-
67
-
-
84859972859
-
Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins
-
Znameroski E.A., Coradetti S.T., Roche C.M., Tsai J.C., Iavarone A.T., Cate J.H., Glass N.L. Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc. Natl. Acad. Sci. USA 2012, 109:6012-6017.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 6012-6017
-
-
Znameroski, E.A.1
Coradetti, S.T.2
Roche, C.M.3
Tsai, J.C.4
Iavarone, A.T.5
Cate, J.H.6
Glass, N.L.7
-
68
-
-
84893489724
-
Evidence for transceptor function of cellodextrin transporters in Neurospora crassa
-
Znameroski E.A., Li X., Tsai J.C., Galazka J.M., Glass N.L., Cate J.H. Evidence for transceptor function of cellodextrin transporters in Neurospora crassa. J. Biol. Chem. 2014, 289:2610-2619.
-
(2014)
J. Biol. Chem.
, vol.289
, pp. 2610-2619
-
-
Znameroski, E.A.1
Li, X.2
Tsai, J.C.3
Galazka, J.M.4
Glass, N.L.5
Cate, J.H.6
|