-
1
-
-
43049124536
-
Method of producing L-malic acid by fermentation
-
November, US patent
-
Abe S, Akira F, Ken-Ichiro T. November 1962. Method of producing L-malic acid by fermentation. US patent 3,063,910.
-
(1962)
, vol.3
, Issue.63
, pp. 910
-
-
Abe, S.1
Akira, F.2
Ken-Ichiro, T.3
-
4
-
-
0025301129
-
Localization of pyruvate carboxylase in organic acid-producing Aspergillus strains
-
Bercovitz A, Peleg Y, Battat E, Rokem JS, Goldberg I. 1990. Localization of pyruvate carboxylase in organic acid-producing Aspergillus strains. Appl. Environ. Microbiol. 56:1594-1597.
-
(1990)
Appl. Environ. Microbiol.
, vol.56
, pp. 1594-1597
-
-
Bercovitz, A.1
Peleg, Y.2
Battat, E.3
Rokem, J.S.4
Goldberg, I.5
-
5
-
-
0026155122
-
Optimization of L-malic acid production by Aspergillus flavus in a stirred fermentor
-
Battat E, Peleg Y, Bercovitz A, Rokem JS, Goldberg I. 1991. Optimization of L-malic acid production by Aspergillus flavus in a stirred fermentor. Biotechnol. Bioeng. 37:1108-1116.
-
(1991)
Biotechnol. Bioeng.
, vol.37
, pp. 1108-1116
-
-
Battat, E.1
Peleg, Y.2
Bercovitz, A.3
Rokem, J.S.4
Goldberg, I.5
-
6
-
-
43049090802
-
Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export
-
Zelle RM, de Hulster E, van Winden WA, de Waard P, Dijkema C, Winkler AA, Geertman J-MA, van Dijken JP, Pronk JT, van Maris AJA. 2008. Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export. Appl. Environ. Microbiol. 74:2766-2777.
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 2766-2777
-
-
Zelle, R.M.1
de Hulster, E.2
van Winden, W.A.3
de Waard, P.4
Dijkema, C.5
Winkler, A.A.6
Geertman, J.M.A.7
van Dijken, J.P.8
Pronk, J.T.9
van Maris, A.J.A.10
-
8
-
-
44049083061
-
Metabolic engineering of Escherichia coli for the production of malic acid
-
Moon SY, Hong SH, Kim TY, Lee SY. 2008. Metabolic engineering of Escherichia coli for the production of malic acid. Biochem. Eng. J. 40:312-320.
-
(2008)
Biochem. Eng. J.
, vol.40
, pp. 312-320
-
-
Moon, S.Y.1
Hong, S.H.2
Kim, T.Y.3
Lee, S.Y.4
-
9
-
-
33749538256
-
Whole genome comparison of Aspergillus flavus and A
-
Payne GA, Nierman WC, Wortman JR, Pritchard BL, Brown D, Dean RA, Bhatnagar D, Cleveland TE, Machida M, Yu J. 2006. Whole genome comparison of Aspergillus flavus and A. oryzae. Med. Mycol. 44:9-11.
-
(2006)
oryzae. Med. Mycol.
, vol.44
, pp. 9-11
-
-
Payne, G.A.1
Nierman, W.C.2
Wortman, J.R.3
Pritchard, B.L.4
Brown, D.5
Dean, R.A.6
Bhatnagar, D.7
Cleveland, T.E.8
Machida, M.9
Yu, J.10
-
10
-
-
44849094233
-
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
-
doi:10.1186/1471-2164-9-245.
-
Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J. 2008. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 9:245. doi:10.1186/1471-2164-9-245.
-
(2008)
BMC Genomics
, vol.9
, pp. 245
-
-
Vongsangnak, W.1
Olsen, P.2
Hansen, K.3
Krogsgaard, S.4
Nielsen, J.5
-
11
-
-
41949120307
-
A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species
-
Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. 2008. A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc. Natl. Acad. Sci. U. S. A. 105:4387-4392.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 4387-4392
-
-
Andersen, M.R.1
Vongsangnak, W.2
Panagiotou, G.3
Salazar, M.P.4
Lehmann, L.5
Nielsen, J.6
-
12
-
-
29244442741
-
Genome sequencing and analysis of Aspergillus oryzae
-
Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K-I, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J-I, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, et al. 2005. Genome sequencing and analysis of Aspergillus oryzae. Nature 438:1157-1161.
-
(2005)
Nature
, vol.438
, pp. 1157-1161
-
-
Machida, M.1
Asai, K.2
Sano, M.3
Tanaka, T.4
Kumagai, T.5
Terai, G.6
Kusumoto, K.I.7
Arima, T.8
Akita, O.9
Kashiwagi, Y.10
Abe, K.11
Gomi, K.12
Horiuchi, H.13
Kitamoto, K.14
Kobayashi, T.15
Takeuchi, M.16
Denning, D.W.17
Galagan, J.E.18
Nierman, W.C.19
Yu, J.20
Archer, D.B.21
Bennett, J.W.22
Bhatnagar, D.23
Cleveland, T.E.24
Fedorova, N.D.25
Gotoh, O.26
Horikawa, H.27
Hosoyama, A.28
Ichinomiya, M.29
Igarashi, R.30
Iwashita, K.31
Juvvadi, P.R.32
Kato, M.33
Kato, Y.34
Kin, T.35
Kokubun, A.36
Maeda, H.37
Maeyama, N.38
Maruyama, J.I.39
Nagasaki, H.40
Nakajima, T.41
Oda, K.42
Okada, K.43
Paulsen, I.44
Sakamoto, K.45
Sawano, T.46
Takahashi, M.47
Takase, K.48
Terabayashi, Y.49
Wortman, J.R.50
more..
-
13
-
-
79953138924
-
Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae
-
Vongsangnak W, Hansen K, Nielsen J. 2011. Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae. Biotechnol. Bioeng. 108:1130-1139.
-
(2011)
Biotechnol. Bioeng.
, vol.108
, pp. 1130-1139
-
-
Vongsangnak, W.1
Hansen, K.2
Nielsen, J.3
-
14
-
-
85022103610
-
The R Development Core Team.
-
The R Foundation for Statistical Computing, Vienna, Austria.
-
The R Development Core Team. 2012. R: a language and environment for statistical computing. The R Foundation for Statistical Computing, Vienna, Austria.
-
(2012)
R: a language and environment for statistical computing
-
-
-
15
-
-
84877309040
-
Enriching the gene set analysis ofgenome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
-
Varemo L, Nielsen J, Nookaew I. 2013. Enriching the gene set analysis ofgenome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 41: 4378-4391.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 4378-4391
-
-
Varemo, L.1
Nielsen, J.2
Nookaew, I.3
-
17
-
-
84884189377
-
plier: implements the Affymetrix PLIER algorithm
-
Affymetric Inc, Crispin JM, PICR., R package, version 1.28.0. Affymetrix, Santa Clara, CA.
-
Affymetric Inc, Crispin JM, PICR. plier: implements the Affymetrix PLIER algorithm. R package, version 1.28.0. Affymetrix, Santa Clara, CA.
-
-
-
-
18
-
-
33644872577
-
Limma: linear models for microarray data
-
Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (ed), Springer, New York, NY.
-
Smyth GK. 2005. Limma: linear models for microarray data, p 397-420. In Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (ed), Bioinformatics and computational biology solutions using {R} and bioconductor. Springer, New York, NY.
-
(2005)
Bioinformatics and computational biology solutions using {R} and bioconductor.
, pp. 397-420
-
-
Smyth, G.K.1
-
19
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57:289-300.
-
(1995)
J. R. Stat. Soc. Series B Stat. Methodol.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
20
-
-
14544268137
-
Uncovering transcriptional regulation of metabolism by using metabolic network topology
-
Patil KR, Nielsen J. 2005. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. U. S. A. 102:2685-2689.
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 2685-2689
-
-
Patil, K.R.1
Nielsen, J.2
-
21
-
-
84862228827
-
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources
-
Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, Wortman JR. 2012. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Res. 40:D653-D659.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Arnaud, M.B.1
Cerqueira, G.C.2
Inglis, D.O.3
Skrzypek, M.S.4
Binkley, J.5
Chibucos, M.C.6
Crabtree, J.7
Howarth, C.8
Orvis, J.9
Shah, P.10
Wymore, F.11
Binkley, G.12
Miyasato, S.R.13
Simison, M.14
Sherlock, G.15
Wortman, J.R.16
-
22
-
-
78049304837
-
Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
-
doi:10.1371/journal.pcbi.1000859.
-
Bordel S, Agren R, Nielsen J. 2010. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput. Biol. 6:e1000859. doi:10.1371/journal.pcbi.1000859.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Bordel, S.1
Agren, R.2
Nielsen, J.3
-
23
-
-
77954291914
-
BioMet toolbox: genome-wide analysis of metabolism
-
doi:10.1093/nar/gkq404.
-
Cvijovic M, Olivares-Hernández R, Agren R, Dahr N, Vongsangnak W, Nookaew I, Patil KR, Nielsen J. 2010. BioMet toolbox: genome-wide analysis of metabolism. Nucleic Acids Res. 38:W144-W149. doi:10.1093/nar/gkq404.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Cvijovic, M.1
Olivares-Hernández, R.2
Agren, R.3
Dahr, N.4
Vongsangnak, W.5
Nookaew, I.6
Patil, K.R.7
Nielsen, J.8
-
24
-
-
41049102359
-
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
-
doi:10.1186/1752-0509-2-17.
-
Oliveira A, Patil K, Nielsen J. 2008. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst. Biol. 2:17. doi:10.1186/1752-0509-2-17.
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 17
-
-
Oliveira, A.1
Patil, K.2
Nielsen, J.3
-
25
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden J, André B, Collado-Vides J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281:827-842.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 827-842
-
-
van Helden, J.1
André, B.2
Collado-Vides, J.3
-
26
-
-
78651272522
-
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
-
doi:10.1093/nar/gkq964.
-
Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Lourenço AB, dos Santos SC, Cabrito TR, Francisco AP, Madeira SC, Aires RS, Oliveira AL, Sá-Correia I, Freitas AT. 2011. YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res. 39:D136-D140. doi:10.1093/nar/gkq964.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Abdulrehman, D.1
Monteiro, P.T.2
Teixeira, M.C.3
Mira, N.P.4
Lourenço, A.B.5
dos Santos, S.C.6
Cabrito, T.R.7
Francisco, A.P.8
Madeira, S.C.9
Aires, R.S.10
Oliveira, A.L.11
Sá-Correia, I.12
Freitas, A.T.13
-
27
-
-
0030003064
-
Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae
-
Schmitt AP, McEntee K. 1996. Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 93:5777-5782.
-
(1996)
Proc. Natl. Acad. Sci. U. S. A.
, vol.93
, pp. 5777-5782
-
-
Schmitt, A.P.1
McEntee, K.2
-
28
-
-
0032931265
-
Identification of enzymes and quantification of metabolic fluxes in the wild type and in a recombinant Aspergillus oryzae strain
-
Pedersen H, Carlsen M, Nielsen J. 1999. Identification of enzymes and quantification of metabolic fluxes in the wild type and in a recombinant Aspergillus oryzae strain. Appl. Environ. Microbiol. 65:11-19.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 11-19
-
-
Pedersen, H.1
Carlsen, M.2
Nielsen, J.3
-
30
-
-
77449103113
-
Identification, analysis, and prediction of protein ubiquitination sites
-
Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM. 2010. Identification, analysis, and prediction of protein ubiquitination sites. Proteins 78:365-380.
-
(2010)
Proteins
, vol.78
, pp. 365-380
-
-
Radivojac, P.1
Vacic, V.2
Haynes, C.3
Cocklin, R.R.4
Mohan, A.5
Heyen, J.W.6
Goebl, M.G.7
Iakoucheva, L.M.8
-
31
-
-
0029669455
-
Morphology and physiology of an α-amylase producing strain of Aspergillus oryzae during batch cultivations
-
Carlsen M, Spohr AB, Nielsen J, Villadsen J. 1996. Morphology and physiology of an α-amylase producing strain of Aspergillus oryzae during batch cultivations. Biotechnol. Bioeng. 49:266-276.
-
(1996)
Biotechnol. Bioeng.
, vol.49
, pp. 266-276
-
-
Carlsen, M.1
Spohr, A.B.2
Nielsen, J.3
Villadsen, J.4
-
32
-
-
6344237317
-
PP2A phosphatase activity is required for stress and Tor kinase regulation of yeast stress response factor Msn2p
-
Santhanam A, Hartley A, Düvel K, Broach JR, Garrett S. 2004. PP2A phosphatase activity is required for stress and Tor kinase regulation of yeast stress response factor Msn2p. Eukaryot. Cell 3:1261-1271.
-
(2004)
Eukaryot. Cell
, vol.3
, pp. 1261-1271
-
-
Santhanam, A.1
Hartley, A.2
Düvel, K.3
Broach, J.R.4
Garrett, S.5
|