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Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.

Biotechnology for biofuels

Alipour A, Tsuchimoto S, Sakai H, Ohmido N, Fukui K.
PMID: 24020916
Biotechnol Biofuels. 2013 Sep 10;6(1):129. doi: 10.1186/1754-6834-6-129.

BACKGROUND: Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features...

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Alipour A, Tsuchimoto S, Sakai H, et al. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnol Biofuels. 2013;6(1):129doi: 10.1186/1754-6834-6-129.
Alipour, A., Tsuchimoto, S., Sakai, H., Ohmido, N., & Fukui, K. (2013). Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnology for biofuels, 6(1), 129. https://doi.org/10.1186/1754-6834-6-129
Alipour, Atefeh, et al. "Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L." Biotechnology for biofuels vol. 6,1 (2013): 129. doi: https://doi.org/10.1186/1754-6834-6-129
Alipour A, Tsuchimoto S, Sakai H, Ohmido N, Fukui K. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnol Biofuels. 2013 Sep 10;6(1):129. doi: 10.1186/1754-6834-6-129. PMID: 24020916; PMCID: PMC3852365.
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Correction: Direct production of biodiesel from high-acid value Jatropha oil with solid acid catalyst derived from lignin.

Biotechnology for biofuels

Pua FL, Fang Z, Zakaria S, Guo F, Chia CH.
PMID: 22958652
Biotechnol Biofuels. 2012 Sep 07;5(1):66. doi: 10.1186/1754-6834-5-66.

No abstract available.

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Pua FL, Fang Z, Zakaria S, et al. Correction: Direct production of biodiesel from high-acid value Jatropha oil with solid acid catalyst derived from lignin. Biotechnol Biofuels. 2012;5(1):66doi: 10.1186/1754-6834-5-66.
Pua, F. L., Fang, Z., Zakaria, S., Guo, F., & Chia, C. H. (2012). Correction: Direct production of biodiesel from high-acid value Jatropha oil with solid acid catalyst derived from lignin. Biotechnology for biofuels, 5(1), 66. https://doi.org/10.1186/1754-6834-5-66
Pua, Fei-Ling, et al. "Correction: Direct production of biodiesel from high-acid value Jatropha oil with solid acid catalyst derived from lignin." Biotechnology for biofuels vol. 5,1 (2012): 66. doi: https://doi.org/10.1186/1754-6834-5-66
Pua FL, Fang Z, Zakaria S, Guo F, Chia CH. Correction: Direct production of biodiesel from high-acid value Jatropha oil with solid acid catalyst derived from lignin. Biotechnol Biofuels. 2012 Sep 07;5(1):66. doi: 10.1186/1754-6834-5-66. PMID: 22958652; PMCID: PMC3477030.
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Simultaneous utilization of glucose and xylose for lipid production by Trichosporon cutaneum.

Biotechnology for biofuels

Hu C, Wu S, Wang Q, Jin G, Shen H, Zhao ZK.
PMID: 21864398
Biotechnol Biofuels. 2011 Aug 24;4(1):25. doi: 10.1186/1754-6834-4-25.

BACKGROUND: Biochemical conversion of lignocellulose hydrolysates remains challenging, largely because most microbial processes have markedly reduced efficiency in the presence of both hexoses and pentoses. Thus, identification of microorganisms capable of efficient and simultaneous utilization of both glucose and...

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Hu C, Wu S, Wang Q, et al. Simultaneous utilization of glucose and xylose for lipid production by Trichosporon cutaneum. Biotechnol Biofuels. 2011;4(1):25doi: 10.1186/1754-6834-4-25.
Hu, C., Wu, S., Wang, Q., Jin, G., Shen, H., & Zhao, Z. K. (2011). Simultaneous utilization of glucose and xylose for lipid production by Trichosporon cutaneum. Biotechnology for biofuels, 4(1), 25. https://doi.org/10.1186/1754-6834-4-25
Hu, Cuimin, et al. "Simultaneous utilization of glucose and xylose for lipid production by Trichosporon cutaneum." Biotechnology for biofuels vol. 4,1 (2011): 25. doi: https://doi.org/10.1186/1754-6834-4-25
Hu C, Wu S, Wang Q, Jin G, Shen H, Zhao ZK. Simultaneous utilization of glucose and xylose for lipid production by Trichosporon cutaneum. Biotechnol Biofuels. 2011 Aug 24;4(1):25. doi: 10.1186/1754-6834-4-25. PMID: 21864398; PMCID: PMC3174874.
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The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.

Biotechnology for biofuels

Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C.
PMID: 24834124
Biotechnol Biofuels. 2014 Apr 24;7:66. doi: 10.1186/1754-6834-7-66. eCollection 2014.

BACKGROUND: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and...

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Kunze G, Gaillardin C, Czernicka M, et al. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Biotechnol Biofuels. 2014;7:66doi: 10.1186/1754-6834-7-66.
Kunze, G., Gaillardin, C., Czernicka, M., Durrens, P., Martin, T., Böer, E., Gabaldón, T., Cruz, J. A., Talla, E., Marck, C., Goffeau, A., Barbe, V., Baret, P., Baronian, K., Beier, S., Bleykasten, C., Bode, R., Casaregola, S., Despons, L., Fairhead, C., Giersberg, M., Gierski, P. P., Hähnel, U., Hartmann, A., Jankowska, D., Jubin, C., Jung, P., Lafontaine, I., Leh-Louis, V., Lemaire, M., Marcet-Houben, M., Mascher, M., Morel, G., Richard, G. F., Riechen, J., Sacerdot, C., Sarkar, A., Savel, G., Schacherer, J., Sherman, D. J., Stein, N., Straub, M. L., Thierry, A., Trautwein-Schult, A., Vacherie, B., Westhof, E., Worch, S., Dujon, B., Souciet, J. L., Wincker, P., Scholz, U., & Neuvéglise, C. (2014). The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Biotechnology for biofuels, 766. https://doi.org/10.1186/1754-6834-7-66
Kunze, Gotthard, et al. "The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest." Biotechnology for biofuels vol. 7 (2014): 66. doi: https://doi.org/10.1186/1754-6834-7-66
Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Biotechnol Biofuels. 2014 Apr 24;7:66. doi: 10.1186/1754-6834-7-66. eCollection 2014. PMID: 24834124; PMCID: PMC4022394.
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Genome sequencing and transcriptome analysis of .

Biotechnology for biofuels

Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F.
PMID: 28912831
Biotechnol Biofuels. 2017 Sep 07;10:209. doi: 10.1186/s13068-017-0897-7. eCollection 2017.

BACKGROUND: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete RESULTS: Sequence comparison of the cellulase-negative strain QM9978 to...

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Ivanova C, Ramoni J, Aouam T, et al. Genome sequencing and transcriptome analysis of . Biotechnol Biofuels. 2017;10:209doi: 10.1186/s13068-017-0897-7.
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 . Biotechnology for biofuels, 10209. https://doi.org/10.1186/s13068-017-0897-7
Ivanova, Christa, et al. "Genome sequencing and transcriptome analysis of ." Biotechnology for biofuels vol. 10 (2017): 209. doi: https://doi.org/10.1186/s13068-017-0897-7
Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F. Genome sequencing and transcriptome analysis of . Biotechnol Biofuels. 2017 Sep 07;10:209. doi: 10.1186/s13068-017-0897-7. eCollection 2017. PMID: 28912831; PMCID: PMC5588705.
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Single cell oil production by .

Biotechnology for biofuels

Zhao C, Fang H, Chen S.
PMID: 28852423
Biotechnol Biofuels. 2017 Aug 23;10:202. doi: 10.1186/s13068-017-0889-7. eCollection 2017.

BACKGROUND: Single cell oil (SCO) production from lignocelluloses by oleaginous microorganisms is still high in production cost, making the subsequent production of biofuels inviable economically in such an era of low oil prices. Therefore, how to upgrade the final...

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Zhao C, Fang H, Chen S. Single cell oil production by . Biotechnol Biofuels. 2017;10:202doi: 10.1186/s13068-017-0889-7.
Zhao, C., Fang, H., & Chen, S. (2017). Single cell oil production by . Biotechnology for biofuels, 10202. https://doi.org/10.1186/s13068-017-0889-7
Zhao, Chen, et al. "Single cell oil production by ." Biotechnology for biofuels vol. 10 (2017): 202. doi: https://doi.org/10.1186/s13068-017-0889-7
Zhao C, Fang H, Chen S. Single cell oil production by . Biotechnol Biofuels. 2017 Aug 23;10:202. doi: 10.1186/s13068-017-0889-7. eCollection 2017. PMID: 28852423; PMCID: PMC5568358.
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Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions.

Biotechnology for biofuels

Santos CA, Zanphorlin LM, Crucello A, Tonoli CCC, Ruller R, Horta MAC, Murakami MT, de Souza AP.
PMID: 27006690
Biotechnol Biofuels. 2016 Mar 22;9:71. doi: 10.1186/s13068-016-0487-0. eCollection 2016.

BACKGROUND: The conversion of biomass-derived sugars via enzymatic hydrolysis for biofuel production is a challenge. Therefore, the search for microorganisms and key enzymes that increase the efficiency of the saccharification of cellulosic substrates remains an important and high-priority area...

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Santos CA, Zanphorlin LM, Crucello A, et al. Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. Biotechnol Biofuels. 2016;9:71doi: 10.1186/s13068-016-0487-0.
Santos, C. A., Zanphorlin, L. M., Crucello, A., Tonoli, C. C. C., Ruller, R., Horta, M. A. C., Murakami, M. T., & de Souza, A. P. (2016). Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. Biotechnology for biofuels, 971. https://doi.org/10.1186/s13068-016-0487-0
Santos, Clelton A, et al. "Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions." Biotechnology for biofuels vol. 9 (2016): 71. doi: https://doi.org/10.1186/s13068-016-0487-0
Santos CA, Zanphorlin LM, Crucello A, Tonoli CCC, Ruller R, Horta MAC, Murakami MT, de Souza AP. Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. Biotechnol Biofuels. 2016 Mar 22;9:71. doi: 10.1186/s13068-016-0487-0. eCollection 2016. PMID: 27006690; PMCID: PMC4802607.
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Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization.

Biotechnology for biofuels

Wang J, Wang Y, Wang X, Zhang D, Wu S, Zhang G.
PMID: 27034717
Biotechnol Biofuels. 2016 Mar 31;9:79. doi: 10.1186/s13068-016-0490-5. eCollection 2016.

BACKGROUND: SpyTag is a peptide that can form an irreversible covalent linkage to its 12 kDa partner SpyCatcher via a spontaneous isopeptide bond. Herein, we fused SpyTag at the N-terminal of lichenase and SpyCatcher at C-terminal so that the...

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Wang J, Wang Y, Wang X, et al. Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization. Biotechnol Biofuels. 2016;9:79doi: 10.1186/s13068-016-0490-5.
Wang, J., Wang, Y., Wang, X., Zhang, D., Wu, S., & Zhang, G. (2016). Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization. Biotechnology for biofuels, 979. https://doi.org/10.1186/s13068-016-0490-5
Wang, Jindan, et al. "Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization." Biotechnology for biofuels vol. 9 (2016): 79. doi: https://doi.org/10.1186/s13068-016-0490-5
Wang J, Wang Y, Wang X, Zhang D, Wu S, Zhang G. Enhanced thermal stability of lichenase from Bacillus subtilis 168 by SpyTag/SpyCatcher-mediated spontaneous cyclization. Biotechnol Biofuels. 2016 Mar 31;9:79. doi: 10.1186/s13068-016-0490-5. eCollection 2016. PMID: 27034717; PMCID: PMC4815112.
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Moderate alkali-thermophilic ethanologenesis by locally isolated .

Biotechnology for biofuels

Ahmad QU, Yang ST, Manzoor M, Qazi JI.
PMID: 28450886
Biotechnol Biofuels. 2017 Apr 24;10:105. doi: 10.1186/s13068-017-0785-1. eCollection 2017.

BACKGROUND: Biofuels obtained from first-generation (1G) sugars-starch streams have been proven unsustainable as their constant consumption is not only significantly costly for commercial scale production systems, but it could potentially lead to problems associated with extortionate food items for...

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Ahmad QU, Yang ST, Manzoor M, et al. Moderate alkali-thermophilic ethanologenesis by locally isolated . Biotechnol Biofuels. 2017;10:105doi: 10.1186/s13068-017-0785-1.
Ahmad, Q. U., Yang, S. T., Manzoor, M., & Qazi, J. I. (2017). Moderate alkali-thermophilic ethanologenesis by locally isolated . Biotechnology for biofuels, 10105. https://doi.org/10.1186/s13068-017-0785-1
Ahmad, Qurat-Ul-Ain, et al. "Moderate alkali-thermophilic ethanologenesis by locally isolated ." Biotechnology for biofuels vol. 10 (2017): 105. doi: https://doi.org/10.1186/s13068-017-0785-1
Ahmad QU, Yang ST, Manzoor M, Qazi JI. Moderate alkali-thermophilic ethanologenesis by locally isolated . Biotechnol Biofuels. 2017 Apr 24;10:105. doi: 10.1186/s13068-017-0785-1. eCollection 2017. PMID: 28450886; PMCID: PMC5402650.
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Process relevant screening of cellulolytic organisms for consolidated bioprocessing.

Biotechnology for biofuels

Antonov E, Schlembach I, Regestein L, Rosenbaum MA, Büchs J.
PMID: 28450887
Biotechnol Biofuels. 2017 Apr 24;10:106. doi: 10.1186/s13068-017-0790-4. eCollection 2017.

BACKGROUND: Although the biocatalytic conversion of cellulosic biomass could replace fossil oil for the production of various compounds, it is often not economically viable due to the high costs of cellulolytic enzymes. One possibility to reduce costs is consolidated...

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Antonov E, Schlembach I, Regestein L, et al. Process relevant screening of cellulolytic organisms for consolidated bioprocessing. Biotechnol Biofuels. 2017;10:106doi: 10.1186/s13068-017-0790-4.
Antonov, E., Schlembach, I., Regestein, L., Rosenbaum, M. A., & Büchs, J. (2017). Process relevant screening of cellulolytic organisms for consolidated bioprocessing. Biotechnology for biofuels, 10106. https://doi.org/10.1186/s13068-017-0790-4
Antonov, Elena, et al. "Process relevant screening of cellulolytic organisms for consolidated bioprocessing." Biotechnology for biofuels vol. 10 (2017): 106. doi: https://doi.org/10.1186/s13068-017-0790-4
Antonov E, Schlembach I, Regestein L, Rosenbaum MA, Büchs J. Process relevant screening of cellulolytic organisms for consolidated bioprocessing. Biotechnol Biofuels. 2017 Apr 24;10:106. doi: 10.1186/s13068-017-0790-4. eCollection 2017. PMID: 28450887; PMCID: PMC5402656.
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Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in S.

Biotechnology for biofuels

Papapetridis I, van Dijk M, van Maris AJA, Pronk JT.
PMID: 28450888
Biotechnol Biofuels. 2017 Apr 26;10:107. doi: 10.1186/s13068-017-0791-3. eCollection 2017.

CONCLUSIONS: Deletion of

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Papapetridis I, van Dijk M, van Maris AJA, et al. Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in S. Biotechnol Biofuels. 2017;10:107doi: 10.1186/s13068-017-0791-3.
Papapetridis, I., van Dijk, M., van Maris, A. J. A., & Pronk, J. T. (2017). Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in S. Biotechnology for biofuels, 10107. https://doi.org/10.1186/s13068-017-0791-3
Papapetridis, Ioannis, et al. "Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in S." Biotechnology for biofuels vol. 10 (2017): 107. doi: https://doi.org/10.1186/s13068-017-0791-3
Papapetridis I, van Dijk M, van Maris AJA, Pronk JT. Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in S. Biotechnol Biofuels. 2017 Apr 26;10:107. doi: 10.1186/s13068-017-0791-3. eCollection 2017. PMID: 28450888; PMCID: PMC5406903.
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Network reconstruction and systems analysis of plant cell wall deconstruction by .

Biotechnology for biofuels

Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL.
PMID: 28947916
Biotechnol Biofuels. 2017 Sep 21;10:225. doi: 10.1186/s13068-017-0901-2. eCollection 2017.

BACKGROUND: Plant biomass degradation by fungal-derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides....

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Samal A, Craig JP, Coradetti ST, et al. Network reconstruction and systems analysis of plant cell wall deconstruction by . Biotechnol Biofuels. 2017;10:225doi: 10.1186/s13068-017-0901-2.
Samal, A., Craig, J. P., Coradetti, S. T., Benz, J. P., Eddy, J. A., Price, N. D., & Glass, N. L. (2017). Network reconstruction and systems analysis of plant cell wall deconstruction by . Biotechnology for biofuels, 10225. https://doi.org/10.1186/s13068-017-0901-2
Samal, Areejit, et al. "Network reconstruction and systems analysis of plant cell wall deconstruction by ." Biotechnology for biofuels vol. 10 (2017): 225. doi: https://doi.org/10.1186/s13068-017-0901-2
Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL. Network reconstruction and systems analysis of plant cell wall deconstruction by . Biotechnol Biofuels. 2017 Sep 21;10:225. doi: 10.1186/s13068-017-0901-2. eCollection 2017. PMID: 28947916; PMCID: PMC5609067.
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