Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysis
}, volume={348}, ISSN={["1873-2976"]}, DOI={10.1016/j.biortech.2022.126780}, journal={BIORESOURCE TECHNOLOGY}, author={Bing, Ryan G. and Straub, Christopher T. and Sulis, Daniel B. and Wang, Jack P. and Adams, Michel W. W. and Kelly, Robert M.}, year={2022}, month={Mar} } @article{liu_gao_sun_li_zhang_wang_zhou_sulis_wang_chiang_et al._2022, title={Dimerization of PtrMYB074 and PtrWRKY19 mediates transcriptional activation of PtrbHLH186 for secondary xylem development in Populus trichocarpa}, ISSN={["1469-8137"]}, DOI={10.1111/nph.18028}, journal={NEW PHYTOLOGIST}, author={Liu, Huizi and Gao, Jinghui and Sun, Jiatong and Li, Shuang and Zhang, Baofeng and Wang, Zhuwen and Zhou, Chenguang and Sulis, Daniel Barletta and Wang, Jack P. and Chiang, Vincent L. and et al.}, year={2022}, month={Mar} } @article{chen_neubauer_wang_2022, title={Enhancing HR Frequency for Precise Genome Editing in Plants}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.883421}, journal={FRONTIERS IN PLANT SCIENCE}, author={Chen, Hao and Neubauer, Matthew and Wang, Jack P.}, year={2022}, month={May} } @article{yu_zhou_li_li_lin_wang_chiang_li_2022, title={p A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa}, volume={3}, ISSN={["2590-3462"]}, DOI={10.1016/j.xplc.2021.100250}, number={1}, journal={PLANT COMMUNICATIONS}, author={Yu, Jing and Zhou, Chenguang and Li, Danning and Li, Shuang and Lin, Ying-Chung Jimmy and Wang, Jack P. and Chiang, Vincent L. and Li, Wei}, year={2022}, month={Jan} } @article{matthews_wang_sederoff_chiang_williams_2021, title={A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa}, volume={19}, ISSN={["2001-0370"]}, DOI={10.1016/j.csbj.2020.11.046}, journal={COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, author={Matthews, Megan L. and Wang, Jack P. and Sederoff, Ronald and Chiang, Vincent L. and Williams, Cranos M.}, year={2021}, pages={168–182} } @article{vries_brouckaert_chanoca_kim_regner_timokhin_sun_de meester_van doorsselaere_goeminne_et al._2021, title={CRISPR-Cas9 editing of CAFFEOYL SHIKIMATE ESTERASE 1 and 2 shows their importance and partial redundancy in lignification in Populus tremula x P. alba}, ISSN={["1467-7652"]}, DOI={10.1111/pbi.13651}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Vries, Lisanne and Brouckaert, Marlies and Chanoca, Alexandra and Kim, Hoon and Regner, Matthew R. and Timokhin, Vitaliy I. and Sun, Yi and De Meester, Barbara and Van Doorsselaere, Jan and Goeminne, Geert and et al.}, year={2021}, month={Aug} } @article{lin_sun_song_chen_shi_yang_liu_tunlaya-anukit_liu_loziuk_et al._2021, title={Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.727932}, journal={FRONTIERS IN PLANT SCIENCE}, author={Lin, Chien-Yuan and Sun, Yi and Song, Jina and Chen, Hsi-Chuan and Shi, Rui and Yang, Chenmin and Liu, Jie and Tunlaya-Anukit, Sermsawat and Liu, Baoguang and Loziuk, Philip L. and et al.}, year={2021}, month={Oct} } @article{bing_sulis_wang_adams_kelly_2021, title={Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose}, volume={13}, ISSN={1758-2229 1758-2229}, url={http://dx.doi.org/10.1111/1758-2229.12943}, DOI={10.1111/1758-2229.12943}, number={3}, journal={Environmental Microbiology Reports}, publisher={Wiley}, author={Bing, Ryan G. and Sulis, Daniel B. and Wang, Jack P. and Adams, Michael W. W. and Kelly, Robert M.}, year={2021}, month={Mar}, pages={272–293} } @article{liu_liu_yu_wang_sun_li_lin_chiang_li_wang_2021, title={Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood}, volume={186}, ISSN={["1532-2548"]}, url={https://doi.org/10.1093/plphys/kiab038}, DOI={10.1093/plphys/kiab038}, number={1}, journal={PLANT PHYSIOLOGY}, publisher={Oxford University Press (OUP)}, author={Liu, Baoguang and Liu, Juan and Yu, Jing and Wang, Zhifeng and Sun, Yi and Li, Shuang and Lin, Ying-Chung Jimmy and Chiang, Vincent L. and Li, Wei and Wang, Jack P.}, year={2021}, month={May}, pages={250–269} } @article{wang_mao_guo_gao_liu_li_lin_chen_wang_chiang_et al._2020, title={MYB Transcription Factor161 Mediates Feedback Regulation of Secondary wall-associated NAC-Domain1 Family Genes for Wood Formation}, volume={9}, url={https://doi.org/10.1104/pp.20.01033}, DOI={10.1104/pp.20.01033}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Wang, Zhifeng and Mao, Yuli and Guo, Yanjiao and Gao, Jinghui and Liu, Xinying and Li, Shuang and Lin, Ying-Chung Jimmy and Chen, Hao and Wang, Jack P. and Chiang, Vincent L. and et al.}, year={2020}, month={Nov}, pages={pp.01033.2020} } @article{matthews_wang_sederoff_chiang_williams_2020, title={Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa}, url={https://doi.org/10.1371/journal.pcbi.1007197}, DOI={10.1371/journal.pcbi.1007197}, journal={PLOS Computational Biology}, author={Matthews, Megan L. and Wang, Jack P. and Sederoff, Ronald and Chiang, Vincent L. and Williams, Cranos M.}, editor={Roy, SushmitaEditor}, year={2020}, month={Apr} } @article{kim_li_karlen_smith_shi_liu_yang_tunlaya-anukit_wang_chang_et al._2020, title={Monolignol Benzoates Incorporate into the Lignin of Transgenic Populus trichocarpa Depleted in C3H and C4H}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85082016107&partnerID=MN8TOARS}, DOI={10.1021/acssuschemeng.9b06389}, number={9}, journal={ACS Sustainable Chemistry and Engineering}, author={Kim, H. and Li, Q. and Karlen, S.D. and Smith, R.A. and Shi, R. and Liu, J. and Yang, C. and Tunlaya-Anukit, S. and Wang, J.P. and Chang, H.-M. and et al.}, year={2020}, pages={3644–3654} } @misc{sulis_wang_2020, title={Regulation of Lignin Biosynthesis by Post-translational Protein Modifications}, volume={11}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2020.00914}, journal={FRONTIERS IN PLANT SCIENCE}, author={Sulis, Daniel B. and Wang, Jack P.}, year={2020}, month={Jul} } @article{liu_wang_2020, title={Tracheid Associated Transcription Factors in Loblolly Pine.}, volume={2}, url={http://europepmc.org/abstract/med/32050028}, DOI={10.1093/treephys/tpaa014}, journal={Tree physiology}, author={Liu, B and Wang, JP}, year={2020}, month={Feb} } @article{straub_bing_wang_chiang_adams_kelly_2020, title={Use of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplar}, volume={13}, ISSN={["1754-6834"]}, DOI={10.1186/s13068-020-01675-2}, number={1}, journal={BIOTECHNOLOGY FOR BIOFUELS}, author={Straub, Christopher T. and Bing, Ryan G. and Wang, Jack P. and Chiang, Vincent L. and Adams, Michael W. W. and Kelly, Robert M.}, year={2020}, month={Mar} } @article{yeh_wang_miao_ma_kao_hsu_yu_hung_lin_kuan_et al._2019, title={A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time}, volume={29}, ISSN={["1549-5469"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85071056042&partnerID=MN8TOARS}, DOI={10.1101/gr.245951.118}, number={8}, journal={GENOME RESEARCH}, author={Yeh, Chung-Shu and Wang, Zhifeng and Miao, Fang and Ma, Hongyan and Kao, Chung-Ting and Hsu, Tzu-Shu and Yu, Jhong-He and Hung, Er-Tsi and Lin, Chia-Chang and Kuan, Chen-Yu and et al.}, year={2019}, month={Aug}, pages={1343–1351} } @article{yan_liu_kim_liu_huang_yang_lin_chen_yang_wang_et al._2019, title={CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa}, volume={222}, ISSN={["1469-8137"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055556739&partnerID=MN8TOARS}, DOI={10.1111/nph.15505}, number={1}, journal={NEW PHYTOLOGIST}, author={Yan, Xiaojing and Liu, Jie and Kim, Hoon and Liu, Baoguang and Huang, Xiong and Yang, Zhichang and Lin, Ying-Chung Jimmy and Chen, Hao and Yang, Chenmin and Wang, Jack P. and et al.}, year={2019}, month={Apr}, pages={244–260} } @misc{wang_liu_sun_chiang_sederoff_2019, title={Enzyme-Enzyme Interactions in Monolignol Biosynthesis}, volume={9}, ISSN={["1664-462X"]}, url={http://dx.doi.org/10.3389/fpls.2018.01942}, DOI={10.3389/fpls.2018.01942}, journal={FRONTIERS IN PLANT SCIENCE}, author={Wang, Jack P. and Liu, Baoguang and Sun, Yi and Chiang, Vincent L. and Sederoff, Ronald R.}, year={2019}, month={Jan} } @article{wang_matthews_naik_williams_ducoste_sederoff_chiang_2019, title={Flux modeling for monolignol biosynthesis}, volume={56}, ISSN={0958-1669}, url={http://dx.doi.org/10.1016/J.COPBIO.2018.12.003}, DOI={10.1016/j.copbio.2018.12.003}, journal={Current Opinion in Biotechnology}, publisher={Elsevier BV}, author={Wang, Jack P and Matthews, Megan L and Naik, Punith P and Williams, Cranos M and Ducoste, Joel J and Sederoff, Ronald R and Chiang, Vincent L}, year={2019}, month={Apr}, pages={187–192} } @article{chen_wang_liu_li_lin_shi_yang_gao_zhou_li_et al._2019, title={Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Populus trichocarpa}, volume={31}, url={https://doi.org/10.1105/tpc.18.00620}, DOI={10.1105/tpc.18.00620}, number={3}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Chen, Hao and Wang, Jack P. and Liu, Huizi and Li, Huiyu and Lin, Ying-Chung Jimmy and Shi, Rui and Yang, Chenmin and Gao, Jinghui and Zhou, Chenguang and Li, Quanzi and et al.}, year={2019}, month={Mar}, pages={602–626} } @article{matthews_wang_sederoff_chiang_williams_2019, title={Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa}, volume={6}, url={https://doi.org/10.1101/677047}, DOI={10.1101/677047}, publisher={Cold Spring Harbor Laboratory}, author={Matthews, Megan L. and Wang, Jack P. and Sederoff, Ronald and Chiang, Vincent L. and Williams, Cranos M.}, year={2019}, month={Jun} } @article{straub_khatibi_wang_conway_williams-rhaesa_peszlen_chiang_adams_kelly_2019, title={Quantitative fermentation of unpretreated transgenic poplar by Caldicellulosiruptor bescii}, volume={10}, ISSN={["2041-1723"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85070390326&partnerID=MN8TOARS}, DOI={10.1038/s41467-019-11376-6}, number={1}, journal={NATURE COMMUNICATIONS}, publisher={Springer Science and Business Media LLC}, author={Straub, Christopher T. and Khatibi, Piyum A. and Wang, Jack P. and Conway, Jonathan M. and Williams-Rhaesa, Amanda M. and Peszlen, Ilona M. and Chiang, Vincent L. and Adams, Michael W. W. and Kelly, Robert M.}, year={2019}, month={Aug} } @misc{myburg_hussey_wang_street_mizrachi_2019, title={Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks}, volume={10}, ISSN={["1664-462X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85068483814&partnerID=MN8TOARS}, DOI={10.3389/fpls.2019.00775}, journal={FRONTIERS IN PLANT SCIENCE}, author={Myburg, Alexander A. and Hussey, Steven G. and Wang, Jack P. and Street, Nathaniel R. and Mizrachi, Eshchar}, year={2019}, month={Jun} } @article{li_lin_wang_zhang_li_chen_shi_tunlaya-anukit_liu_wang_et al._2019, title={The AREB1 Transcription Factor Influences Histone Acetylation to Regulate Drought Responses and Tolerance in Populus trichocarpa}, volume={31}, url={http://dx.doi.org/10.1105/tpc.18.00437}, DOI={10.1105/tpc.18.00437}, number={3}, journal={Plant Cell}, author={Li, S. and Lin, Y.-C.J. and Wang, P. and Zhang, B. and Li, M. and Chen, S. and Shi, R. and Tunlaya-Anukit, S. and Liu, X. and Wang, Z. and et al.}, year={2019}, month={Mar}, pages={663–686} } @article{naik_wang_sederoff_chiang_williams_ducoste_2018, title={Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis}, volume={13}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0193896}, DOI={10.1371/journal.pone.0193896}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Naik, Punith and Wang, Jack P. and Sederoff, Ronald and Chiang, Vincent and Williams, Cranos and Ducoste, Joel J.}, editor={Cullen, DanielEditor}, year={2018}, month={Mar}, pages={e0193896} } @article{wang_matthews_williams_shi_yang_tunlaya-anukit_chen_li_liu_lin_et al._2018, title={Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-03863-z}, DOI={10.1038/s41467-018-03863-z}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Jack P. and Matthews, Megan L. and Williams, Cranos M. and Shi, Rui and Yang, Chenmin and Tunlaya-Anukit, Sermsawat and Chen, Hsi-Chuan and Li, Quanzi and Liu, Jie and Lin, Chien-Yuan and et al.}, year={2018}, month={Apr}, pages={1579} } @article{lin_chen_li_li_wang_shi_tunlaya-anukit_shuai_wang_ma_et al._2017, title={Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa}, volume={114}, ISSN={["0027-8424"]}, url={http://europepmc.org/abstract/med/29078399}, DOI={10.1073/pnas.1714422114}, number={45}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Lin, Ying-Chung Jimmy and Chen, Hao and Li, Quanzi and Li, Wei and Wang, Jack P. and Shi, Rui and Tunlaya-Anukit, Sermsawat and Shuai, Peng and Wang, Zhifeng and Ma, Hongyan and et al.}, year={2017}, month={Nov}, pages={E9722–E9729} } @article{shi_wang_lin_li_sun_chen_sederoff_chiang_2017, title={Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa}, volume={245}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85009291513&partnerID=MN8TOARS}, DOI={10.1007/s00425-016-2640-1}, number={5}, journal={PLANTA}, author={Shi, Rui and Wang, Jack P. and Lin, Ying-Chung and Li, Quanzi and Sun, Ying-Hsuan and Chen, Hao and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2017}, month={May}, pages={927–938} } @inbook{wang_tunlaya-anukit_shi_yeh_chuang_isik_yang_liu_li_loziuk_et al._2016, title={A Proteomic-Based Quantitative Analysis of the Relationship Between Monolignol Biosynthetic Protein Abundance and Lignin Content Using TransgenicPopulus trichocarpa}, volume={5}, ISBN={9781118883303 9781118883266}, url={http://dx.doi.org/10.1002/9781118883303.ch4}, DOI={10.1002/9781118883303.ch4}, booktitle={Recent Advances in Polyphenol Research}, publisher={John Wiley & Sons, Ltd}, author={Wang, Jack P. and Tunlaya-Anukit, Sermsawat and Shi, Rui and Yeh, Ting-Feng and Chuang, Ling and Isik, Fikret and Yang, Chenmin and Liu, Jie and Li, Quanzi and Loziuk, Philip L. and et al.}, editor={Kumi Yoshida, Veronique Cheynier and Quideau, StephaneEditors}, year={2016}, month={Dec}, pages={89–107} } @article{lin_li_tunlaya-anukit_shi_sun_wang_liu_loziuk_edmunds_miller_et al._2016, title={A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa}, volume={12}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-016-0978-Y}, DOI={10.1007/s11295-016-0978-y}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Lin, Chien-Yuan and Li, Quanzi and Tunlaya-Anukit, Sermsawat and Shi, Rui and Sun, Ying-Hsuan and Wang, Jack P. and Liu, Jie and Loziuk, Philip and Edmunds, Charles W. and Miller, Zachary D. and et al.}, year={2016}, month={Mar} } @article{lin_wang_li_chen_liu_loziuk_song_williams_muddiman_sederoff_et al._2015, title={4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa}, volume={8}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925201417&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2014.12.003}, number={1}, journal={MOLECULAR PLANT}, author={Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Chen, Hsi-Chuan and Liu, Jie and Loziuk, Philip and Song, Jina and Williams, Cranos and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2015}, month={Jan}, pages={176–187} } @article{liu_hai_wang_cao_xu_jia_yang_wang_dai_cheng_2015, title={Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth}, volume={126}, ISSN={["1876-7737"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84930933098&partnerID=MN8TOARS}, DOI={10.1016/j.jprot.2015.05.032}, journal={JOURNAL OF PROTEOMICS}, author={Liu, Jinwen and Hai, Guanghui and Wang, Chong and Cao, Shenquan and Xu, Wenjing and Jia, Zhigang and Yang, Chuanping and Wang, Jack P. and Dai, Shaojun and Cheng, Yuxiang}, year={2015}, month={Aug}, pages={94–108} } @article{loziuk_parker_li_lin_wang_li_sederoff_chiang_muddiman_2015, title={Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa}, volume={14}, ISSN={["1535-3907"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84942916917&partnerID=MN8TOARS}, DOI={10.1021/acs.jproteome.5b00233}, number={10}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Loziuk, Philip L. and Parker, Jennifer and Li, Wei and Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2015}, month={Oct}, pages={4158–4168} } @article{wang_chuang_loziuk_chen_lin_shi_qu_muddiman_sederoff_chiang_2015, title={Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis}, volume={112}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1510473112}, DOI={10.1073/pnas.1510473112}, abstractNote={Although phosphorylation has long been known to be an important regulatory modification of proteins, no unequivocal evidence has been presented to show functional control by phosphorylation for the plant monolignol biosynthetic pathway. Here, we present the discovery of phosphorylation-mediated on/off regulation of enzyme activity for 5-hydroxyconiferaldehyde