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62) JC Stevens, L Das, JK Mobley,  AO Shardrack, BC Lynn, DW Rodgers, J Shi (2019). Understanding laccase-ionic liquid interactions toward biocatalytic lignin conversion in aqueous ionic liquidsACS Sustainable Chemistry & Engineering [Link]

61) JC Stevens, J Shi (2019) Biocatalysis in ionic liquids for lignin valorization: Opportunities and recent developments, Biotechnology Advances, 107418. [Link]

60) JA Belgodere, SA Zamin, RM Kalinoski, CE Astete, JC Penrod, KM Hamel, BC Lynn, JS Rudra, J Shi, JP Jung (2019) Modulating mechanical properties of collagen–lignin composites, ACS Applied Bio Materials, 2,8,3562-3572 (Supplemental Cover) [Link]

59) PD Muley, JK Mobley, X Tong, B Novak, J Stevens, D Moldovan, J Shi, D Boldor (2019) Rapid microwave-assisted biomass delignification and lignin depolymerization in deep eutectic solvents, Energy Conversion and Management, 196, 1080-1088. [Link]

58) L Dodge, RM Kalinoshi, L Das, J Bursavich, PD Muley, D Boldor, J Shi (2019) Sequential extraction and characterization of lignin derived compounds from thermochemically processed biorefinery lignins, Energy and Fuels, 33 (5), 4322-4330. [Link]


57) W Li, K Amos, M Li, Y Pu, S Debolt, AJ Ragauskas, J Shi (2018)Fractionation and characterization of lignin streams from unique high-lignin content endocarp feedstocks, Biotechnology for Biofuels, 11: 304 [Link]

56) RA Kalinoski, J Shi (2018).Hydrogels derived from lignocellulosic compounds: Evaluation of the compositional, structural, mechanical and antimicrobial properties, Industrial Crops and Products,128: 323-330 [Link]

55) W Li, Y Zhang, L Das, Y Wang, M Li, N Wanninayake, Y Pu, DY Kim, YT Cheng, AJ Ragauskas, J Shi (2018). Linking lignin source with structural and electrochemical properties of lignin-derived carbon materials, RSC Advances, 6 (8): 10408-10420 [Link]

54) L Das, M Li, JC Stevens, W Li, Y Pu, AJ Ragauskas, J Shi (2018). Characterization and catalytic transfer hydrogenolysis of deep eutectic solvent extracted sorghum lignin to phenolic compounds, ACS Sustainable Chemistry & Engineering, 6 (8): 10408-10420 [Link]

53) E Liu, M Li, L Das, Y Pu, T Frazier,  B Zhao, M Crocker, AJ Ragauskas, J Shi (2018). Understanding lignin fractionation and characterization from engineered switchgrass treated by an aqueous ionic liquidACS Sustainable Chemistry & Engineering, 6(5): 6612-6623. [Link]


52) E Liu, L Das, M Crocker, B Zhao, J Shi (2017). Impact of dilute sulfuric acid, ammonium hydroxide and ionic liquid pretreatment on the fractionation and characterization of engineered switchgrass, BioEnergy Research, 10: 1079–1093 [Link]

51) L Das, E Liu, A Saeed, DW Williams, H Hong, C Li, AE Ray, J Shi (2017). Industrial hemp as a potential biofuels crop in comparison with kenaf, switchgrass and biomass sorghum, Bioresource Technology, 244: 641-649 [Link]

50) L Das, S Xu, J Shi. Catalytic oxidation and depolymerization of lignin in aqueous ionic liquid (2017). Frontiers in Energy Research, 5:21 [Link]

49) Y Zheng, J Shi, M Tu, YS Cheng (2017) Principles and development of lignocellulosic biomass pretreatment for biofuels. Published by Elsevier, In Advance in Bioenergy, 2: 1-68 [Link]

48) J Shi, D Wu, L Zhang, BA Simmons, S Singh, B Yang, CE Wyman (2017) Dynamic changes of substrate reactivity and enzyme adsorption on partially hydrolyzed cellulose. Biotechnology and Bioengineering, 114(3), 503-515. [Link]

47) J Sun, J Shi, NVSN Murthy Konda, D Campos, D Liu, S Nemser, J Shamshina, T Dutta, P Berton, G Gurau, RD Rogers, BA Simmons and S Singh (2017). Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation. Biotechnology for Biofuels 10(1): 154. [Link]


46) T Dutta, Shi J, Sun J, Zhang X, Cheng G, Simmons BA, and Singh S (2016) Ionic liquid pre-treatment of lignocellulosic biomass for biofuels and chemicals. In Ionic Liquids in the Biorefinery Concept: Challenges and Perspectives, Rafal Bogel-Lukasik Edition, Published by the Royal Society of Chemistry [Link]

45) J Sun, S Konda, J Shi, R Parthasarathi, T Dutta, F Xu, CD Scown, BA Simmons, S Singh (2016) CO2 enabled process integration for the production of cellulosic ethanol using bionic liquids, Energy & Environmental Science, 9: 2822-2834 [Link]

44) J Shi, S Pattathil, R Parthasarathi, NA Anderson, JI Kim, S Venketachalam, MG Hahn, C Chapple, BA Simmons, S Singh (2016) Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency. Green Chemistry, 18: 4884-4895 (back cover)  [Link]

43) H Wang, B Zhang, S Xiu, R Li, J Shi (2016) Densification and pyrolysis of lignocellulosic biomass for renewable energy. Current Organic Chemistry, 20: 2480-2488 [Link]

42) F Xu, J Sun, S Konda, J Shi, T Dutta, CD Scown, B Simmons, S Singh (2016) Transforming biomass conversion with ionic liquids: process intensification and the development of a high-gravity, one-pot process for the production of cellulosic ethanol. Energy & Environmental Science, 9, 1042-1049 [Link]

41) YF Li, J Shi, MC Nelson, PH Chen, J Graf, Y Li, Z Yu (2016) Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover, Bioresource Technology, 200, 744-752 [Link]


40) R Parthasarathi, K Balamurugan, J Shi, V Subramanian, BA Simmons, S Singh (2015) Theoretical insights into the role of water in the dissolution of cellulose using IL/water mixed solvent systems. The Journal of Physical Chemistry B, 119, 14339–14349 (Cover article) [Link]

39) Shi J, George K, Sun N, He W, Stavila V, Lee TS, Simmons BA, Singh S (2015) Impact of pretreatment technologies on saccharification and isopentenol fermentation of mixed lignocellulosic feedstocks, BioEnergy Research, 8, 1004-1013 [Link]

38) George A, Brandt A, Tran K, Zahari S, Klein-Marcuschamer D, Sun N, Sathitsuksanoh N, Shi J, Stavila V, Parthasarathi R, Singh S, Holmes BM, Welton T, Simmons BA, Hallett JP (2015) Design of low-cost ionic liquids for lignocellulosic biomass pretreatment, Green Chemistry, 17, 1728-1734 [Link]

37) Sathitsuksanoh N, Sawant M, Truong Q, Tan J, Canlas CG, Sun N, Zhang W, Renneckar S, Prasomsri T, Shi J, Çetinkol Ö, Singh S, Simmons BA, George A (2015) How alkyl chain length of alcohols affects lignin fractionation and ionic liquid recycle during lignocellulose pretreatment? BioEnergy Research, 8, 973-981 [Link]


36) Shi J, Balamurugan K, Parthasarathi R, Sathitsuksanoh N,  Zhang S, Stavila V, Subramanian V, Simmons BA, Singh S (2014) Understanding the role of water during ionic liquid pretreatment of lignocellulose: co-solvent or anti-solvent? Green Chemistry, 16, 3830-3840 [Link]

35) Socha, AM, Parthasarathi R, Shi J, Pattathil S, Whyte D, Bergeron M, Venkatachalam S, Hahn MG, Simmons BA, and Singh S (2014) Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose, Proceedings of the National Academy of Sciences111, E3587-E3595 (featured research in Berkeley Lab News, Science Daily, Biofuels Digest, R&D magazine) [Link]

34) Shi J, Chinn, MS, Sharma RS (2014) Interactions between fungal growth, substrate utilization, and enzyme production during solid substrate cultivation of Phanerochaete chrysosporium on cotton stalks. Bioprocess and Biosystems Engineering, 37, 2463-2473 [Link]

33) Kai D, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, and Northen TR, (2014) Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS), ACS Chemical Biology, 9, 1470–1479 (Cover article) [Link]

32) Sun N, Parthasarathia N, Socha AM, Shi J, Zhang J, Stavila V, Sale KL, Simmons BA, Singh S (2014) Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by chemistry and computation, Green Chemistry, 16, 2546-2557 [Link]

31) Shi J, Xu F, Wang Z, Stiverson JA, Yu ZT, Li Y (2014). Effects of microbial and non-microbial factors of liquid anaerobic digestion effluent as inoculum for solid-state anaerobic digestion of corn stover, Bioresource Technology, 157:188–196 [Link]

30) Konda MNVSN, Shi J, Singh S, Blanch HW, Simmons BA, Klein-Marcuschamer D (2014) Understanding cost drivers and economic potential of two variants of ionic liquid pretreatment for cellulosic biofuel production, Biotechnology for Biofuels7:86 [Link]


29) Shi J, Gladden JM, Sathitsuksanoh N, Kambam P, Sandoval L, Mitra D, Zhang S, George A,  Singer SW, Simmons BA, Singh S (2013). One-pot ionic liquid (IL) pretreatment and saccharification of switchgrass, Green Chemistry15, 2579-2589 (featured research in Science Daily, R&D magazine; cover story on Biofuels Digest) [Link]

28) Shi J, Wang Z, Stiverson JA, Yu ZT, Li Y (2013). Reactor performance and microbial community dynamics during solid-state anaerobic digestion of corn stover at mesophilic and thermophilic conditions, Bioresource Technology136: 574–581 [Link]

27) Shi J, Thompson VS, Yancey NA, Stavila V, Simmons BA, Singh S (2013) Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment efficiency, Biofuels, 4(1): 63–72 (highlighted research in Berkeley Lab News, Science Daily, and DOE Pulse) [Link]

26) Xu F, Shi J, Lv W, Yu Z and Li Y (2013) Comparison of different anaerobic digestion effluents as inocula and nitrogen sources for solid-state anaerobic digestion of corn stover, Waste Management33(1):26-32 [Link]


25) Shi J, Qing Q, Zhang T, Lloyd TA and Wyman CE (2012) Aqueous processing of cellulosic biomass for biological and chemical conversion to ethanol and other fuels. In Fundamentals of Materials for Energy and Environmental Sustainability, David Ginley and David Cahen edition, Materials Research Society and Cambridge University Press [Link]

24) Brown D, Shi J, Li Y (2012) Comparison of solid-state to liquid anaerobic digestion of lignocellulosic feedstocks for biogas production, Bioresource Technology124: 379–386 [Link]

23) Liew LN, Shi J, Li Y (2012) Methane production from solid-state anaerobic digestion of lignocellulosic biomass, Biomass & Bioenergy, 46: 125–132 [Link]

22) Cui Z, Wan C, Shi J, Sykes RW, Li Y (2012) Enzymatic digestibility of corn stover fractions in response to fungal pretreatment, Industrial & Engineering Chemistry Research, 51 (21): 7153–7159 (highlighted research in ACS News and Science Daily) [Link]

21) Cui Z, Shi J, Wan C and Li Y (2012) Comparison of alkaline- and fungi-assisted wet-storage of corn stover, Bioresource Technology109: 98-104 [Link]

20) Shi J, Sharma-Shivappa RS, and Chinn MS (2012) Interactions between fungal growth, substrate utilization and enzyme production during shallow stationary cultivation of Phanerochaete chrysosporium on cotton stalks, Enzyme and Microbial Technology51 (1): 1-8 [Link]

2011 and Prior Years

19) Tanjore D, Shi J, and Wyman CE (2011) Water-only and dilute acid pretreatment of lignocellulosic biomass. In Chemical and Biochemical Catalysis for Next Generation Biofuels (RSC Energy Series), Blake A. Simmons edition, Royal Society of Chemistry, Cambridge, UK [Link]

18) Cui Z, Shi J, and Li Y (2011) Solid-state anaerobic digestion of spent wheat straw from horse stall for biogas production, Bioresource Technology,102 (20):9432-37 [Link]

17) Liew LN, Shi J, and Li Y (2011) Enhancing solid-state anaerobic digestion of fallen leaves through simultaneous alkaline treatment, Bioresource Technology, 102 (19):8828-8834 [Link]

16) Shi J, Pu Y, Yang B, Ragauskas A, and Wyman CE (2011) Comparison of microwaves to fluidized sand baths for heating tubular reactors for hydrothermal and dilute acid batch pretreatment of corn stover. Bioresource Technology, 102(10): 5952-61 [Link]

15) Falls M, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Garlock RJ, Balan V, Dale BE, Pallapolu VR, Lee YY, Kim Y, Mosier NS, Ladisch MR, Hames B, Thomas SR, Donohoe BS, Vinzant TB, Elander RT, Sierra R, Holtzapple MT (2011) Investigation of enzyme formulation on pretreated switchgrass. Bioresource Technology, 102(24): 11072-79 [Link]

14) Shi J, Ebrik MA, Yang B, Wyman CE (2011) Sugar yields from dilute sulfuric acid and sulfur dioxide pretreatments and subsequent enzymatic hydrolysis of switchgrass, Bioresource Technology, 102(20):8930-38 [Link]

13) Pallapolu VR, Lee YY, Garlock RJ, Balan V, Dale BE, Kim Y, Mosier NS, Ladisch MR, Falls M, Holtzapple MT, Sierra R, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Donohoe BS, Vinzant TB, Elander RT, Hames B, Thomas SR, Warner RE (2011). Effects of enzyme loading and β-glucosidase on enzymatic hydrolysis of switchgrass processed by leading pretreatment technologies. Bioresource Technology102(24): 11115-20 [Link]

12) Shi J, Ebrik MA, Redmond T, Yang B, Garlock RJ, Balan V, Dale BE, Pallapolu VR, Lee YY, Kim Y, Mosier NS, Ladisch MR, Holtzapple MT, Falls M, Sierra R, Donohoe BS, Vinzant TB, Elander RT, Hames B, Thomas SR, Warner RE, Wyman CE, et al. (2011) Application of cellulase and hemicellulase to pure xylan, pure cellulose, and switchgrass solids from leading pretreatments. Bioresource Technology, 102(24): 11080-88 [Link]

11) Garlock RJ, Balan V, Dale BE, Pallapolu VR, Lee YY, Kim Y, Mosier NS, Ladisch MR, Holtzapple MT, Falls M, Sierra R, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Donohoe BS, Vinzant TB, Elander RT, Hames B, Thomas SR, Warner RE (2011). Comparative material balances around leading pretreatment technologies for the conversion of switchgrass to soluble sugars. Bioresource Technology102(24): 11063-71 [Link]

10) Donohoe BS, Vinzant TB, Elander RT, Pallapolu VR, Lee YY, Garlock RJ, Balan V, Dale BE, Kim, Y, Moiser N, Ladisch MR, Falls M, Sierra R, Holtzapple MT, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Hames B, Thomas SR, Warner RE (2011). Native and pretreated switchgrass surface and ultrastructural imaging analysis of various leading pretreatment technologies. Bioresource Technology, 102(24): 11097-104  [Link]

9) Kim, Y, Moiser N, Ladisch MR, Pallapolu VR, Lee YY, Garlock RJ, Balan V, Dale BE, Donohoe BS, Vinzant TB, Elander RT, Falls M, Sierra R, Holtzapple MT, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Warner RE (2011) Comparative study on enzymatic digestibility of switchgrass varieties and harvests processed by leading pretreatment technologies. Bioresource Technology. 102(24): 11089-96 (highlighted research in Science Daily) [Link]

8) Tao L, Aden A, Elander RT, Pallapolu VR, Lee YY, Garlock RJ, Balan V, Dale BE, Kim Y, Mosier NS, Ladisch MR, Falls M, Holtzapple MT, Sierra R, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Hames B, Thomas SR, Warner RE (2011). Process and technoeconomic analysis of leading pretreatment technologies for lignocellulosic ethanol production using switchgrass. Bioresource Technology, 102(24): 11105-14 [Link]

7) Wyman CE, Balan V, Dale BE, Elander RT, Falls M, Holtzapple MT, Hames B, Ladisch MR, Lee YY, Mosier NS, Pallapolu VR, Shi J, Thomas SR, Warner RE (2011). Comparative data on effects of leading pretreatments and enzyme loadings and formulations on sugar yields from different switchgrass sources. Bioresource Technology 102(24): 11052-62 [Link]

6) Li N, Tompsett GA, Zhang T, Shi J, Wyman CE, and Huber GW (2011) Renewable gasoline from aqueous phase hydrodeoxygenation of aqueous sugar solutions prepared by hydrolysis of maple wood. Green Chemistry13, 91-101 [Link]

5) Lee JM, Shi J, Venditti RA, Jameel H (2009) Autohydrolysis pretreatment of coastal bermuda grass for increased enzyme hydrolysis. Bioresource Technology, 100 (24): 6434-6441 [Link]

4) Shi J, Sharma-Shivappa RR, Chinn MS (2009) Microbial pretreatment of cotton stalks by submerged cultivation of Phanerochaete chrysosporiumBioresource Technology, 100 (19): 4388-4395 [Link]

3) Shi J, Sharma-Shivappa RR, Chinn MS, Howell N (2009) Effects of microbial pretreatment on enzymatic hydrolysis and fermentation of cotton stalks to ethanol production. Biomass and Bioenergy, 33 (1): 88-96 (One of the Top 25 most cited papers 2009-2014) [Link]

2) Shi J, Chinn MS, Sharma-Shivappa RR (2008) Microbial pretreatment of cotton stalks by solid-state cultivation of Phanerochaete chrysosporiumBioresource Technology, 99(14): 6556-6564 [Link]

1) Shi J, Sharma-Shivappa RR, Howell N, Shivappa RB, and Dean RA (2007) Challenge in quantification of ligninolytic enzymes from Phanerochaete chrysosporium cultivation for pretreatment of cotton stalks. Transaction of the ASABE, 50 (6): 2347-2354 (ASABE paper award 2008) [Link]


2) Shi J, Ebrik M, Yang B, Wyman CE (2009) The potential of cellulosic ethanol production from municipal solid waste: a technical and economic evaluation. University of California Energy Institute. Development & Technology. Paper EDT-015 [Link]

1) Li Y, Shi J, Reeder R (2011) Storing lignocellulosic biomass as silage. The Ohio State University Extension-Agriculture and Natural Resources, Fact Sheet: AEX 651.1-11 [Link]


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