static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and...

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1. Mohnen, et al., Cell wall polysaccharide synthesis, Biomass Recalcitrance, 2008 2. Ding, et al., Identifying Molecular Structural Features of Biomass Recalcitrance Using Nondestructive Microscopy and Spectroscopy, Microcopy and Microanalysis, 2008 3. Keller, et al., Microbial goods from single cells and metagenomes, Current Opinion in Microbiology, 2008 4. Lynd, et al., How biotech can transform biofuels, Nature Biotechnology, 2008 5. Xi, et al., Agrobacterium-mediated transformation of switchgrass and inheritance of the transgenes BER-133R1, BioEnergy Research, 2008 6. Ljungdahl, et al., Contribution of domain interactions and calcium binding to the stability of carbohydrate-Active enzymes, Bioenergy, 2008 7. Ding, et al., A Biophysical Perspective of the Cellulosome: New Opportunities for Biomass Conversion, Current Opinion in Biotechnology, 2008 8. York, et al., Biochemical control of xylan biosynthesis — which end is up?, Current Opinion Plant Biology, 2008 9. Blumer-Schuette, et al., Extremely thermophilic microorganisms for biomass conversion: status and prospects, Current Opinion in Biotechnology, 2008 10. Mohnen, et al., Pectin Structure and Biosynthesis, Current Opinion Plant Biology, 2008 11. Bordner, et al., Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces, BMC Bioinformatics, 2008 12. Zhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 13. Hong, et al., Simple protein purification through affinity adsorption on regenerated amorphous cellulose followed by intein self-cleavage, Journal of Chromatography, 2008 14. Hong, et al., Bioseparation of recombinant cellulose binding module- protein by affinity adsorption on an ultra-high-capacity cellulosic adsorbent, Analytica Chimica Acta, 2008 15. Moxley, et al., Efficient Sugar Release by the Cellulose Solvent-Based Lignocellulose Fractionation Technology and Enzymatic Cellulose Hydrolysis, Journal of Agricultural and Food Chemistry, 2008 16. Yuan, et al., Plants to power: bioenergy to fuel the future, Trends in Plant Science, 2008

Transcript of static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and...

Page 1: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

1. Mohnen, et al., Cell wall polysaccharide synthesis, Biomass Recalcitrance, 20082. Ding, et al., Identifying Molecular Structural Features of Biomass Recalcitrance

Using Nondestructive Microscopy and Spectroscopy, Microcopy and Microanalysis, 2008

3. Keller, et al., Microbial goods from single cells and metagenomes, Current Opinion in Microbiology, 2008

4. Lynd, et al., How biotech can transform biofuels, Nature Biotechnology, 20085. Xi, et al., Agrobacterium-mediated transformation of switchgrass and inheritance of

the transgenes BER-133R1, BioEnergy Research, 20086. Ljungdahl, et al., Contribution of domain interactions and calcium binding to the

stability of carbohydrate-Active enzymes, Bioenergy, 20087. Ding, et al., A Biophysical Perspective of the Cellulosome: New Opportunities for

Biomass Conversion, Current Opinion in Biotechnology, 20088. York, et al., Biochemical control of xylan biosynthesis — which end is up?, Current

Opinion Plant Biology, 20089. Blumer-Schuette, et al., Extremely thermophilic microorganisms for biomass

conversion: status and prospects, Current Opinion in Biotechnology, 200810. Mohnen, et al., Pectin Structure and Biosynthesis, Current Opinion Plant Biology,

200811. Bordner, et al., Comprehensive inventory of protein complexes in the Protein Data

Bank from consistent classification of interfaces, BMC Bioinformatics, 200812. Zhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 200813. Hong, et al., Simple protein purification through affinity adsorption on regenerated

amorphous cellulose followed by intein self-cleavage, Journal of Chromatography, 2008

14. Hong, et al., Bioseparation of recombinant cellulose binding module-protein by affinity adsorption on an ultra-high-capacity cellulosic adsorbent, Analytica Chimica Acta, 2008

15. Moxley, et al., Efficient Sugar Release by the Cellulose Solvent-Based Lignocellulose Fractionation Technology and Enzymatic Cellulose Hydrolysis, Journal of Agricultural and Food Chemistry, 2008

16. Yuan, et al., Plants to power: bioenergy to fuel the future, Trends in Plant Science, 2008

17. Goel, et al., System estimation from metabolic time-series data, Bioinformatics, 2008

18. Mao, et al., DOOR: a database for prokaryotic operons, Nucleic Acids Research, 2008

19. Cole, et al., Possible impacts of the US EPA Notice of Proposed Rulemaking on the biofuels industry, Industrial Biotechnology, 2008

20. Petridis, et al., Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomass, Journal of Physics, 2008

21. Sykes, et al., Within tree variability of lignin composition in Populus, Wood Science and Technology, 2008

22. Zhang, et al., A sweet and out-of-the-box solution for the hydrogen economy: Is sugar-powered car science fiction?, Energy and Environmental Science, 2009

23. Zhang, et al., Advances in cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF), ACS Symposium Series, 2009

Page 2: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

24. Burris, et al., An improved tissue culture system for embyrogenic callus production and plant regeneration in switchgrass (Panicum virgatum L.) BER-130R1, Bioenergy Research, 2009

25. Zhu, et al., Direct quantitative determination of adsorbed cellulase on lignocellulosic biomass with its application to study cellulase desorption for potential recycling, Analyst, 2009

26. Slavov, et al., Extensive pollen flow in two ecologically contrasting populations of Populus trichocarpa, Molecular Ecology, 2009

27. Zhulin (Jouline), et al., It Is Computation Time for Bacteriology!, Journal of Bacteriology, 2009

28. Yin, et al., Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome, New Phytologist, 2009

29. Desikan, et al., Nanomechanical Methods to Study Single Cells, Accessing Uncultivated Microorganisms, 2009

30. Jiang, et al., Perdeuterated pyridinium molten salt (ionic liquid) for direct dissolution and NMR analysis of plant cell walls, Green Chemistry, 2009

31. Yang, et al., Poplar genomics: State of the science, Critical Reviews in Plant Sciences, 2009

32. Mazarei, et al., Protoplast isolation and transient gene expression in switchgrass, Panicum virgatum L., Biotechnology Journal, 2009

33. Keller, et al., Single-Cell Genomics, Accessing Uncultivated Microorganisms, 200934. Ye, et al., Spontaneous high-yield production of hydrogen from cellulosic materials

and water catalyzed by enzyme cocktails, ChemSusChem, 200935. Zhao, et al., Two poplar methyl salicylate esterases display comparable biochemical

properties but divergent expression patterns, Phytochemistry, 200936. Zhou, et al., RepPop: a database for repetitive elements in Populus trichocarpa,

BMC Genomics, 200937. Yang, Transcriptomic and metabolomic profiling of Zymomonas mobilis during

aerobic and anaerobic fermentations, BMC Genomics, 200938. Li, et al., Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass,

Biotechnology for Biofuels, 200939. Karpinets, Phenotype fingerprinting suggests the involvement of single-genotype

consortia in degradation of aromatic compounds by Rhodopseudomonas palustris, PLoS One, 2009

40. Keller, et al., Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level, et al., Microbiology and Molecular Biology Reviews, 2009

41. Hisano, et al., Genetic modification of lignin biosynthesis for improved biofuel production, Journal of In Vitro Cellular and Developmental Biology – Plant, 2009

42. Guyett, et al., Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase, Carbohydrate Research, 2009

43. Liu, et al., Fast identification of thermostable beta-glucosidase mutants on cellobiose by a novel combinatorial selection/screening approach, Biotechnology and Bioengineering, 2009

44. Raman, et al., Impact of pretreated switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis, PLoS One, 2009

Page 3: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

45. Zhou, et al., Cellulose hydrolysis in evolving substrate morphologies I: a general modeling formalism, Biotechnology and Bioengineering, 2009

46. Zhou, et al., Cellulose hydrolysis in evolving substrate morphologies II: numerical results and analysis, Biotechnology and Bioengineering, 4/27/2009

47. Xu, et al., Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation, Protein Science, 2009

48. Yang, et al., Efficient degradation of lignocellulosic plant biomass without pretreatment by the thermophilic anaerobe, Anaerocellum thermophilum DSM 6725, Applied and Environmental Microbiology, 2009

49. Sathitsuksanoh, et al., Saccharification of a potential bioenergy crop, Phragmites australis (common reed), by lignocellulose fractionation followed by enzymatic hydrolysis at decreased cellulase loadings, Industrial & Engineering Chemistry Research, 5/28/2009

50. Drost, et al., A Microarray-Based Genotyping and Genetic Mapping Approach for Highly Heterozygous Outcrossing Species Localizes a Large Fraction of the Unassembled Populus trichocarpa Genome Sequence, Plant Journal, 2009

51. Kataeva, et al., Genome Sequence of the Anaerobic, Thermophilic, and Cellulolytic Bacterium "Anaerocellum thermophilum" DSM 6725, Journal of Bacteriology, 2009

52. Ye, et al., Identification of the Flavin-dependent Monooxygenase-encoding YUCCA Gene Family in Populus trichocarpa and Their Expression in Vegetative Tissues and in Response to Hormone and Environmental Stresses, Plant Cell, Tissue and Organ Culture (PCTOC) - Journal of Plant Biotechnology, 2009

53. Chou, et al., Recent developments in parameter estimation and structure identification of biochemical and genomic systems, Mathematical Biosciences, 2009

54. Miller, et al., The DOE BioEnergy Science Center - a U.S. Department of Energy Bioenergy Research Center, Journal of In Vitro Cellular and Developmental Biology – Plant, 2009

55. Ghimire, et al., The mycorrhizal fungus, Sebacina vermifera, enhances seed germination and biomass production in switchgrass (Panicum virgatum L), BioEnergy Research, 2009

56. Wang, et al., Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration, Microbial Cell Factories, 6/4/2009

57. Gu, et al., Enzymatic characterization and comparison of various Poaceae UDP-GlcA 4-Epimerase Isoforms, Journal of Biochemistry, 6/15/2009

58. Liu, et al., Does the Cellulose-Binding Module Move on the Cellulose Surface?, Cellulose, 6/19/2009

59. Wang, et al., Cell-free protein synthesis energized by slowly-metabolized maltodextrin, BMC Biotechnology, 6/28/2009

60. Zhu, et al., Comparative study of corn stover pretreated by dilute acid and cellulose solvent‐based lignocellulose fractionation: Enzymatic hydrolysis, supramolecular structure, and substrate accessibility, Biotechnology and Bioengineering, 2009

61. Lee, et al., Effects of gold patterning on the bending profile and frequency response of a microcantilever, Journal of Applied Physics, 7/27/2009

62. Yin, et al., The cellulose synthase superfamily in fully sequenced plants and algae, BMC Plant Biology, 7/31/2009

Page 4: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

63. Yang, et al., Identification of galacturonic acid-1-P kinase: a new member of the GHMP kinase super family in plants and comparison with galactose-1-P kinase, Journal of Biological Chemistry, 8/7/2009

64. Samuel, et al., Structural characterization and comparison of switchgrass ball milled lignin before and after dilute acid pretreatment, Applied Biochemistry and Biotechnology, 8/24/2009

65. Zhang, et al., Cellulase Assays, Biofuels: Methods and Protocols, 200966. Chen, Genomics of Secondary Metabolism in Populus: Interactions with Biotic and

Abiotic Environments, Critical Reviews in Plant Sciences, 200967. Mao, et al., pDAWG: an Integrated Database for Plant Cell-Wall Genes, BioEnergy

Research, 200968. Liu, et al., The family 1 glycoside hydrolase from Clostridium cellulolyticum H10 is a

cellodextrin glucohydrolase., Applied Biochemistry and Biotechnology, 200969. Kong, et al., Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are

Functional Orthologs to PARVUS/AtGATL1 in Arabidopsis, Molecular Plant, 200970. Cheng, et al., Populus community mega-genomics: coming of age, Critical Reviews

in Plant Sciences, 9/5/200971. Caffall, et al., Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the

Biosynthe sis of Pectin and Xylan in Cell Walls and Seed Testa, Molecular Plant, 9/11/2009

72. Sykes, et al., High Throughput Screening of Plant Cell Wall Composition Using Pyrolysis Molecular Beam Mass Spectroscopy, Biofuels: Methods and Protocols, 9/18/2009

73. Sathitsuksanoh, et al., Bamboo saccharification through cellulose solvent-based biomass pretreatment followed by enzymatic hydrolysis at ultra-low cellulase loadings, Bioresource Technology, 9/25/2009

74. Caffall, et al., The structure, function, and biosynthesis of plant cell wall pectic polysaccharides, Carbohydrate Research, 9/28/2009

75. Yang, et al., Improved genome annotation for Zymomonas mobilis, Nature Biotechnology, 2009

76. Schulz, et al., Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer, Journal of Chemical Theory and Computation, 2009

77. Podar, et al., Single Cell Whole Genome Amplification of Uncultivated Organisms, Uncultivated Microorganisms Microbiology Monographs, 2009

78. Xu, et al., Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom, BMC Bioinformatics, 10/9/2009

79. Ulrich, et al., The MiST2 database: a comprehensive genomics resource on microbial signal transduction, Nucleic Acids Research, 10/9/2009

80. Yang, et al., Natural variation for nutrient-use and remobilization efficiencies in switchgrass BER-124R1, BioEnergy Research, 10/14/2009

81. Shen, et al., A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production BER-120R1, BioEnergy Research, 10/16/2009

82. Shen, et al., Developmental control of lignification in stems of lowland switchgrass variety Alamo and the effects on saccharification efficiency, BioEnergy Research, 10/20/2009

83. Patten, et al., Probing native lignin macromolecular configuration in Arabidopsis thaliana in specific cell wall types: Further insights into limited substrate

Page 5: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

degeneracy and assembly of the lignins of ref8, fah 1–2 and C4H::F5H lines, Molecular BioSystems, 10/22/2009

84. Ranjan, et al., Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus, BioEnergy Research, 12009

85. Voit, et al., Estimation of Metabolic Pathway Systems from Different Data Sources, IET Systems Biology, 2009

86. Zhang, et al., Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations (SyPaB): Challenges and opportunities, Biotechnology and Bioengineering, 2009

87. Kalluri, et al., Shotgun proteome profile of Populus developing xylem, Proteomics, 2009

88. Tran, et al., De novo computational prediction of non-coding RNA genes in prokaryotic genomes, et al., Bioinformatics, et al., 11/15/2009

89. Liu, et al., A single molecule study of cellulase hydrolysis of crystalline cellulose, Spie-Int Soc Optical Engineering, 2009

90. Machina, et al., Automated piecewise power-law modeling of biological systems, Journal of Biotechnology, et al., 2009

91. Yang, et al., Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov., International Journal of Systematic and Evolutionary Microbiology, 2009

92. Dixon, et al., DOE Bioenergy Center Special Issue. The Bioenergy Sciences Center (BESC), BioEnergy Research, 2009

93. Mielenz, et al., Fermentation of soybean hulls to ethanol while preserving protein value, Bioresource Technology, 2009

94. Decker, et al., High-Throughput Screening Techniques for Biomass Conversion, Bioenergy Research, 2009

95. Zhou, et al., Large scale analyses of glycosylation in cellulases, Genomics, Proteomics and Bioinformatics, 2009

96. Kang, et al., Micropropagation of Populus trichocarpa 'Nisqually-1': The genotype deriving the Populus reference genome, Plant Cell, Tissue and Organ Culture (PCTOC) - Journal of Plant Biotechnology, 2009

97. Pu, et al., NMR Characterization of C3H and HCT Down-regulated Alfalfa Lignin, BioEnergy Research, 2009

98. Mann, et al., Rapid assessment of lignin content and structure in switchgrass (Panicum virgatum L.) grown under different environmental conditions, BioEnergy Research, 2009

99. Smith, et al., Supercomputers Tackle BIOFUEL Production Problems, SciDAC Review, 2009

100. Davison, et al., The goals and research of the BioEnergy Sciences Center (BESC): Developing cost-effective and sustainable means of producing biofuels by overcoming biomass recalcitrance, Bioenergy Research, 2009

101. Foston, et al., Variations in Cellulosic Ultrastructure of Poplar BER-123R1, BioEnergy Research, 2009

102. Bochner, et al., Phenotype MicroArray Profiling of Zymomonas mobilis ZM4, Applied Biochemistry and Biotechnology, 2009

103. VanFossen, et al., Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences, Applied and Environmental Microbiology, 2009

Page 6: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

104. Hamilton-Brehm, et al., Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park, Applied and Environmental Microbiology, 2009

105. Tetard, et al., New modes for subsurface atomic force microscopy through nanomechanical coupling, Nature Nanotechnology, 2009

106. Kim, et al., Piezoresistive cantilever array sensor for consolidated bioprocess monitoring, Scanning, 2009

107. Stewart, et al., China-U.S. Workshop on Biotechnology of Bioenergy Plants, Ecotoxicology, 2010

108. Xu, et al., Computational Challenges in Deciphering Genomic Structures of Bacteria, Journal of Computer Science and Technology, 2010

109. Wuichet, et al., Evolution and phyletic distribution of two-component signal transduction systems, Current Opinion in Microbiology, 2010

110. Lindedam, et al., Near Infrared Spectroscopy as a Screening Tool for Sugar Release and Chemical Composition of Wheat Straw, Journal of Biobased Materials and Bioenergy, 2010

111. Slavov, et al., Salient Biological Features, Systematics, and Genetic Variation of Populus, Genetics and Genomics of Populus, 2010

112. Samuel, et al., Solid-state NMR characterization of switchgrass cellulose after dilute acid pretreatment, Biofuels, 2010

113. Escamilla-Treviño, et al., Switchgrass (Panicum virgatum L.) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties, New Phytologist, 2010

114. Kausch, et al., Transgenic perennial biofuel feedstocks and strategies for bioconfinement, Biofuels, 2010

115. Jung, et al., Surface Characterization of Dilute Acid Pretreated Populus deltoides by ToF-SIMS, Energy and Fuels, 2010

116. Studer, et al., Engineering of a High-Throughput Screening System to Identify Cellulosic Biomass, Pretreatments, and Enzyme Formulations that Enhance Sugar Release., Biotechnology and Bioengineering, 2010

117. Xie, et al., PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis, PNAS, 2010

118. Vogel, et al., Genome sequencing and analysis of the model grass Brachypodium distachyon, Nature, 2010

119. Zeng, et al., Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy, BioEnergy Research, 2010

120. Zhao, et al., An NAC transcription factor orchestrates multiple features of cell wall development in Medicago truncatula, Plant Journal, 2010

121. Abulencia, et al., Accessing Microbial Communities Relevant to Biofuels Production, Manual of Industrial Microbiology and Biotechnology, 2010

122. Yin, et al., Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8, Plant Physiology, 2010

123. Mielenz, et al., Improving microbial robustness using systems biology, Manual of Industrial Microbiology and Biotechnology, 2010

124. Chen, et al., Macromolecular replication during lignin biosynthesis, Phytochemistry, 2010

125. Himmel, et al., Microbial enzyme systems for biomass conversion: emerging paradigms, Biofuels, 2010

Page 7: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

126. Sannigrahi, et al., Poplar as a feedstock for biofuels: A review of compositional characteristics, Biofuels, Bioproducts and Biorefining (Biofpr), 2010

127. Zhang, et al., The non-cellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: Heterologous expression, characterization, and processivity., Applied Microbiology and Biotechnology, 2010

128. Ye, et al., Thermophilic alpha-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability, Journal of Molecular Catalysis B: Enzymatic, 2010

129. Zhou, et al., GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems, BMC Microbiology, 3/4/2010

130. Petridis, et al., A Molecular Mechanics Force Field for Lignin, Journal of Computational Chemistry, 2010

131. Gu, et al., Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family, Journal of Biological Chemistry, 2010

132. Yin, et al., Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome, PNAS, 2010

133. Myung, et al., Fructose-1,6-bisphosphatase from a hyper-thermophilic bacterium Thermotoga maritime: Characterization, metabolite stability, and its implications, Process Biochemistry, 2010

134. Li, et al., Increased Crystalline Cellulose Activity via Combinations of Amino Acid Changes in the Family 9 Catalytic Domain and Family 3c Cellulose Binding Module of Thermobifida fusca Cel9A, Applied and Environmental Microbiology, 2010

135. Selig, et al., Lignocellulose recalcitrance screening by integrated high- throughput hydrothermal pretreatment and enzymatic, Industrial Biotechnology, 2010

136. Yang, et al., Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae, PNAS, 2010

137. Darvill, et al., Plant Cell Walls, Plant Cell Walls, 2010138. Yang, et al., The Zymomonas mobilis regulator Hfq and related Saccharomyces

cerevisiae proteins contribute to tolerance against multiple lignocellulosic pretreatment inhibitors, BMC Microbiology, 2010

139. Kang, et al., Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP-binding cassette transporter confers resistance to four aminoglycoside antibiotics, Plant Cell Reports, 2010

140. Chen, et al., A High - Throughput Transient Gene Expression System for Switchgrass (Panicum virgatum L.) Seedlings, Biotechnology for Biofuels, 2010

141. Hu, et al., Chemical Profiles of Switchgrass, Bioresource Technology, 2010142. Shaw, et al., Natural Competence in Thermoanaerobacter and

Thermoanaerobacterium Species, Applied and Environmental Microbiology, 2010143. Slavov, et al., Population substructure in continuous and fragmented stands of

Populus trichocarpa, Heredity, 2010144. Hubbell, et al., Effect of acid-chlorite delignification on cellulose degree of

polymerization, Bioresource Technology, 2010145. Moon, et al., Sustainable Use of Biotechnology for Bioenergy Feedstocks, et al.,

Environmental Management, 2010146. Zhang, et al., Biofuel production by in vitro synthetic pathway biotransformation,

Current Opinion in Biotechnology, 2010

Page 8: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

147. Zhou, et al., Cellulose hydrolysis in evolving substrate morphologies III: time scale analysis, Biotechnology and Bioengineering, 2010

148. Izquierdo, et al., Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost, Applied and Environmental Microbiology, 2010

149. Elkins, et al., Engineered microbial systems for enhanced conversion of lignocellulosic biomass, Current Opinion in Biotechnology, 2010

150. Liu, et al., Engineering of Clostridium phytofermentans endoglucanase Cel5A for improved thermostability, Applied and Environmental Microbiology, 2010

151. Zhang, et al., Glycoside hydrolase family 9 processive endoglucanase from Clostridium phytofermentans: Heterologous expression, purification, and synergy with family 48 cellobiohydrolase, Bioresource Technology, 2010

152. Yang, et al., Identification of a novel UDP-sugar Pyrophosphorylase with a broad substrate specificity In Trypanosoma cruzi, Biochemical Journal, 2010

153. Wuichet, et al., Origins and Diversification of a Complex Signal Transduction System in Prokaryotes, Science Signaling, 2010

154. Voit, et al., Parameter Estimation in Canonical Biological Systems Models, International Journal of Systems Synthetic Biology, 2010

155. Tetard, et al., Spectroscopy and atomic force microscopy of biomass, Ultramicroscopy, 2010

156. Zhu, et al., Virus-Induced Gene Silencing Offers a Functional Genomics Platform for Studying Plant Cell Wall Formation, Molecular Plant, 2010

157. Gu, et al., Biosynthesis of a New UDP-sugar, UDP-2-acetamido-2-deoxyxylose, in the Human Pathogen Bacillus cereus Subspecies cytotoxis NVH 391-98, Journal of Biological Chemistry, 2010

158. Kalluri, et al., Bioenergy Research: A new paradigm in multidisciplinary research, Journal of the Royal Society Interface, 2010

159. Yang, et al., Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis, Biochemical Journal, 2010

160. Saar, et al., Label-free, real-time monitoring of biomass processing with stimulated Raman scattering microscopy, Angewandte Chemie, 2010

161. Lacayo, et al., Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements, Plant Physiology, 2010

162. Voelker, et al., Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar, Plant Physiology, 2010

163. Foston, et al., Changes In Lignocellulosic Supramolecular And Ultrastructure During Dilute Acid Pretreatment Of Populus And Switchgrass, Biomass and Bioenergy, 2010

164. Andrews, et al., "Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2", Annuals of Bioanalytical Chemistry, 2010

165. Andrews, et al., Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting, Annuals of Bioanalytical Chemistry, 2010

166. Zhang, et al., Renewable carbohydrates are a potential high-density hydrogen carrier, International Journal of Hydrogen Energy, 2010

167. Mazumder, et al., Structural analysis of arabinoxylans isolated from ball milled switchgrass biomass, et al., Carbohydrate Research, 2010

168. Alahuhta, et al., Structure of a fibronectin type III-like module from Clostridium thermocellum, et al., Acta Crystallographica - Section F, 2010

Page 9: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

169. David, et al., Switchgrass as an energy crop for biofuel production: A review of its ligno-cellulosic chemical properties, Energy and Environmental Science, 2010

170. Zhao, et al., Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch, PNAS, 2010

171. Alahuhta, et al., The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A, Journal of Molecular Biology, 2010

172. Vuong, et al., Glycoside hydrolases: Catalytic base / nucleophile diversity, Biotechnology and Bioengineering, 2010

173. Bomble, et al., Modeling the Cellulosome Using Multiscale Methods, ACS Symposium Series - Computational Modeling in Lignocellulosic Biofuel Production, 2010

174. Moinuddin, et al., Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMP (caffeic acid O-methyl transferase) mutant Atomt1, Organic and Biomolecular Chemistry, 2010

175. Wang, et al., A novel FRET approach for in situ investigation of cellulase–cellulose interaction, Analytical and Bioanalytical Chemistry, 2010

176. Tripathi, et al., Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant, Applied and Environmental Microbiology, 2010

177. Kausch, et al., Gene flow in genetically engineered perennial grasses: lessons for modification of dedicated bioenergy crops, Biotechnology in Agriculture and Forestry, 2010

178. Kausch, et al., Genetic modification in dedicated bioenergy crops and strategies for gene confinement., Biotechnology in Agriculture and Forestry, 2010

179. Zhang, et al., One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges, Engineering in Life Sciences, 2010

180. Xu, et al., "Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin–dockerin complex and its variants", Protein Engineering, Design and Selection, 2010

181. Zhou, et al., Identification of Novel Proteins Involved in Plant Cell-Wall Synthesis Based on Protein−Protein Interaction Data, Journal of Proteome Research, 8/5/2010

182. Olson, et al., Deletion of Cel48S from Clostridium thermocellum, et al., PNAS, 2010183. Chou, et al., GolgiP: prediction of Golgi resident proteins in plants, Bioinformatics,

2010184. Rollin, et al., Increasing cellulose accessibility is more important than removing

lignin: A comparison of cellulose solvent-based lignocellulose fractionation and soaking in aqueous ammonia, Biotechnology and Bioengineering, 8/30/2010

185. Yang, et al., Genomic aspects of research involving polyploid plants, Plant Cell, Tissue and Organ Culture (PCTOC), 8/31/2010

186. Lee, et al., Mathematical modeling of monolignol biosynthesis in Populus xylem, Mathematical Biosciences, 2010

187. DeMartini, et al., Small scale and automatable high-throughput compositional analysis of biomass, et al., Biotechnology and Bioengineering, 2010

188. Gu, et al., Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose-4-epimerase, et al., Microbiology, 2010

189. Li, et al., A new framework for identifying cis-regulatory motifs in prokaryotes, Nucleic Acids Research, 9/29/2010

Page 10: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

190. Foston, et al., Changes in the Structure of the Cellulose Fiber Wall during Dilute Acid Pretreatment in Populus Studied by 1H and 2H NMR, Energy and Fuels, 9/30/2010

191. DiFazio, et al., The Populus Genome Project, Principles and Practices of Plant Genomics Volume 3, 9/30/2010

192. Bergenstrahle, et al., Simulation studies of the insolubility of cellulose, Carbohydrate Research, 2010

193. DeMartini, et al., Changes in composition and sugar release across the annual rings of Populus wood and implications on recalcitrance, Bioresource Technology, 2010

194. Elkins, et al., Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T, Journal of Bacteriology, 2010

195. Wang, et al., Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis, Bioresource Technology, 2010

196. Wang, et al., Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants, PNAS, 2010

197. Jiang, et al., Rapid determination of lignin content via direct dissolution and 1H NMR analysis of the plant cell walls, ChemSusChem, 2010

198. Jiang, et al., "Time-Resolved NMR: Extracting the Topology of Complex Enzyme Networks", Biophysical Journal, 2010

199. Ziebell, et al., Increase in 4-coumaryl alcohol units during lignification in alfalfa (Medicago sativa) alters the extractability and molecular weight of lignin, Journal of Biological Chemistry, 10/4/2010

200. Zhang, et al., Ethanol Production From Paper Sludge by Simultaneous Saccharification and Co-Fermentation Using Recombinant Xylose-Fermenting Microorganisms, Biotechnology and Bioengineering, 10/10/2010

201. Saharay, et al., Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS, PloS One, 10/12/2010

202. Blumer-Schuette, et al., Phylogenetic, microbiological and glycoside hydrolase diversity within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor, Applied Environmental Microbiology, 10/22/2010

203. Tyler, et al., Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon, BMC Genomics, 10/25/2010

204. Ghimire, et al., Biodiversity of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma, Fungal Diversity, 12010

205. Sathitsuksanoh, et al., Cellulose solvent-based pretreatment breaks highly ordered hydrogen bonds in cellulose fibers of switchgrass, Biotechnology and Bioengineering, 11/12/2010

206. Yin, et al., Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus, PloS One, 11/22/2010

207. Jung, et al., Direct analysis of cellulose in poplar stem by matrix-assisted laser desorption/ionization imaging mass spectrometry, Rapid Communications in Mass Spectrometry, 11/30/2010

208. Huang, et al., Analysis of biofuels production from sugar based on three criteria: Thermodynamics, bioenergetics, and product separation, Energy and Environmental Science, 12010

209. Beckham, et al., Application of computational science for understanding enzymatic deconstruction of cellulose, Current Opinion in Biotechnology, 12010

Page 11: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

210. Park, et al., CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database, et al., Glycobiology, 2010

211. Sannigrahi, et al., Pseudo-lignin and pretreatment chemistry, Energy and Environmental Science, 2010

212. Dagel, et al., In Situ Imaging of Single Carbohydrate-Binding Modules on Cellulose Microfibrils, Journal of Physical Chemistry B, 2010

213. Yao, et al., QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity, Journal of Physical Chemistry B, 12/17/2010

214. Atsumi, et al., Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, Molecular Systems Biology, 12/21/2010

215. Yin, et al., Glycosyltransferases of the GT8 Family, Annual Plant Reviews, Plant Polysaccharides, Biosynthesis and Bioengineering, 12/22/2010

216. Podkaminer, et al., "Enzyme inactivation by ethanol and development of a kinetic model for thermophilic simultaneous saccharification and fermentation at 50°C with Thermoanaerobacterium saccharolyticum ALK2", Biotechnology and Bioengineering, 2010

217. Blumer-Schuette, et al., Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjannonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor lactoaceticus, Journal of Bacteriology, 2011

218. Chen, et al., Genome-wide discovery of missing genes in biological pathways of prokaryotes, BMC Bioinformatics, 2011

219. Mann, et al., pANIC: A versatile set of Gateway-compatible vectors for gene overexpression and RNAi-mediated down-regulation in monocots, Plant Transformation Technologies, 2011

220. Alahuhta, et al., Structure of CBM4 from Clostridium thermocellum cellulase K, Acta Crystallographica - Section F, 2011

221. Chen, et al., The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom, The Plant Journal, 2011

222. Zhang, et al., Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis, Microbial Biotechnology, 2011

223. Fu, et al., Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass, BioEnergy Research, 2011

224. Srivastava, et al., "The Folylpolyglutamate Synthetase Plastidial Isoform is Required for Postembryonic Root Development in Arabidopsis", Plant Physiology, 2011

225. Dam, et al., Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725, Nucleic Acids Research Advance, 2011

226. Zhang, et al., Renewable Hydrogen Carrier — Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy, Energies, 2011

227. Lee, et al., Analysis of Operating Principles with S-system Models, Mathematical Biosciences, 2011

228. Liu, et al., Cellobiohydrolase Hydrolyzes Crystalline Cellulose on Hydrophobic Faces, Journal of Biological Chemistry, 2011

229. Selig, et al., High-Throughput Determination of Glucan and Xylan Fractions in Lignocelluloses, Biotechnology Letters, 2/2/2011

Page 12: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

230. Chundawat, et al., Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals, The Annual Review of Chemical and Biomolecular Engineering, 2/4/2011

231. Sizova, et al., Cellulose- and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost, Applied and Environmental Microbiology, 2/11/2011

232. Cartmell, et al., "The structure and function of an arabinan-specific a-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases", Journal of Biological Chemistry, 2/16/2011

233. Yang, et al., Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics, Plant Science, 2/17/2011

234. Wang, et al., Biohydrogenation from Biomass Sugar Mediated by in vitro Synthetic Enzymatic Pathways, Chemistry and Biology, 2011

235. Fu, et al., Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass, PNAS, 2011

236. Studer, et al., Lignin content in natural Populus variants affects sugar release, PNAS, 2011

237. Bar-Peled, et al., Plant Nucleotide Sugar Formation, Interconversion, and Salvage by Sugar Recycling, Annual Review of Plant Biology, 2011

238. Tsai, et al., Poplar Genome Microarrays, Genetics, Genomics and Breeding of Crop Plants: Poplar, 2011

239. Srivastava, et al., The plastidial folylpolyglutamate synthetase and root apical meristem maintenance, Plant Signaling and Behavior, 2011

240. Yang, et al., Discovery and annotation of small proteins using genomics, proteomics, and computational approaches, Genome Research, 3/2/2011

241. VanFossen, et al., Glycoside Hydrolase Inventory Drives Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus, Biotechnology and Bioengineering, 3/11/2011

242. Cai, et al., MicroSyn: A user friendly tool for detection of microsynteny in a gene family, BMC Bioinformatics, 3/18/2011

243. Myung, et al., Ultra-Stable Phosphoglucose Isomerase Through Immobilization of Cellulose-Binding Module-Tagged Thermophilic Enzyme on Low-Cost High-Capacity Cellulosic Adsorbent, Biotechnology Progress, 3/21/2011

244. Petridis, et al., Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes, ACS Symposium Series - Computational Modeling in Lignocellulosic Biofuel Production, 2011

245. Higashide, et al., Metabolic Engineering of Clostridium cellulolyticum for Isobutanol Production from Cellulose, et al., Applied and Environmental Microbiology, 2011

246. Samuel, et al., HSQC (heteronuclear single quantum coherence) 13C–1H correlation spectra of whole biomass in perdeuterated pyridinium chloride–DMSO system: An effective tool for evaluating pretreatment, Fuel, 4/11/2011

247. Lochner, et al., Label-free quantitative proteomics distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis, Applied Environmental Microbiology, 4/15/2011

248. Zhu, et al., Maltodextrin-Powered Enzymatic Fuel Cell through a Non-Natural Enzymatic Pathway, Journal of Power Sources, 4/22/2011

249. Pu, et al., Application of quantitative (31)P NMR in biomass lignin and biofuel precursors characterization, Energy and Environmental Science, 2011

250. Sukharnikov, et al., Cellulases: ambiguous nonhomologous enzymes in a genomic perspective, Trends in Biotechnology, 2011

Page 13: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

251. Srivastava, et al., Collection and analysis of expressed sequence tags derived from laser capture microdissected switchgrass (Panicum virgatum L. Alamo) vascular tissues, BioEnergy Research, 2011

252. Ye, et al., Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis, Plant Science, 2011

253. Wilson, et al., Microbial diversity of cellulose hydrolysis, Current Opinion in Microbiology, 2011

254. Deshpande, et al., Plant Genetics for Study of the Roles of Root Exudates and Microbes in the Soil, Root Genomics, 2011

255. DiFazio, et al., Populus: A premier pioneer system for plant genomics, Genetics, Genomics and Breeding of Crop Plants, 2011

256. Mazarei, et al., Switchgrass (Panicum virgatum L.) cell suspension cultures: Establishment, characterization, and application, Plant Science, 2011

257. Ye, et al., "Fusion of a family 9 cellulose-binding module improves catalytic potential of Clostridium thermocellum cellodextrin phosphorylase on insoluble cellulose", Applied Microbiology and Biotechnology, 5/3/2011

258. Zhang, et al., One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtillis, Metabolic Engineering, 5/3/2011

259. Tetard, et al., Virtual Resonance and Frequency Difference Generation by van der Waals Interaction, Physical Review Letters, 5/6/2011

260. Lee, et al., Integrative Analysis of Transgenic Alfalfa (Medicago sative L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis, PloS Computational Biology, 5/16/2011

261. Correia, et al., The structure and function of an arabinoxylan-specific xylanase, Journal of Biological Chemistry, 5/20/2011

262. Chung, et al., Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes, Journal of Industrial Microbiology and Biotechnology, 5/22/2011

263. Shao, et al., Conversion for Avicel and AFEX pretreated corn stover by Clostridium thermocellum and simultaneous saccharification and fermentation: Insights into microbial conversion of pretreated cellulosic biomass, Bioresource Technology, 2011

264. Zhou, et al., Developmental Analysis of a Medicago truncatula smooth leaf margin1 Mutant Reveals Context-Dependent Effects on Compound Leaf development, The Plant Cell, 2011

265. Bomble, et al., Modeling the Self-assembly of the Celluosome Enzyme Complex, The Journal of Biological Chemistry, 2011

266. Zhang, et al., Substrate channeling and enzyme complexes for biotechnological applications, Biotechnology Advances, 6/7/2011

267. Raman, et al., "Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation", BMC Microbiology, 6/14/2011

268. Mohnen, et al., Plants Get Hyp to O-Glycosylation, Science, 6/17/2011269. Liao, et al., A minimal set of bacterial cellulases for consolidated bioprocessing of

lignocelluloses, Biotechnology Journal, 2011270. Huang, et al., Energy Efficiency Analysis: Biomass-to-Wheel Efficiency Related with

Biofuels Production, Fuel Distribution, and Powertrain System, PloS One, 2011

Page 14: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

271. Zhang, et al., Simpler Is Better: High-Yield and Potential Low-Cost Biofuels Production through Cell-Free Synthetic Pathway Biotransformation (SyPaB), ACS Catalysis, 2011

272. Yang, et al., Enzymatic hydrolysis of cellulosic biomass, Biofuels, 2011273. Zhang, et al., "Toward low-cost biomanufacturing through in vitro synthetic biology:

bottom-up design", Journal of Materials Chemistry, 7/4/2011274. Yang, et al., Innovative Biological Solutions to Challenges in Sustainable Biofuels

Production, Biofuel Production-Recent Developments and Prospects, 7/5/2011275. Zhang, et al., Hydrogen Production from Carbohydrates: A mini-review, ACS

Symposium Series, 7/11/2011276. Mann, et al., Switchgrass (Panicum virgatum L.) ubiquitin gene (PvUbi1 and PvUbi2)

promoters for use in plant transformation, BMC Biotechnology, 7/11/2011277. Studer, et al., Co-hydrolysis of hydrothermal and dilute acid pretreated Populus

slurries to support development of a high-throughput pretreatment system, Biotechnology for Biofuels, 7/12/2011

278. Brown, et al., Complete Genome Sequence of the Haloalkaliphilic, Hydrogen Producing Halanaerobium hydrogenoformans, Journal of Bacteriology, 7/14/2011

279. Kostylev, et al., Determination of the catalytic base in family 48 glycosyl hydrolases, Applied Environmental Microbiology, 7/15/2011

280. Liao, et al., One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP, Applied Microbiology and Biotechnology, 7/16/2011

281. Farkas, et al., Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon, Pyrococcus furiosus, needed for construction of a stable replicating shuttle vector, Applied Environmental Microbiology, 7/22/2011

282. Mao, et al., SEAS: A system for SEED-Based Pathway Enrichment Analysis, PloS One, 7/22/2011

283. Zhang, et al., Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences, Genetica, 7/23/2011

284. Xu, et al., Silencing of 4-coumarate:coenzyme A ligase in switchgrass leads to reduced lignin content and improved fermentable sugar yields for biofuel production, New Phytologist, 7/25/2011

285. Voit, et al., What if the Fit is Unfit? Criteria for Biological Systems Estimation Beyond Residual Errors, Applied Statistics for Biological Networks, 2011

286. Zhang et al., What is vital (and not vital) to advance economically-competitive biofuels production, Process Biochemistry, 2011

287. Dagel, et al., "DOPI and PALM Imaging of Single Carbohydrate Binding Modules Bound to Cellulose Nanocrystals", SPIE Proc. Proc, 2011

288. Li, et al., Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases, Biotechnology for Biofuels, 8/4/2011

289. Xu, et al., Multifunctional Enzyme Systems for Plant Cell Wall Degradation, Comprehensive Biotechnology (Second Edition), 8/5/2011

290. Ge, et al., "Pollen Viability and Longevity of Switchgrass (Panicum virgatum L.)", Crop Science, 8/11/2011

291. Joyce, et al., Designing the perfect plant feedstock for biofuel production: using the whole buffalo to diversify fuels and products, Biotechnology Advances, 8/12/2011

292. Zhang, et al., Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass, Crop Science, 8/12/2011

Page 15: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

293. Ghimire, et al., Enhancement of Switchgrass (Panicum virgatum L.) Biomass Production under Drought Conditions by the Ectomycorrihizal Fungus Sebacina vermifera, Applied and Environmental Microbiology, 8/12/2011

294. Brown, et al., Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum, PNAS, 8/16/2011

295. Ye, et al., Evolution and divergence in the coding and promoter regions of the Populus gene family encoding xyloglucan endotransglycosylase / hydrolases, Tree Genetics and Genomes, 8/18/2011

296. Samuel, et al., Structural Changes in switchgrass lignin and hemicelluloses during pretreatments by NMR analysis, Polymer Degradation and Stability, 8/25/2011

297. Shao, et al., Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum, Applied Microbiology and Biotechnology, 8/27/2011

298. Wang, et al., Evaluations of Cellulose Accessibilities of Lignocelluloses by Solute Exclusion and Protein Adsorption Techniques, Biotechnology and Bioengineering, 8/30/2011

299. Davison, et al., Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion, Aqueous Pretreatment of Plant Biomass for Biological and, 2011

300. Pu, et al., Challenges of the utilization of wood polymers: how can they be overcome?, Applied Microbiology and Biotechnology, 2011

301. Tetard, et al., Optomechanical spectroscopy with broadband interferometric and quantum cascade laser sources, Optics Letters, 2011

302. Yuan, et al., US-China collaborative biofuel research: towards a global solution for petroleum replacement, Biofuels, 2011

303. Yuan, et al., Biomass feedstock: diversity as a solution, Biofuels, 2011304. Tetard, et al., Nanometrology of delignified Populus using mode synthesizing atomic

force microscopy, Nanotechnology, et al., 9/5/2011305. Stewart, Bioenergy plants in the United States and China, et al., Plant Science,

9/5/2011306. DeMartini, et al., Application of monoclonal antibodies to investigate plant cell wall

deconstruction for biofuels production, Energy and Environmental Science, 9/6/2011307. Gallego-Giraldo, et al., Salicylic acid mediates the reduced growth of lignin down-

regulated plants, PNAS, 9/11/2011308. Ye, et al., Transgenic Populus trees for forest products, bioenergy, and functional

genomics, Critical Reviews in Plant Sciences, 9/12/2011309. Biagioni, et al., Orthogonal projection to latent structures solution properties for

chemometrics and systems biology data, Journal of Chemometrics, 9/27/2011310. Mann, et al., Gateway-compatible vectors for high-throughput gene functional

analysis in switchgrass (Panicum virgatum L.) and other monocot species, Plant Biotechnology Journal, 9/28/2011

311. Li, et al., Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes, Nucleic Acids Research, 9/29/2011

312. Argyros, et al., High Ethanol Titers from Cellulose using Metabolically Engineered Thermophilic, Anaerobic Microbes, Applied Environmental Microbiology, 9/30/2011

313. Wang, et al., Spatial and temporal dynamics of cellulose degradation and biofilm formation by Caldicellulosiruptor obsidiansis and Clostridium thermocellum, AMB Express, 2011

Page 16: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

314. Ellis, et al., "Closing the Carbon Balance for Fermentation by Clostridium thermocellum (ATCC 27405)", Bioresource Technology, 2011

315. Rodgers-Melnick, et al., Contrasting Patterns of Evolution Following Whole Genome versus Tandem Duplication Events in Populus, Genome Research, 10/5/2011

316. Shen, et al., Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks, New Phytologist, 10/11/2011

317. Lochner, et al., Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass, Journal of Proteome Research, 10/11/2011

318. Escamilla-Treviño, et al., Potential of Plants from the Genus Agave as Bioenergy Crops, BioEnergy Research, 10/14/2011

319. Foston, et al., Chemical, ultrastructural and supermolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance, Energy and Environmental Science, 10/20/2011

320. Tetard, et al., Optical and plasmonic spectroscopy with cantilever shaped materials, Journal of Physics D: Applied Physics, 10/21/2011

321. Abraham, et al., Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics, Journal of Proteome Research, 12011

322. Alahuhta, et al., A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase, Acta Crystallographica - Section F, 12011

323. Casler, et al., The Switchgrass Genome: Tools and Strategies, The Plant Genome, 12011

324. Broach, et al., Biosynthesis of UDP-glucuronic acid and UDP-galacturonic acid in Bacillus cereus subsp. Cytotoxis NVH 391-98, The FEBS Journal, 12011

325. Kulkarni, et al., The ability of land plants to synthesize glucuronoxylans predates the evolution of tracheophytes, Glycobiology, 11/2/2011

326. DeMartini, et al., Composition and hydrothermal pretreatment and enzymatic saccharification performance of grasses and legumes from a mixed species prarie, Biotechnology for Biofuels, 11/15/2011

327. Yin, et al., Evolution of Plant Nucleotide-Sugar Interconversion Enzymes, PloS One, 11/18/2011

328. Ozdemir, et al., S-layer homology (SLH) domain proteins Csac_0678 and Csac_2722 implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus, Applied and Environmental Microbiology, 11/19/2011

329. Atmodjo, et al., Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall pectin biosynthetic homogalacturonan–galacturonosyltransferase complex, PNAS, 11/21/2011

330. Wilson, et al., Processive and nonprocessive cellulases for biofuel production—lessons from bacterial genomes and structural analysis, Applied Microbiology and Biotechnology, 11/24/2011

331. You, et al., Enhanced microbial cellulose utilization of recalcitrant cellulose by an ex vivo cellulosome-microbe complex, Applied and Environmental Microbiology, 12011

Page 17: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

332. You, et al., Simple Cloning via direct transformation of PCR product (DNA multimer) to Escherichia coli and Bacillus subtilis, Applied and Environmental Microbiology, 12011

333. Sannigrahi, et al., Characterization of Fermentation Residues from the Production of Bio-Ethanol from Lignocellulosic Feedstocks, Journal of Biobased Materials and Bioenergy, 12011

334. Chen, et al., Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution, Carbohydrate Research, 12/8/2011

335. Olson, et al., Recent progress in consolidated bioprocessing, Current Opinion in Biotechnology, 12/14/2011

336. Yang, et al., In-microbe formation of nucleotide sugars in engineered Escherichia coli, Analytical Biochemistry, et al., 12/20/2011

337. Wisniewski-Dye, et al., Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments, PLoS Genetics, 12/22/2011

338. Lindedam, et al., Cultivar variation and selection potential relevant to the production of cellulosic ethanol from wheat straw, Biomass and Bioenergy, 12/29/2011

339. Sangha, et al., Molecular simulation as a tool for studying lignin, Environmental Progress and Sustainable Energy, 12/30/2011

340. Vishnivetskaya, et al., Cellulolytic Microorganisms from Thermal Environments, Extremophiles: Microbiology and Biotechnology, 2012

341. Yang, et al., Ethanol-tolerant Gene Identification in Clostridium thermocellum using Pyro-resequencing for Metabolic Engineering, Microbial Metabolic Engineering: Methods and Protocols, 2012

342. Yang, et al., Genomics on Pretreatment Inhibitor Tolerance of Zymomonas mobilis, Microbial Stress Tolerance for Biofuel (book chapter), 2012

343. Kostylev, et al., Synergistic interactions in cellulose hydrolysis, Biofuels, 2012344. Kwit, et al., Gene flow matters in switchgrass (Panicum virgatum L.,) a potential

widespread biofuel feedstock, Ecological Applications, 2012345. Zhang, et al., Genomic Arrangement of Regulons in Bacterial Genomes, PLoS One,

1/3/2012346. Li, et al., Combined inactivation of the Clostridium cellulolyticum lactate and malate

dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations, Biotechnology for Biofuels, 1/4/2012

347. Martinez, et al., "Biosynthesis of UDP-4-keto-6-deoxyglucose and UDP-rhamnose in Pathogenic Fungi Magnaporthe grisea and Botryotinia fuckeliana", The Journal of Biological Chemistry, 1/6/2012

348. Syed, et al., BESC knowledgebase public portal, Bioinformatics, 1/11/2012349. Fu, et al., Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in

various morphological alterations and leads to improved biomass production, Plant Biotechnology Journal, 1/12/2012

350. Chen, et al., A polymer of caffeyl alcohol in plant seeds, PNAS, 1/17/2012351. Foston, et al., Solid-State Selective C-13 Excitation and Spin Diffusion NMR To

Resolve Spatial Dimensions in Plant Cell Walls, Journal of Agricultural and Food Chemistry, 2012

352. Wang, et al., Determination of cellulase colocalization on cellulose fiber with quantitative FRET measured by acceptor photobleaching and spectrally unmixing fluorescence microscopy, Analyst, 2/7/2012

Page 18: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

353. Lee, et al., Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality, Biotechnology for Biofuels, 2/8/2012

354. Sun, et al., Thermophilic Thermotoga maritima ribose-5 phosphate isomerase RpiB: Optimized heat treatment purification and basic characterization, Protein Expression and Purification, 2/8/2012

355. Nag, et al., Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa, Database, 2/9/2012

356. Holwerda, et al., A defined growth medium with very low background carbon for culturing Clostridium thermocellum, Journal of Industrial Microbiology and Biotechnology, 2/14/2012

357. You, et al., Mini-scaffoldin enhanced mini-cellulosome hydrolysis performance on low-accessibility cellulose (Avicel) more than on high-acccessibility amorphous cellulose, Biochemical Engineering Journal, 2/15/2012

358. Wang, et al., Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding?, Annals of Botany, 2/28/2012

359. Brunecky, et al., Structure and function of the Clostridium thermocellum cellobiohydrolase A X1-module repeat: enhancement through stabilization of the CbhA complex, Acta Crystallographica - Section D, 2012

360. Zhang, et al., A new high-energy density hydrogen carrier—carbohydrate—might be better than methanol, International Journal of Energy Research, 3/3/2012

361. Zhou, et al., Qserver: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters, PLoS One, 3/5/2012

362. Induri, et al., Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus, Tree Physiology, 3/8/2012

363. Izquierdo, et al., Complete Genome Sequence of Clostridium clariflavum DSM 19732, Standards In Genomic Sciences, 3/12/2012

364. Hoover, et al., Eliminating the scattering ambiguity in multifocal, multimodal, multiphoton imaging systems, Journal of Biophotonics, 3/28/2012

365. Sun, et al., MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress, PLoS One, 3/28/2012

366. Tuskan, et al., The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis, Tree Genetics and Genomes, 3/28/2012

367. Li, et al., Chemical Composition and Characterization of Cellulose for Agave as a Fast Growing, Drought Tolerant Biofuels Feedstock, RSC Advances, 3/29/2012

368. Farkas, et al., The Recombinogenic Properties of the Pyrococcus furiosus COM1 Strain Enable Rapid Selection of Targeted Mutants, Applied Environmental Microbiology, 2012

369. Hu, et al., Pseudo-lignin formation and its impact on enzymatic hydrolysis, Bioresource Technology, 2012

370. Ye, et al., Engineering a large protein by combined rational and random approaches: stabilizing the Clostridium thermocellum cellobiose phosphorylase, Molecular BioSystems, 2012

371. Sathitsuksanoh, et al., Cellulose solvent-based pretreatment for corn stove rand avicel: concentrated phosphoric acid versus ionic liquid [BMIM]C1, Cellulose, 2012

372. Mann, et al., Very bright orange fluorescent plant: endoplasmic reticulum targeting of orange fluorescent proteins as visual reporters in transgenic plants, BMC Biotechnology, 4/3/2012

Page 19: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

373. Sangha, et al., Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory study, The Journal of Physical Chemistry B, 4/4/2012

374. Wei, et al., Tracking dynamics of plant biomass compositing by changes in substrate structure, microbial community, and enzyme activity, Biotechnology for Biofuels, 4/10/2012

375. Zhu, et al., Deep oxidation of glucose in enzymatic fuel cells through a synthetic enzymatic pathway containing a cascade of two thermostable dehydrogenases, Biosensors and Bioelectronics, 4/11/2012

376. Sathitsuksanoh, et al., Cellulose solvent - and organic solvent-based lignocellulose fractionation enabled efficient sugar release from a variety of lignocellulosic feedstocks, Bioresource Technology, 4/21/2012

377. McKee, et al., Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains, PNAS, 4/24/2012

378. Basen, et al., Engineering a Hyperthermophilic Archaeon for Temperature-Dependent Product Formation, mBio, 4/27/2012

379. van der Lelie, et al., The metagenome of an anaerobic microbial community decomposing poplar wood chips, PLoS One, 2012

380. Guss, et al., Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum, Biotechnology for Biofuels, 5/6/2012

381. Duceppe, et al., Assessment of Genetic Variability of Cell Wall Degradability for the Selection of Alfalfa with Improved Saccharification Efficiency, BioEnergy Research, 5/9/2012

382. Bar-Peled, et al., The Synthesis and Origin of the Pectic Polysaccharide Rhamnogalacturonan II - Insights from Nucleotide Sugar Formation and Diversity, Frontiers in Plant Science, 5/11/2012

383. Olson, et al., Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles, Journal of Biological Engineering, 5/11/2012

384. Cui, et al., Enzymatic Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment, Industrial & Engineering Chemistry Research, 5/14/2012

385. Bennetzen, et al., Reference genome sequence of the model plant Setaria, Nature Biotechnology, 5/15/2012

386. Olson, et al., Transformation of Clostridium Thermocellum by Electroporation, Methods in Enzymology, 5/17/2012

387. Pena, et al., Methods for Structural Characterization of the Products of Cellulose - and Xyloglucan-Hydrolyzing Enzymes, Methods in Enzymology, 5/17/2012

388. You, et al., Easy preparation of a large-size random gene mutagenesis library in Escherichia coli, Analytical Biochemistry, 5/22/2012

389. Brown, et al., Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2, Journal of Bacteriology, 5/25/2012

390. Karpinets, et al., Analyzing large biological datasets with association networks, Nucleic Acids Research, 5/25/2012

391. Blumer-Schuette, et al., Caldicellulosiruptor core and pan genomes reveal determinants for non-cellulosomal thermophilic deconstruction of plant biomass, Journal of Bacteriology, 5/25/2012

392. Hu, et al., Pretreatment and Lignocellulosic Chemistry, BioEnergy Research, 5/25/2012

Page 20: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

393. Foston, et al., C-13 cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall, Analyst, 5/29/2012

394. Yin, et al., dbCAN: a web resource for automated carbohydrate-active enzyme annotation, Nucleic Acids Research, 5/29/2012

395. Leuze, et al., Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA, Gene Regulation and Systems Biology, 5/30/2012

396. Li, et al., Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes, Biotechnology for Biofuels, 6/6/2012

397. Podkaminer, et al., Ethanol and anaerobic conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous saccharification and fermentation (tSSF), Biotechnology for Biofuels, 6/15/2012

398. Mao, et al., The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces, Nucleic Acids Research, 6/26/2012

399. Brosse, et al., Miscanthus: a fast-growing crop for biofuels and chemicals production, Biofuels, Biproducts & Biorefining, 2012

400. Hyatt, et al., Gene and Translation Initiation Site Prediction in Metagenomic Sequences, Bioinformatics, 7/12/2012

401. Archambault-Leger, et al., Integrated analysis of hydrothermal flowthrough pretreatment, Biotechnology for Biofuels, 7/19/2012

402. Yang, et al., Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress, BMC Genomics, 7/23/2012

403. You, et al., Facilitated Substrate Channeling in a Self-Assembled Trifunctional Enzyme Complex, Angewandte Chemie, 7/23/2012

404. Frock, et al., Extreme thermophiles: moving beyond single-enzyme biocatalysis, Current Opinion in Chemical Engineering, 7/25/2012

405. Davison, et al., The Increasing Importance and Capabilities of Biomass Characterization, Industrial Biotechnology, 7/31/2012

406. Pattathil, et al., Changes in Cell Wall Carbohydrate Extractability Are Correlated with Reduced Recalcitrance of HCT Downregulated Alfalfa Biomass, Industrial Biotechnology, 7/31/2012

407. Tetard, et al., "Development of New Methods in Scanning Probe Microscopy for Lignocellulosic Biomass Characterization", Industrial Biotechnology, 2012

408. Slavov, et al., Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa, New Phytologist, 2012

409. Himmel, et al., Challenges for Assessing the Performance of Biomass Degrading Biocatalysts, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

410. Ding, et al., Imaging Cellulose Using Atomic Force Microscopy, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

411. Zeng, et al., Coherent Raman Microscopy Analysis of Plant Cell Walls, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

412. Pattathil, et al., Immunological Approaches to Plant Cell Wall and Biomass Characterization: Glycome Profiling, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

413. Wilson, et al., Cellulase Processivity, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

Page 21: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

414. Liu, et al., Single-Molecule Tracking of Carbohydrate-Binding Modules on Cellulose Using Fluorescence Microscopy, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

415. Gilbert, et al., Bioprospecting Metagenomics for New Glycoside Hydrolases, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

416. Hamilton-Brehm, et al., Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

417. Decker, et al., Reducing the Effect of Variable Starch Levels in Biomass Recalcitrance Screening, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

418. Brunecky, et al., Analysis of Transgenic Glycoside Hydrolases Expressed in Plants: T. reesei CBH I and A. celluloyticus EI, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

419. Mazumder, et al., Structural Characterization of the Heteroxylans from Poplar and Switchgrass, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

420. Corea, et al., Laser Microdissection and Genetic Manipulation Technologies to Probe Lignin Heterogeneity and Configuration in Plant Cell Walls, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

421. Chen, et al., Lignin-Degrading Enzyme Activities, Methods in Molecular Biology Biomass Conversion: Methods and Protocols, 2012

422. Kulkarni, et al., Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses, Industrial Biotechnology, 2012

423. Chou, et al., Estimation of dynamic flux profiles from metabolic time series data, BMC Systems Biology, 8/9/2012

424. Wang, et al., Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis, BMC Plant Biology, 8/9/2012

425. Urbanowicz, et al., 4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein, PNAS, 8/14/2012

426. Zhou, et al., Identification and characterization of petiolule-like pulvinus mutants with abolished nyctinastic leaf movement in the model legume Medicago truncatula, New Phytologist, 8/14/2012

427. Mearls, et al., Formation and characterization of non-growth states in Clostridium thermocellum: spores and L-forms, BMC Microbiology, 8/16/2012

428. Foston, et al., Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance, Industrial Biotechnology, 8/16/2012

429. Nageswara-Rao, et al., Genetic diversity and structure of natural and agronomic switchgrass (Panicum virgatum L.) populations, Genetic Resources and Crop Evolution, 8/16/2012

430. Chung, et al., "Methylation by a Unique alpha-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725", PLoS One, 8/22/2012

431. Cao, et al., Chemical transformations of Populus trichocarpa during dilute acid pretreatment, RCS Advances, 2012

432. Chen, et al., Novel seed coat lignins in the Cactaceae: structure, distribution and implications for the evolution of lignin diversity, The Plant Journal, 9/7/2012

433. Foston, et al., NMR a critical tool to study the production of carbon fiber from carbon, Carbon, 9/14/2012

Page 22: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

434. Farkas, et al., Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii, Journal of Industrial Microbiology and Biotechnology, 9/19/2012

435. Hu, et al., Impact of Pseudolignin versus Dilute Acid-Pretreated Lignin on Enzymatic Hydrolysis of Cellulose, ACS Sustainable Chemistry and Engineering, 9/25/2012

436. Tschaplinski, et al., Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog, Biotechnology for Biofuels, 9/28/2012

437. Jung, et al., 3D Chemical Image using TOF-SIMS Revealing the Biopolymer Component Spatial and Lateral Distributions in Biomass, Angewandte Chemie, 9/28/2012

438. Podkaminer, et al., Characterization of xylan utilization and discovery of a new endoxylanase in Thermoanaerobacterium saccharolyticum through targeted gene deletions, Applied and Environmental Microbiology, 9/28/2012

439. Kumar, et al., Carbohydrate Derived-Pseudo-Lignin can retard cellulose biological conversion, Biotechnology and Bioengineering, 2012

440. Sukharnikov, et al., Sequence, Structure, and Evolution of cellulases in the glycoside Hydrolase Family 48, The Journal of Biological Chemistry, 10/10/2012

441. Waller, et al., Exchange of Type II Dockerin-Containing Subunits of the C. thermocellum Cellulosome as revealed by SNAP-tags, FEMS Microbiology Letters, 10/10/2012

442. Uppalapati, et al., Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations, Bioenergy Research, 10/14/2012

443. Abraham, et al., Putting the pieces together: high-performance LC-MS/MS provides network-pathway-, and protein-level perspectives in Populus, Molecular and Cellular Proteomics, 10/16/2012

444. Gjersing, et al., Rapid determination of sugar content in biomass hydrolysates using nuclear magnetic resonance spectroscopy, Biotechnology and Bioengineering, 10/18/2012

445. Wullschleger, et al., Revisiting the sequencing of the first tree genome: Populus trichocarpa, Tree Physiology, 10/25/2012

446. Czarnecki, et al., Evidence for a contribution of ALA synthesis to plastid-to-nucleus signaling, Frontiers in Plant Science, 10/29/2012

447. Gao, et al., Application of High Throughput Pretreatment and Co-Hydrolysis System to Thermochemical Pretreatment - Part 1: Dilute Acid, Biotechnology and Bioengineering, 12012

448. Ye, et al., Evolutionary analyses of non-family genes in plants, The Plant Journal, 11/4/2012

449. De Souza, et al., Composition and Structure of Sugarcane cell wall polysaccharides: implications for second-generation bioethanol production, Bioenergy Research, 11/6/2012

450. Lee, et al., Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach, PLOS Computational Biology, 11/8/2012

451. Yee, et al., Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach, Biotechnology for Biofuels, 11/12/2012

452. Ding, et al., How Does Plant Cell Wall Nanoscale Architecture Correlate With Enzymatic Digestibility?, Science, 11/23/2012

Page 23: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

453. Sathitsuksanoh, et al., New lignocellulose pretreatments using cellulose solvents: a review, Journal of Chemical Technology and Biotechnology, 11/30/2012

454. Olson, et al., The role of the CipA scaffoldin protein in cellulose solubilization as determined by targeted gene deletion and complementation in Clostridium thermocellum, Journal of Bacteriology, 12012

455. Deng, et al., Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum, Metabolic Engineering, 12012

456. Li, et al., Complete genome sequence of Clostridium sp. Strain BNL1100, a cellulolytic mesophile isolated from corn stover, Journal of Bacteriology, 12012

457. Xu, et al., Overexpression of AtLov1 in Switchgrass alters plant architecture, lignin content, and flowering time, Plos One, 12012

458. Kumar, et al., Comparison of Laboratory Delignification Methods, their selectivity, and impacts on physiochemical characteristics of cellulosic biomass, Bioresource Technology, 12/5/2012

459. Mao, et al., CINPER: An interactive web system for pathway prediction for prokaryotes, PLOS One, 12/7/2012

460. Shao, et al., Kinetic modeling of xylan hydrolysis in co- and countercurrent liquid hot water flow-through pretreatments, Bioresource Technology, 12/10/2012

461. Porth, et al., Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations, New Phytologist, 12/20/2012

462. Ramanna, et al., Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing, Methods and Protocols Series; Methods in Molecular Biology, Volume 975, 2013

463. Tan, et al., An Arabidopsis cell wall proteoglycan consists of pectin and arabinoxylan covalently linked to an arabinogalactan protein, The Plant Cell, 2013

464. Hamilton-Brehm, et al., Thermodesulfobacterium geofontis sp. Nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park, Extremophiles, 1/4/2013

465. Zhang, et al., Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.), The Plant Journal, 1/5/2013

466. DeMartini, et al., Investigating plant cell wall components that affect biomass recalcitrance in poplar and switchgrass, Energy & Environmental Science, 1/8/2013

467. Hardin, et al., Standardization of Switchgrass Sample Collection for cell wall and biomass trait analysis, Bioenergy Research, 1/17/2013

468. Ma, et al., Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency, Genomics, Proteomics & Bioinformatics, 1/25/2013

469. Pu, et al., Assessing the molecular structure basis for biomass recalcitrance during dilute acid and hydrothermal pretreatments, Biotechnology for Biofuels, 1/28/2013

470. Muchero, et al., Genome anchored QTLs for biomass productivity in hybrid populus grown under contrasting environments, PLOS ONE, 1/29/2013

471. Bartley, et al., Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall hydroxycinnamic acid content and saccharification, Plant Physiology, 2013

472. Currie, et al., Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolytim, Biotechnology for Biofuels, 2013

473. GhattyVenkataKrishna, et al., Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel may affect cellobiohydrolase directional specificity, Biophysical Journal, 2013

Page 24: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

474. Fried, et al., Self-assembly and application of cellulosomal components, Bionanotechnology: Biological Self-assembly and its Applications, 2013

475. Samuel, et al., Investigation of the fate of poplar lignin during autohydrolysis pretreatment to understand the biomass recalcitrance, RCS Advances, 2/4/2013

476. Mao, et al., Barcode Server: A visualization-based genome analysis system, PLoS ONE, 2/15/2013

477. Zhou, et al., An atypical glycolysis in Clostridium thermocellum, Applied and Environmental Microbiology, 2/22/2013

478. Wyman, et al., Chemical and Biological Deconstruction of Aqueous Phase Processing, Catalysis for the Conversion of Biomass and Its Derivatives, 2013

479. Alahuhta, et al., The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction, Acta Crystallographica - Section D, 2013

480. Bhandiwad, et al., Metabolic engineering of thermoanaerobacterium thermosaccharolyticum for increased n-butanol production, Advances in Microbiology, 2013

481. Chung, et al., Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus, Journal of Industrial Microbiology and Biotechnology, 3/10/2013

482. Martin del Campo, et al., High-Yield Production of Dihydrogen from Xylose by Using a Synthetic Enzyme Cascade in a Cell-Free System, Angewandte Chemie, 3/19/2013

483. Li, et al., "Chromatographic determination of 1, 4-b-xylooligosaccharides of different chain lengths to follow xylan deconstruction in biomass conversion", Journal of Industrial Microbiology & Biotechnology, 3/19/2013

484. Trajano, et al., Comparison of the effectiveness of a fluidized sand bath and a steam chamber for reactor heating, Industrial & Engineering Chemistry Research, 3/19/2013

485. Serba, et al., Linkage maps of lowland and upland tetraploid switchgrass ecotypes, Bioenergy Research, 3/24/2013

486. You, et al., Enzymatic transformation of nonfood biomass to starch, PNAS, 2013487. Shen, et al., Enhanced characteristics of genetically modified switchgrass (Panicum

virgatum L.) for high biofuel production, Biotechnology for Biofuels, 2013488. Chung, et al., Construction of a stable replicating shuttle vector for

Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus, PLoS One, 4/3/2013

489. Passian, et al., Comments on the paper 'A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces', Ultramicroscopy, 4/4/2013

490. Resch, et al., Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction, Energy and Environmental Science, 4/8/2013

491. Saha, et al., Self-rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis, The Plant Journal, 4/9/2013

492. Holwerda, et al., Testing alternative kinetic models for utilization of crystalline cellulose (Avicel) by batch cultures of Clostridium thermocellum, Biotechnology and Bioengineering, 4/11/2013

Page 25: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

493. Holwerda, et al., Development and evaluation of methods to infer biosynthesis and substrate consumption in cultures of cellulolytic microorganisms, , Biotechnology and Bioengineering, 4/11/2013

494. Elkins, et al., Complete genome sequence of the hyperthermophilic sulfate-reducing bacterium thermodesulfobacterium geofontis OPF15, Genome Announcements, 4/11/2013

495. van der Veen, et al., Characterization of Clostridium thermocellum strains with disrupted fermentation end product pathways, Journal of Industrial Microbiology & Biotechnology, 4/15/2013

496. Zhu, et al., Isolation and diversity analysis of resistance gene homologues from switchgrass, G3: Genes, Genomes, Genetics, 4/15/2013

497. Wang, et al., Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy, Journal of Environmental Sciences, 4/15/2013

498. Ma, et al., Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions, Nucleic Acids Research, 4/17/2013

499. Flowers, et al., SMET: Systematic multiple enzyme targeting - a method to rationally design optimal strains for target chemical overproduction, Biotechnology Journal, 4/24/2013

500. Wyman, et al., Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals - Introduction, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

501. Lynd, et al., Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment, et al., Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

502. Trajano (McKenzie), et al., Fundamentals of biomass pretreatment at Low pH, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

503. Sannigrahi, et al., Fundamentals of biomass pretreatment by fractionation, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

504. Kumar, et al., Physical and chemical features of pretreated biomass that influence macro-micro-accessibility and biological processing, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

505. Pu, et al., Plant biomass characterization: application of solution- and solid-state NMR spectroscopy, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

506. Qing, et al., Xylooligosaccharides production, quantification, and characterization in context of lignocellulosic biomass pretreatment, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

507. DeMartini, et al., High-throughput pretreatment and hydrolysis systems for screening biomass species in aqueous pretreatment of plant biomass, Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013

508. Li, et al., Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 2: dilute alkali, Biotechnology and Bioengineering, 2013

Page 26: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

509. Ragauskas, et al., When to accept no … to yesterday's solutions, Biofuels, Bioproducts and Biorefining, 2013

510. Nageswara-Rao, et al., Advances in biotechnology and genomics of switchgrass, Biotechnology for Biofuels, 2013

511. Kataeva, et al., Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature, Energy and Environmental Science, 2013

512. Atmodjo, et al., Evolving views of pectin biosynthesis, Annual Review of Plant Biology, 5/8/2013

513. Brown, et al., Genome sequences of industrially relevant saccharomyces cerevisiae strain M3707, isolated from a sample of distillers yeast and four haploid derivatives, Genome Announcements, 2013

514. Chung, et al., Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement, Biotechnology for Biofuels, 2013

515. Cha, et al., Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass, Biotechnology for Biofuels, 2013

516. Gilna, et al., Cellulosic biofuels, Science Omega Review, 2013517. Zeng, et al., Lignin plays a negative role in the biochemical process for producing

lignocellulosic biofuels, Current Opinion in Biotechnology, 2013518. Atalla, et al., Irreversible transformations of native celluloses, upon exposure to

elevated temperatures, Carbohydrate Polymers, 6/15/2013519. Zhao, et al., Loss of function of cinnamyl alcohol dehydrogenase 1 leads to

unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula, PNAS, 6/28/2013

520. Abraham, et al., Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus, Journal of Proteome Research, 2013

521. Meng, et al., Determination of porosity of lignocellulosic biomass before and after pretreatment by using Simons' stain and NMR techniques, Bioresource Technology, 7/8/2013

522. GhattyVenkataKrishna, et al., Effect of the amyloid B hairpin's structure on the handedness of helices formed by its aggregates, FEBS Letters, 7/8/2013

523. Kostylev, et al., Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion, Biochemistry, 7/9/2013

524. Ma, et al., An integrated toolkit for accurate prediction and analysis of cis regulatory motifs at a genome scale, Bioinformatics, 7/10/2013

525. Zhang, et al., Cellulases: Characteristics, sources, production, and applications, Bioprocessing Technologies in Biorefinery for Sustainable Production of Fuels, Chemicals, and Polymers, 7/12/2013

526. Yang, et al., Systems biology analysis of zymomonas mobilis ZM4 ethanol stress responses, Plos One, 7/16/2013

527. Tobimatsu, et al., "Coexistence but Independent Biosynthesis of Catechyl and Guaiacyl/Syringyl Lignin Polymers in Seed Coats", Plant Cell, 7/31/2013

528. Mostofian, et al., Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution, Cellulose, 2013

Page 27: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

529. Lian, et al., "Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: a quantum mechanical/molecular mechanical study", Cellulose, 2013

530. Trajano, et al., The fate of lignin during hydrothermal pretreatment, Biotechnology for biofuels, 2013

531. Blumer-Schuette, et al., Thermophilic lignocellulose deconstruction, FEMS Microbiology Review, 2013

532. Taghavi, et al., Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a novel solventogenic Clostridium species isolated from anaerobic sludge, Genome Announcements, 8/8/2013

533. Linville, et al., Kinetic modeling of batch fermentation for Populus hydrolysate tolerant mutant and wild type strains of Clostridium thermocellum, Bioresource Technology, 8/20/2013

534. Xu, et al., Improving activity of minicellulosomes by integration of intra- and intermolecular synergies, Biotechnology for Biofuels, 8/30/2013

535. Voit, et al., Characterizability of metabolic pathway systems from time series data, Mathematical Biosciences, 2013

536. Voit, et al., Biochemical Systems Theory: A Review, ISRN Biomathematics, 2013537. GhattyVenkataKrishna, et al., Dynamics of water in the amphiphilic pore of amyloid

beta fibrils, Chemical Physics Letters, 9/4/2013538. Rodgers-Melnick, et al., Predicting whole genome protein interaction networks from

primary sequence data in model and non-model organisms using ENTS, BMC Genomics, 9/10/2013

539. Wilson, et al., Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress, Biotechnology for Biofuels, 9/12/2013

540. Sathitsuksanoh, et al., Overcoming biomass recalcitrance by combining genetically modified switchgrass and cellulose solvent-based lignocellulose pretreatment, Plos One, 9/27/2013

541. Cha, et al., Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, caldicellulosiruptor bescii, Journal of Industrial Microbiology and Biotechnology, 2013

542. Ratnaparkhe, et al., Analyses using cell wall glycan-directed monoclonal antibodies reveal xylan-degration by two microbial glycosyl hydrolases in cell walls from poplar and switchgrass biomass, Journal of Bioremediation & Biodegradation, 2013

543. Zhao, et al., Molecular and biochemical characterization of the jasmonic acid methyltransferase gene from black cottonwood (Populus trichocarpa), Phytochemistry, 2013

544. Li, et al., Investigation of lignin deposition on cellulose during hydrothermal pretreatment, its effect on cellulose hydrolysis, and underlying mechanisms, , Biotechnology and Bioengineering, 10/12/2013

545. Linville, et al., Biotechnology and Bioengineering, Industrial robustness: understanding the mechanism of tolerance for the populus hydrolysate-tolerant mutant strain of clostridium thermocellum, Plos One, 10/21/2013

546. King, et al., Biolistic transformation of elite genotypes of switchgrass (Panicum virgatum L.), Plant Cell Reports, 12013

547. Baxter, et al., Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress, Biofuels, 12013

548. Mao, et al., DOOR 2.0: presenting operons and their functions through dynamic and integrated views, Nucleic Acids Research, 11/7/2013

Page 28: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

549. Bhandiwad, et al., "Metabolic engineering of Thermoanaerobacterium Saccharolyticum for n-butanol production", Metabolic Engineering, 11/9/2013

550. Dykstra, et al., Development of a multi-point quantitation method of simultaneously measure enzymatic and structural components of the Clostridium thermocellum Cellulosome protein complex, Journal of Proteome Research, 11/15/2013

551. Ding, et al., Overview of Lignocellulose: Structure and Chemistry, Biological Concerstion of Biomass for Fuels and Chemicals: Exploration from Natural Utilization Systems, 11/18/2013

552. Liu, et al., Advances in the measurement and characterization of biomass structure and processing, Biological Concerstion of Biomass for Fuels and Chemicals: Exploration from Natural Utilization Systems, 11/18/2013

553. Iwata, et al., Coarse but efficient identification of metabolic pathway systems, International Journal of Systems Biology, 11/20/2013

554. Liu, et al., Advanced genetic tools for plant biotechnology, Nature Reviews Genetics, 11/26/2013

555. Xie, et al., High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress, Plant Biotechnology Journal, 11/28/2013

556. Dumitrache, et al., Tracking the cellulolytic activity of clostridium thermocellum biofilms, Biotechnology for Biofuels, 11/29/2013

557. Shen, et al., A genomics approach to deciphering lignin biosynthesis in switchgrass, Plant Cell, 11/30/2013

558. Alahuhta, et al., Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 A resolution, Acta Crystallographica Section F Structural Biology and Crystallization Communications, 11/30/2013

559. Muchero, et al., Genome resequencing in Populus: revealing large-scale genome variation and implications on specialized-trait genomics, Challenges and Opportunities for the World's Forests in the 21st Century, 12013

560. Wilson, et al., Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass, Biotechnology for Biofuels, 12/2/2013

561. Fineran, et al., Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles, Genome Announcements, 12/12/2013

562. Ding, et al., Size, shape, and arrangement of native cellulose fibrils in maize cell walls, Cellulose, 12/12/2013

563. Reed, et al., Cellulose fermentation by C. thermocellum and a mixed consortium in an automated repetitive batch reactor, Bioresource Technology, 12/12/2013

564. Hu, et al., Suppression of pseudo-lignin formation under dilute acid pretreatment conditions, RCS Advances, 12/16/2013

565. Gao, et al., Fast hemicellulose quantification via a simple one-step acid hydrolysis, , Biotechnology and Bioengineering, 12/17/2013

566. Brunecky, Revealing nature's cellulase diversity: the digestion mechanism of caldicellulosiruptor bescii celA, Science, 2013

567. Sangha, et al., Chemical Factors that control lignin polymerization, The Journal of Physical Chemistry B, 12/30/2013

568. You, et al., Simple Cloning and DNA Assembly in Escherichia coli by Prolonged Overlap Extension PCR, DNA Cloning and Assembly Methods - Methods in Molecular Biolology, 2014

Page 29: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

569. Zhou, et al., The Trans-acting short interfering RNA3 pathway and NO APICAL MERISTEM anttagonistically regulate leaf margin development and lateral organ separation, as revealed by analysis of an argonaute7/lobed leaflet1 mutant in medicago truncatula, The Plant Cell, 2014

570. Zurawski, et al., The Extremely Thermophilic Genus Caldicellulosiruptor: Physiological and Genomic Characteristics for Complex Carbohydrate Conversion to Molecular Hydrogen, Microbial BioEnergy: Hydrogen Production, 2014

571. Brunecky, et al., Basic biological research relevant to feedstock conversion, Compendium of Bioenergy Plants: Corn, 2014

572. Biswal, et al., Aspen pectate lyase PtxtPl1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield, Biotechnology for Biofuels, 1/7/2014

573. Basen, et al., Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii, et al., Bioresource Technology, et al., 1/12/2014

574. Archambault-Leger, et al., "Fluid mechanics relevant to flow through pretreatment of cellulosic biomass", Bioresource Technology, 1/12/2014

575. Kostylev, et al., A Distinct Model of Synergism between a Processive Endocellulase (TfCel9A) and an Exocellulase (TfCel48A) from Thermobifida fusca, Applied and Environmental Microbiology, 1/14/2014

576. Samuel, et al., Structural characterization of lignin in wild-type versus COMT down-regulated switchgrass, Frontiers in Energy Research, 1/20/2014

577. Chen, et al., Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases, The Journals of Physical Chemistry B, 1/29/2014

578. Penning, et al., Validation of PyMBMS as a high-throughput screen for lignin abundance in lignocellulosic biomass of grasses, Bioenergy Research, et al., 1/30/2014

579. Shields_Menard, Draft genome sequence of Rhodococcus rhodochrous Strain ATCC 21198, Genome Announcements, 2014

580. Meng, et al., Recent advances in understanding the role of cellulose accessibility in enzymatic hydrolysis of lignocellulosic substrates, Current Opinion in Biotechnology, 2014

581. Biswas, Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of clostridium thermocellum, Plos One, 2/7/2014

582. Kumar, et al., Strong cellulase inhibition by mannan polysaccharides in cellulose conversion to sugars, , Biotechnology and Bioengineering, 2/12/2014

583. Karpients, et al., "Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants", Molecular Plant-Microbe Interactions, 2/12/2014

584. Escamilla-Trevino, et al., Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.), Plant Molecular Biology, 2014

585. Edwards, et al., Replacing a suite of commercial pectinases with a single enzyme, pectate lyase B, in Saccharomyces cerevisiae fermentations of cull peaches, Journal of Microbiology and Biotechnology, 2014

586. Robinson, et al., Farming for Fuels, et al., Dimensions, 2014587. Chou, et al., "Analysis of strand-specific RNA-seq data using machine learning

reveals the structures of transcription units in Clostridium thermocellum", Nucleic Acids Research, 2014

Page 30: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

588. Hao, et al., A review of xylan and lignin biosynthesis: foundation for studying Arabidopsis irregular xylem mutants with pleiotropic phenotypes, Critical Reviews in Biochemistry and Molecular Biology, 3/3/2014

589. Yin, et al., Functional genomics of drought tolerance in bioenergy crops, Critical Reviews in Plant Sciences, 3/7/2014

590. Kwit, et al., Switchgrass (Panicum virgatum L.) as a bioenergy crop: advantages concerns, and future prospects, Compendium of Bioenergy Plants: Switchgrass, 3/14/2014

591. Reyes-Hernandez, et al., The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana, New Phytologist, 3/18/2014

592. Brown, et al., Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia, Biotechnology for Biofuels, 3/21/2014

593. Lindedam, et al., Evaluation of high throughput screening methods in picking up differences between cultivars of lignocellulosic biomass for ethanol production, Biomass and Bioenergy, 3/21/2014

594. Li, et al., Identification of features associated with plant cell wall recalcitrance to pretreatment by alkaline hydrogen peroxide in diverse bioenergy feedstocks using glycome profiling, RSC Advances, 3/26/2014

595. Kumagai, et al., Simultaneous saccharification and fermentation and a consolidated bioprocessing for Hinoki cypress and Eucalyptus after fibrillation by steam and subsequent wet-disk milling, Bioresource Technology, 2014

596. Kostylev, Cel48A From Thermobifida fusca: Structure and Site Directed Mutagenesis of Key Residues, et al., Biotechnology and Bioengineering, 2014

597. Liu, Coupling alkaline pre-extraction with alkaline-oxidative post-treatment of corn stover to enhance enzymatic hydrolysis and fermentability, Biotechnology for Biofuels, et al., 4/3/2014

598. Li, et al., Agave proves to be a low recalcitrant lignocellulosic feedstock for biofuels production on semi-arid lands, Biotechnology for Biofuels, 4/4/2014

599. Biswas, et al., Production of Cellulolytic Enzymes, Bioprocessing of Renewable Resources to Commodity Bioproducts, 4/4/2014

600. Myung, et al., In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose, Metabolic Engineering, 4/13/2014

601. Uppugundia, et al., A comparative study of ethanol production using dilute acid, ionic liquid and AFEXTM pretreated corn stover, Biotechnology for Biofuels, 4/13/2014

602. Tolbert, et al., Characterization and analysis of the molecular weight of lignin for biorefining studies, Biofuels, Bioproducts and Biorefining, 4/14/2014

603. Ma, et al., DMINDA: an integrated web server for DNA motif indentification and analysis, Nucleic Acids Research, 4/21/2014

604. Baxter, et al., Two-year field analysis of reduced recalcitrance transgenic switchgrass, Plant Biotechnology Journal, 4/21/2014

605. Lin, et al., Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius, Metabolic Engineering, 4/30/2014

606. Zhao, et al., Altering the cell wall and its impact on plant disease: from forage to bioenergy, Annual Review of Phytopathology, 2014

Page 31: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

607. Gao, et al., Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEXtm, and ionic liquid pretreatments, Biotechnology for Biofuels, 5/13/2014

608. Sun, et al., Comparison of changes in cellulose ultrastructure during different pretreatments of poplar, Cellulose, 5/14/2014

609. Ragauskas, et al., Lignin Valorization: Improving lignin processing in the biorefinery, Science, 5/15/2014

610. Yee, et al., Consolidated bioprocessing of transgenic switchgrass by an engineered and evolved Clostridium thermocellum strain, Biotechnology for Biofuels, 5/22/2014

611. Yang, et al., Elucidation of zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics, Frontiers in Microbiology, 5/22/2014

612. Chung, et al., Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii, PNAS, 6/2/2014

613. Zhou, et al., New Insights into clostridia through comparative analyses of their 40 genomes, Bioenergy Research, 6/3/2014

614. Zhou, et al., AST: An automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees, PLOS One, 6/3/2014

615. Mearls, et al., The identification of four histidine kinases that influence sporulation in Clostridium thermocellum, Anaerobe, 6/5/2014

616. Currie, et al., Profile of secreted hydrolases, associated proteins, and SipA in thermoanaerobacterium saccharolyticum during the degradation of hemicellulose, Applied and Environmental Microbiology, 6/6/2014

617. Mybyrg, et al., The genome of Eucalyptus grandis, Nature, 6/19/2014618. Lupoi, et al., High-throughput prediction of eucalypt lignin syringyl/guaiacyl content

using multivariate analysis: a comparison between mid-infrared, near-infrared, and Raman spectroscopies for model development, Biotechnology for Biofuels, 2014

619. Woo, et al., Draft genome sequence of the lignin-degrading Burkholderia sp. Strain LIG30, isolated from wet tropical forest soil, Genome Announcements, 2014

620. Li, et al., Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation, Biotechnology for Biofuels, 2014

621. Bahulikar, et al., Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tall-grass prairie of northern Oklahoma, Applied and Environmental Microbiology, 7/7/2014

622. Poovaiah, et al., Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks, Plant Biotechnology Journal, 7/22/2014

623. Xiao, et al., NIR and Py-mbms coupled with multivariate data analysis as a high-throughput biomass characterization technique: a review, Frontiers in Plant Science, 7/22/2014

624. Nageswara_Rao, et al., Genetic diversity analysis of switchgrass (Panicum virgatum L.) populations using microsatellites and chloroplast sequences, Agroforest Systems, 7/26/2014

625. Akinosho, et al., The emergence of clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications, Frontiers in Chemistry, 7/28/2014

626. Daverdin, et al., Comparative relationships and chromosome evolution in switchgrass (Panicum virgatum) and its genomic model, foxtain millet (Setaria italica), Bioenergy Research, 7/30/2014

Page 32: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

627. Archambault-Leger, et al., Simulated performance of reactor configurations for hot-water pretreatment of sugarcane bagasse, ChemSusChem, 2014

628. Kyrpides, et al., Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains, PLOS One Biology, 2014

629. Pyne, et al., Improved draft genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525) using a hybrid next-generation sequencing approach, Genome Announcements, 2014

630. Zhao, et al., Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis, Phytochemistry, 8/5/2014

631. Chauhan, et al., Integrated metagenomics and metatranscriptomics analyses of root associated soil from transgenic switchgrass, Genome Announcements, 8/14/2014

632. Linville, et al., Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain, BMC Microbiology, 8/16/2014

633. Poovaiah, et al., Transgenic switchgrass (Panicum virgatum L.) biomass is increased by overexpression of switchgrass sucrose synthase (PvSUS1), Biotechnology Journal, et al., 8/21/2014

634. Evans, et al., Population genomics of the model tree Populus trichocarpa identifies signatures of selection and adaptive trait associations, Nature Genetics, 8/24/2014

635. Hao, et al., Loss of Arabidopsis GAUT12/IRX8 causes anther indehiscence and leads to reduced G lignin associated with altered matrix polysaccharide deposition, Frontiers in Plant Science, 8/28/2014

636. Serba, et al., Quantitative trait loci (QTL) underlying biomass yield and plant height in switchgrass, Bioenergy Research, 8/30/2014

637. Socha, et al., Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose, PNAS, 9/2/2014

638. Mostofian, et al., Replica-exhange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium choloride, The Journal of Physical Chemistry B, 9/2/2014

639. Zaharov, et al., "Karhunen-Lo`eve treatment to remove noise and facilitate data analysis in sensing, spectroscopy and other applications", Analyst, 9/8/2014

640. Yang, et al., Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates, Biotechnology for Biofuels, 9/11/2014

641. Urbanowicz, et al., Two arabidopsis proteins synthesize acetylated xylan in vitro, The Plant Journal, 9/14/2014

642. Groom, et al., Heterologous complementation of a pyrF deletion in Caldicellulosiruptor hydrothermalis generates a new host for the analysis of biomass deconstruction, Biotechnology for Biofuels, et al., 9/16/2014

643. Qin, et al., Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective, Science China Life Sciences, 9/18/2014

644. Chung, et al., Deletion of a Gene Cluster Encoding Pectin Degrading Enzymes in Caldicellulosiruptor bescii Reveals an Important Role for Pectin in Plant Biomass Recalcitrance, Biotechnology for Biofuels, 2014

645. Payyavula, et al., Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus, BMC Plant Biology, 10/7/2014

Page 33: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

646. Singh, et al., Comparison of different biomass pretreatment techniques and their impact on chemistry, structure, and recalcitrance, Frontiers in Energy Research, et al., 10/11/2014

647. Sun, et al., Effect of Lignin Content on Changes occurring in Poplar Cellulose Ultrastructure during Dilute Acid Pretreatment, Biotechnology for Biofuels, 10/14/2014

648. Young, et al., Deletion of CelA, the Most Abundant Cellulase in Caldicellulosiruptor bescii, Reveals its Crucial Role in the Deconstruction of Lignocellulosic Biomass, Biotechnology for Biofuels, 10/14/2014

649. Chai, et al., Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam, BMC Evolutionary Biology, 10/14/2014

650. Vishnivetskaya, et al., Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park, Microbial Ecology, 10/16/2014

651. Holwerda, et al., The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading, Biotechnology for Biofuels, 10/21/2014

652. Zhou, et al., "STM/BP-Like KNOXI Is Uncoupled from ARP in the Regulation of Compound Leaf Development in Medicago truncatula", The Plant Cell, 10/30/2014

653. Carmona, et al., Why genetic modification of lignin leads to low-recalcitrance biomass, Physical Chemistry Chemical Physics, 12014

654. Wuddineh, et al., Identification and overexpress of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance, Plant Biotechnology Journal, 11/2/2014

655. Archambault-Leger, et al., Energy, sugar dilution, and economic analysis of hot water flow-through pre-treatment for producing biofuel from sugarcane residues, Biofuels, Bioproducts and Biorefining, 11/10/2014

656. Kalluri, et al., Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance, Plant Biotechnology Journal, 11/11/2014

657. Basen, et al., Single gene insertion drives bioalcohol production by a thermophilic archaeon, PNAS, 11/11/2014

658. Izquierdo, et al., Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellum to utilize hemicellulose and unpretreated plant material, Biotechnology for Biofuels, 11/18/2014

659. Kumagai, et al., Improvement of enzymatic saccharification of Populus and switchgrass by combined pretreatment with steam and wet disk milling, Renewable Energy, 11/22/2014

660. Bali, et al., The effect of alkaline pretreatment methods on cellulose structure and accessibility, Chem Sus Chem Communications, 11/25/2014

661. Li, et al., Pen and Pal are nucleotide-sugar-dehydratases that convert UDP-GlcNAc to UDP-6-deoxy-D-GlcNAc-5,6-ene and then to UDP-4-keto-6-deoxy-L-AltNAc for CMP-pseudaminic acid synthesis in Bacillus thuringiensis, The Journal of Biological Chemistry, 11/25/2014

662. Carmona, et al., Why genetic modification of lignin leads to low-recalcitrance biomass, Physical Chemistry Chemical Physics, 12014

663. Brunner, et al., Vernalization and the chilling requirement to exit bud dormancy: shared or separate regulation?, Frontiers in Plant Science, 12/2/2014

664. Clarkson, et al., A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E, Biotechnology for Biofuels, 12/3/2014

Page 34: static-content.springer.com10.1007... · Web viewZhou, et al., Barcodes for Genomes and Applications, BMC Bioinformatics, 2008 Hong, et al., Simple protein purification through affinity

665. Land, et al., Quality scores for 32,000 genomes, Standards in Genomic Sciences, 12/12/2014

666. Yang, et al., PvNAC1 and PvNAC2 are associated with leaf senescence and nirtrogen use efficiency in switchgrass, Bioenergy Research, 12/16/2014

667. Tan, et al., Changes in cell wall properties coincide with overexpression of extension fusion proteins in suspension cultured tobacco cells, PLoS ONE, 12/23/2014

668. Yang, et al., A NAP-AA03 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves, The Plant Cell, 12/29/2014

669. Trajano, et al., Xylan hydrolysis in Populus trichocarpa x P. deltoides and model substrates during hydrothermal pretreatment, Bioresource Technology, 2014

670. Baxter, et al., Field evaluation of transgenic switchgrass plants overexpressing PvMYB4 for reduced biomass recalcitrance, BioEnergy Research, 2014

671. Pattathil, et al., Insights into plant cell wall structure, architecture and integrity using glycome profiling of native and AFEXtm pretreated biomass, Journal of Experimental Botany, 2014

672. Biswal, et al., Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock, Biotechnology for Biofuels, 2014