J. D. Keasling, et al., Metabolic engineering delivers next

advertisement
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
J. D. Keasling, et al., Metabolic engineering delivers next-generation biofuels, Nature Biotechnology,
2008
J. E. Dueber, et al., Synthetic protein scaffolds provide modular control over metabolic flux, Nature
Biotechnology, 2009
J. Nielsen, et al., Synergies between synthetic biology and metabolic engineering, Nature
Biotechnology, 2011
R. Knight, et al., Unlocking the potential of metagenomics through replicated experimental design,
Nature Biotechnology, 2012
R. Dahl, et al., Engineering dynamic pathway regulation using stress-response promoters, nature
biotechnology, 2013
W. J. Holtz, et al., Engineering Static and Dynamic Control of Synthetic Pathways, Cell, 2010
Y. Xiao, et al., Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear
stress-response genes, Cell, 2012
J. C. Way, et al., Integrating Biological Redesign: Where Synthetic Biology Came From and Where It
Needs to Go, Cell, 2014
N. V. Fedoroff, et al., Radically Rethinking Agriculture for the 21st Century, Science, 2010
J. D. Keasling, Manufacturing molecules through metabolic engineering, Science, 2010
P. C. Ronald, et al., Plant and animal sensors of conserved microbial signatures, Science, 2010
J. A. Banks, et al., The Selaginella genome identifies genetic changes associated with the evolution of
vascular plants, Science, 2011
J. M. Carothers, et al., Model-driven engineering of RNA devices to quantitatively program gene
expression, Science, 2011
J. A. Dietrich, et al., High-throughput metabolic engineering: advances in small-molecule screening and
selection, Annu Rev Biochem, 2010
E. J. Steen, et al., Microbial production of fatty-acid-derived fuels and chemicals from plant biomass,
Nature, 2010
JP Vogel, et al., Genome sequence analysis of the model grass Brachypodium distachyon: insights into
grass genome evolution, Nature, 2010
S. Yilmaz, et al., Multiple displacement amplification compromises quantitative analysis of
metagenomes, Nature Methods, 2010
J. D. Keasling, et al., Synthesis: A constructive debate, Nature, 2012
P. P. Peralta-Yahya, et al., Microbial engineering for the production of advanced biofuels, Nature, 2012
C. C. Liu, et al., An adaptor from translational to transcriptional control enables predictable assembly of
complex regulation, Nature Methods, 2012
V. K. Mutalik, et al., Precise and reliable gene expression via standard transcription and translation
initiation elements, Nat Methods, 2013
V. K. Mutalik, et al., Quantitative estimation of activity and quality for collections of functional genetic
elements, Nat Methods, 2013
J. Kirby, et al., Biosynthesis of plant isoprenoids: perspectives for microbial engineering, Annual Review
of Plant Biology, 2009
H. V. Scheller, et al., Hemicelluloses, Annual Review of Plant Biology, 2010
J. K. Jansson and N. Tas, The microbial ecology of permafrost, Nature Reviews Microbiology, 2014
J. L. Bennetzen, et al., Reference genome sequence of the model plant Setaria, Nat Biotechnol, 2012
F. Zhang, et al., Design of a dynamic sensor-regulator system for production of chemicals and fuels
derived from fatty acids, Nat Biotechnol, 2012
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.
45.
46.
47.
48.
49.
50.
51.
52.
W. Reindl, et al., Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase
activities in microbial communities, Energy & Environmental Science, 2011
O. Wurtzel, et al., A single-base resolution map of an archaeal transcriptome, Genome Research, 2010
K. H. Jung, et al., The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice
kinase super-family, Trends in Plant Science, 2010
Oikawa, et al., Golgi-localized enzyme complexes for plant cell wall biosynthesis, Trends Plant Sci, 2013
J. Keasling, From yeast to alkaloids, Nature Chemical Biology, 2008
V. K. Mutalik, et al., Rationally designed families of orthogonal RNA regulators of translation, Nature
Chemical Biology, 2012
J. Nielsen, et al., Engineering synergy in biotechnology, Nature Chemical Biology, 2014
P.C. Ronald, Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement,
PLoS Biology, 2014
M. J. Dunlop, et al., Engineering microbial biofuel tolerance and export using efflux pumps, Molecular
Systems Biology, 2011
H. H. Chou and J. D. Keasling, Programming adaptive control to evolve increased metabolite
production, Nature Communications, 2013
T. L. Ruegg, et al., An auto-inducible mechanism for ionic liquid resistance in microbial biofuel
production, Nature Communications, 2014
J. K. Jensen, et al., Identification of a xylogalacturonan xylosyltransferase involved in pectin
biosynthesis in Arabidopsis, Plant Cell, 2008
Rautengarten, et al., The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is
indispensable for plant development in Arabidopsis, Plant Cell, 2011
J. Liwanag, et al., Pectin biosynthesis: GALS1 in Arabidopsis thaliana is a beta-1,4-galactan beta-1,4galactosyltransferase, Plant Cell, 2012
K. Baerenfaller, et al., Arabidopsis, Taking the Next Step: Building an Arabidopsis Information Portal,
Plant Cell, 2012
L. Yuan, et al., Allosteric regulation of transport activity by heterotrimerization of Arabidopsis
ammonium transporter complexes in vivo, Plant Cell, 2013
A. Simmons, et al., Next-generation biomass feedstocks for biofuel production, Genome Biology, 2008
S. Miller, et al., EMIRGE: Reconstruction of full length ribosomal genes from microbial community short
read sequencing data, Genome Biology, 2011
P. P. Peralta-Yahya, et al., Identification and microbial production of a terpene-based advanced biofuel,
Nature Communications , 2011
F. Zhang, and J. Keasling, Biosensors and their applications in microbial metabolic engineering, Trends
in Microbiology, 2011
A. Simmons, et al., Advances in modifying lignin for enhanced biofuel production, Current Opinion in
Plant Biology , 2010
M. Socha, et al., Efficient biomass pretreatment using ionic liquids derived from lignin and
hemicellulose, PNAS, 2014
Rautengarten, et al., The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family
of Arabidopsis, PNAS, 2014
J. L. Fortman, et al., Biofuel alternatives to ethanol: pumping the microbial well, Trends in
Biotechnology, 2008
A. Rennie, et al., Identification of a sphingolipid alpha-glucuronosyltransferase that is essential for
pollen function in Arabidopsis, Plant Cell, 2014
53.
54.
55.
56.
57.
58.
59.
60.
61.
62.
63.
64.
65.
66.
67.
68.
69.
70.
71.
72.
73.
74.
75.
76.
R. D. Rosengarten and M. L. Nicotra, Model Systems of Invertebrate Allorecognition, Current Biology,
2011
P. C. Ronald and K. Shirasu, Front-runners in plant-microbe interactions, Current Opinion in Plant
Biology, 2012
O. U. Mason, et al., Metagenomics reveals sediment microbial community response to Deepwater
Horizon oil spill, ISME Journal, 2014
E. Graham, et al., Microbes in thawing permafrost: the unknown variable in the climate change
equation, ISME Journal, 2012
Lauck, et al., Rosetta Backrub-a web server for flexible backbone protein structure modeling and
design, Nucleic Acids Research, 2010
Densmore, et al., Algorithms for automated DNA assembly, Nucleic Acids Research, 2010
R. De Michele, et al., Fluorescent sensors reporting the activity of ammonium transceptors in live cells,
eLife, 2013
S. K. Lee, et al., Metabolic engineering of microorganisms for biofuels production: from bugs to
synthetic biology to fuels, Current Opinion in Biotechnology, 2008
Mukhopadhyay, et al., Importance of systems biology in engineering microbes for biofuel production,
Current Opinion in Biotechnology, 2008
J. M. Carothers, et al., Chemical synthesis using synthetic biology, Current Opinion in Biotechnology,
2009
M. J. Dougherty, and F. H. Arnold, Directed evolution: new parts and optimized function, Current
Opinion in Biotechnology, 2009
M. E. Vega-Sanchez, and P. C. Ronald, Genetic and biotechnological approaches for biofuel crop
improvement, Current Opinion Biotechnology, 2010
Zhang, et al., Metabolic engineering of microbial pathways for advanced biofuels production, Current
Opinion Biotechnology, 2011
W. Blanch, et al., Bioprocessing for biofuels, Curr Opin Biotechnol, 2012
S. Yuzawa, et al., Heterologous production of polyketides by modular type I polyketide synthases in
Escherichia coli, Curr Opin Biotechnol, 2012
T. de Rond, et al., High throughput screening of enzyme activity with mass spectrometry imaging, Curr
Opin Biotechnol, 2014
M. Carothers, et al., Selecting RNA aptamers for synthetic biology: investigating magnesium
dependence and predicting binding affinity, Nucleic Acids Res, 2010
P. S. Dehal, et al., MicrobesOnline: an integrated portal for comparative and functional genomics,
Nucleic Acids Research, 2010
P. Durek, et al., PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update, Nucleic
Acids Research, 2010
T. Bates, et al., GLAMM: Genome-Linked Application for Metabolic Maps, Nucleic Acids Research, 2011
T. S. Ham, et al., Design, implementation and practice of JBEI-ICE: an open source biological part
registry platform and tools, Nucleic Acids Res, 2012
Chivian, et al., MetaMicrobesOnline: phylogenomic analysis of microbial communities, Nucleic Acids
Res, 2013
S. Kumar, et al., Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic
mevalonate pathway in chloroplasts, Metabolic Engineering, 2012
W. Runguphan and J. D. Keasling, Metabolic engineering of Saccharomyces cerevisiae for production of
fatty acid-derived biofuels and chemicals, Metabolic Engineering, 2014
77.
R. S. Bart, et al., Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1mediated immunity to Xanthomonas oryzae pv. oryzae, PLoS Genet, 2010
78.Y. S. Seo, et al., Towards establishment of a rice stress response interactome, PLoS Genet, 2011
79.
Y. J. Tang, et al., Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling, Mass
Spectrometry Reviews, 2009
80.
R. Lamendella, et al., Omics' of the mammalian gut - new insights into function, Current Opinion in
Biotechnology, 2012
81.
S. Borglin, et al., Application of phenotypic microarrays to environmental microbiology, Current
Opinion in Biotechnology, 2012
82.
Eudes, Y., et al., Lignin bioengineering, Current Opinion in Biotechnology, 2014
83.
S. Rodriguez, et al., Production and quantification of sesquiterpenes in Saccharomyces cerevisiae,
including extraction, detection and quantification of terpene products and key related metabolites,
Nature Protocols, 2014
84.
G. M. Estavillo, et al., Isolation of the plant cytosolic fraction for proteomic analysis, Plant Proteomics:
Methods and Protocols, 2013
85.
H. T. Parsons, et al., Separation of the plant golgi apparatus and endoplasmic reticulum by free-flow
electrophoresis, Plant Proteomics: Methods and Protocols, 2013
86.
E. Garcia, et al., Separation and mass spectrometry in microbial metabolomics, Current Opinion in
Microbiology, 2008
87.
A. Rennie and H. V. Scheller, Xylan biosynthesis, Current Opinion in Biotechnology, 2014
88.
J. Bernal, et al., Functional Analysis of the Cellulose Synthase-Like Genes CSLD1, CSLD2, and CSLD4 in
Tip-Growing Arabidopsis Cells, Plant Physiology, 2008
89.
M. Landau, et al., A cytoplasmically inherited barley mutant is defective in photosystem I assembly due
to a temperature-sensitive defect in ycf3 splicing, Plant Physiology, 2009
90.
Harholt, et al., Biosynthesis of Pectin, Plant Physiology, 2010
91.
H. Jung, et al., The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression
of AP2/ERF Transcription Factors, Plant Physiology, 2010
92.
I. Lacayo, et al., Imaging cell wall architecture in single Zinnia elegans tracheary elements, Plant
Physiology, 2010
93.
J. Joshi, et al., MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics
data, Plant Physiology, 2011
94.
Y. Manabe, et al., Loss-of-Function Mutation of REDUCED WALL ACETYLATION2 in Arabidopsis Leads
to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea, Plant Physiology, 2011
95.
T. Parsons, et al., Isolation and proteomic characterization of the Arabidopsis Golgi defines functional
and novel components involved in plant cell wall biosynthesis, Plant Physiol, 2012
96.
Rautengarten, et al., Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for
feruloylation of omega-hydroxy fatty acids in cutin polyester, Plant Physiol, 2012
97.
A. Rennie, et al., S. F. Hansen, et al., E. E. Baidoo, et al., M. Z. Hadi, et al., J. D. Keasling, et al., H. V.
Scheller, Three members of the Arabidopsis glycosyltransferase family 8 are xylan
glucuronosyltransferases, Plant Physiol, 2012
98.
E. Vega-Sanchez, et al., Loss of Cellulose Synthase-Like F6 function affects mixed-linkage glucan
deposition, cell wall mechanical properties and defense responses in vegetative tissues of rice, Plant
Physiology, 2012
99.
L. E. Bartley, et al., Overexpression of a BAHD Acyltransferase, OsAt10, alters rice cell wall
hydroxycinnamic acid content and saccharification, Plant Physiol, 2013
100.
101.
102.
103.
104.
105.
106.
107.
108.
109.
110.
111.
112.
113.
114.
115.
116.
117.
118.
119.
120.
121.
122.
Y. Manabe, et al., RWA Proteins Play Vital and Distinct Roles in Cell Wall O-Acetylation in Arabidopsis
thaliana, Plant Physiology, 2013
S. S. Dey, et al., Mutual Information Analysis Reveals Coevolving Residues in Tat That Compensate for
Two Distinct Functions in HIV-1 Gene Expression, Journal of Biological Chemistry, 2012
H. Pereira, et al., Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus
acidocaldarius, Acta Crystallographica Section D Biological Crystallography, 2009
H. Pereira, et al., Structure of FabH and factors affecting the distribution of branched fatty acids in
Micrococcus luteus, Acta Crystallogr D Biol Crystallogr, 2012
R. McAndrew, et al., Structure of the OsSERK2 leucine-rich repeat extracellular domain, Acta
Crystallogr D Biol Crystallogr, 2014
M. DeAngelis, et al., Anaerobic decomposition of switchgrass by tropical soil-derived feedstockadapted consortia, MBio, 2012
S. Datta, et al., Ionic liquid tolerant hyperthermophilic cellulases for biomass pretreatment and
hydrolysis, Green Chemistry, 2010
Dibble, et al., A facile method for the recovery of ionic liquid and lignin from biomass pretreatment,
Green Chemistry, 2011
George, et al., The effect of ionic liquid cation and anion combinations on the macromolecular structure
of lignins, Green Chemistry, 2011
Ouellet, et al., Impact of ionic liquid pretreated plant biomass on Saccharomyces cerevisiae growth and
biofuel production, Green Chemistry, 2011
T. Zhang, et al., Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid
tolerance, Green Chemistry, 2011
K. M. Torr, et al., The impact of ionic liquid pretreatment on the chemistry and enzymatic digestibility
of Pinus radiata compression wood, Green Chemistry, 2012
Groff, et al., Acid enhanced ionic liquid pretreatment of biomass, Green Chemistry, 2013
Jian Shi, et al., One-pot ionic liquid pretreatment and saccharification of switchgrass, Green Chemistry,
2013
Sun, et al., Understanding pretreatment efficacy of four cholinium and imidazolium ionic liquids by
chemistry and computation, Green Chemistry, 2014
J. Shi, et al., Understanding the Role of Water during Ionic Liquid Pretreatment of Lignocellulose: Cosolvent or Anti-solvent?, Green Chemistry, 2014
Sathitsuksanoh, et al., Lignin fate and characterization during ionic liquid biomass pretreatment for
renewable chemicals and fuels production, Green Chemistry, 2014
Knoch, et al., A beta-glucuronosyltransferase from Arabidopsis thaliana involved in biosynthesis of type
II arabinogalactan has a role in cell elongation during seedling growth, Plant Journal, 2013
J. Lao, et al., The plant glycosyltransferase clone collection for functional genomics, Plant Journal, 2014
R. P. McAndrew, et al., Structure of a three-domain sesquiterpene synthase: a prospective target for
advanced biofuels production, Structure, 2011
Y. Kung, et al., Constructing tailored isoprenoid products by structure-guided modification of
geranylgeranyl reductase, Structure, 2014
Chandrasekaran, et al., K. Deng, et al., C. Y. Koh, et al., T. Takasuka, et al., L. F. Bergeman, et al., B. G.
Fox, et al., P. D. Adams, et al., A. K. Singh, A universal flow cytometry assay for screening
carbohydrate-active enzymes using glycan microspheres, Chem Commun (Camb), 2013
Y. C. Yeh, et al., Functionalizing bacterial cell surfaces with a phage protein, Chem Commun (Camb),
2013
123.
124.
125.
126.
127.
128.
129.
130.
131.
132.
133.
134.
135.
136.
137.
138.
139.
140.
141.
142.
143.
144.
145.
146.
J. Cao, et al., Construction of a rice glycosyltransferase phylogenomic database and identification of
rice-diverged glycosyltransferases, Molecular Plant, 2008
L. Yin, et al., The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal
Arabidopsis Development, Molecular Plant, 2011
X. Chen, et al., Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and
improved biomass saccharification, Mol Plant, 2013
S. Gille, et al., Arabinosylation of a Yariv-Precipitable Cell Wall Polymer Impacts Plant Growth as
Exemplified by the Arabidopsis Glycosyltransferase Mutant ray1, Mol Plant, 2013
R. Sharma, et al., Recent advances in dissecting stress-regulatory crosstalk in rice, Mol Plant, 2013
X. Chen, et al., An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and
XA3 immune receptors, Molecular Plant, 2014
H. Liepman, et al., Arabidopsis - a powerful model system for plant cell wall research, Plant Journal,
2010
Geshi, et al., A galactosyltransferase acting on arabinogalactan protein glycans is essential for embryo
development in Arabidopsis, Plant J, 2013
Y. Tobimatsu, et al., Visualization of Plant Cell Wall Lignification Using Fluorescence-tagged
Monolignols, Plant J, 2013
J. Y. 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.), Plant J, 2013
M. Frederix and A. J. Downie, Quorum Sensing: Regulating the Regulators, Advances in Microbial
Physiology, Vol 58, 2011
S. Okumoto, et al., Quantitative imaging for discovery and assembly of the metabo-regulome, New
Phytologist, 2008
J. Harholt, et al., Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous
endo-xylanase or ferulic acid esterase in the endosperm, Plant Biotechnology Journal, 2010
Eudes, et al., Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin
polymerization and enhance saccharification, Plant Biotechnol J, 2012
Yang, et al., Engineering secondary cell wall deposition in plants, Plant Biotechnol J, 2013
S. A. Eichorst, et al., Community dynamics of cellulose-adapted thermophilic bacterial consortia,
Environ Microbiol, 2013
S. D. McClendon, et al., Thermoascus aurantiacus is a promising source of enzymes for biomass
deconstruction under thermophilic conditions, Biotechnol Biofuels, 2012
D. Petersen, et al., Engineering of plants with improved properties as biofuels feedstocks by vesselspecific complementation of xylan biosynthesis mutants, Biotechnol Biofuels, 2012
G. Cruz, et al., Impact of high biomass loading on ionic liquid pretreatment, Biotechnol Biofuels, 2013
V. Reyes-Ortiz, et al., Addition of a carbohydrate-binding module enhances cellulase penetration into
cellulose substrates, Biotechnol Biofuels, 2013
M. Socha, et al., Comparison of sugar content for ionic liquid pretreated Douglas-fir woodchips and
forestry residues, Biotechnol Biofuels, 2013
N. Sun, et al., Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids,
Biotechnol Biofuels, 2013
Varanasi, et al., Survey of renewable chemicals produced from lignocellulosic biomass during ionic
liquid pretreatment, Biotechnol Biofuels, 2013
Li, D. Tanjore, et al., Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic
hydrolysis of switchgrass, Biotechnology for Biofuels, 2013
147.
148.
149.
150.
151.
152.
153.
154.
155.
156.
157.
158.
159.
160.
161.
162.
163.
164.
165.
166.
167.
168.
169.
N. Uppugundla, et al., A comparative study of ethanol production using dilute acid, ionic liquid and
AFEX pretreated corn stover, Biotechnology for Biofuels, 2014
J. S. 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
M. Konda, et al., Understanding cost drivers and economic potential of two variants of ionic liquid
pretreatment for cellulosic biofuel production, Biotechnology for Biofuels, 2014
J. M. Gladden, et al., Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from
a switchgrass-adapted microbial community, Biotechnology for Biofuels, 2014
X. Gao, et al., Comparison of enzymatic reactivity of corn stover solids prepared by dilute acid, AFEX,
and ionic liquid pretreatments, Biotechnology for Biofuels, 2014
J. C. Harper, et al., Fabrication and testing of a microneedles sensor array for p-cresol detection with
potential biofuel applications, ACS Applied Materials & Interfaces, 2009
S. Shaikh, et al., Isotopomer distributions in amino acids from a highly expressed protein as a proxy for
those from total protein, Analytical Chemistry, 2008
Bharadwaj, et al., Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion,
Analytical Chemistry, 2010
M. S. Kent, et al., Study of Enzymatic Digestion of Cellulose by Small Angle Neutron Scattering,
Biomacromolecules, 2010
Cheng, et al., Neutron Reflectometry and QCM-D Study of the Interaction of Cellulases with Films of
Amorphous Cellulose, Biomacromolecules, 2011
Cheng, et al., Transition of cellulose crystalline structure and surface morphology of biomass as a
function of ionic liquid pretreatment and its relation to enzymatic hydrolysis, Biomacromolecules, 2011
Chang, et al., Droplet-based microfluidic platform for heterogeneous enzymatic assays, Lab Chip, 2013
M. Ma, et al., Optimization of a heterologous mevalonate pathway through the use of variant HMGCoA reductases, Metabolic Engineering, 2011
M. Redding-Johanson, et al., Targeted proteomics for metabolic pathway optimization: Application to
terpene production, Metabolic Engineering, 2011
D. Keasling, Synthetic biology and the development of tools for metabolic engineering, Metab Eng,
2012
Y. Satoh, et al., Engineering of l-tyrosine oxidation in Escherichia coli and microbial production of
hydroxytyrosol, Metab Eng, 2012
Zhang, et al., Enhancing fatty acid production by the expression of the regulatory transcription factor
FadR, Metab Eng, 2012
Alonso-Gutierrez, et al., Metabolic engineering of Escherichia coli for limonene and perillyl alcohol
production, Metab Eng, 2013
Ozaydin, et al., Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes
with roles in isoprenoid production, Metab Eng, 2013
W. Runguphan, et al., Metabolic engineering of Saccharomyces cerevisiae for production of fatty acidderived biofuels and chemicals, Metab Eng, 2013
S. Batth, et al., A targeted proteomics toolkit for high-throughput absolute quantification of
Escherichia coli proteins, Metab Eng, 2014
E. B. Goh et al., Substantial improvements in methyl ketone production in E. coli and insights on the
pathway from in vitro studies, Metab Eng, 2014
R. W. Haushalter, et al., Production of anteiso-branched fatty acids in Escherichia coli, et al., next
generation biofuels with improved cold-flow properties, Metab Eng, 2014
170.
171.
172.
173.
174.
175.
176.
177.
178.
179.
180.
181.
182.
183.
184.
185.
186.
187.
188.
189.
190.
191.
192.
B. Lucks, et al., Engineering mRNA structural regulation of transcription using an RNA-sensing
riboregulator, Faseb Journal, 2010
Butland, et al., Functional interactions of a monothiol glutaredoxin and an iron sulfur cluster carrier
protein with the radical SAM enzyme MiaB, Faseb Journal, 2013
W. Blanch, et al., Addressing the need for alternative transportation fuels: The Joint BioEnergy
Institute, ACS Chemical Biology, 2008
D. Keasling, Synthetic biology for synthetic chemistry, ACS Chemical Biology, 2008
A. Dietrich, et al., A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered
Substrate-Promiscuous P450(BM3), ACS Chemical Biology, 2009
Heins RA, et al., Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases
through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry, ACS Chemical Biology, 2014
Deng, et al., Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and
Nanostructure-Initiator Mass Spectrometry (NIMS), ACS Chemical Biology, 2014
Hajimorad, et al., A framework and model system to investigate linear system behavior in Escherichia
coli, J Biol Eng, 2011
J. Chen, et al., Device Editor visual biological CAD canvas, J Biol Eng, 2012
Li, et al., Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance,
delignification and enzymatic saccharification, Bioresource Technology, 2010
R. Bharadwaj, et al., High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ
regeneration, Bioresource Technology, 2011
Li, et al., Influence of physico-chemical changes on enzymatic digestibility of ionic liquid and AFEX
pretreated corn stover, Bioresource Technology, 2011
J. I. Park, et al., Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the
hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus, Bioresource Technology, 2011
Oleskowicz-Popiel, et al., Co-production of ethanol, biogas, protein fodder and natural fertilizer in
organic farming--evaluation of a concept for a farm-scale biorefinery, Bioresour Technol, 2012
G. Papa, et al., Exploring the effect of different plant lignin content and composition on ionic liquid
pretreatment efficiency and enzymatic saccharification of Eucalyptus globulus L. mutants, Bioresour
Technol, 2012
Varanasi, et al., Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a
function of ionic liquid pretreatment, Bioresour Technol, 2012
J. A. Perez-Pimienta, et al., Comparison of the impact of ionic liquid pretreatment on recalcitrance of
agave bagasse and switchgrass, Bioresour Technol, 2013
P. Oleskowicz-Popiel, et al., Lignocellulosic ethanol production without enzymes--technoeconomic
analysis of ionic liquid pretreatment followed by acidolysis, Bioresource Technology, 2014
Scullin, et al., Optimization of renewable pinene production from the conversion of macroalgae
Saccharina latissima, Bioresour Technol, 2014
W. Weckwerth, et al., The multinational Arabidopsis steering subcommittee for proteomics assembles
the largest proteome database resource for plant systems biology, Journal of Proteome Research, 2008
Chandrasekaran, et al., A Microscale Platform For Integrated Cell-Free Expression And Activity
Screening Of Cellulases, Journal of Proteome Research, 2010
J. Ito, et al., Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central
plant metabolism, Journal of Proteome Research, 2011
Meng, et al., UDP-glucose pyrophosphorylase is not rate limiting, but is essential in Arabidopsis, Plant
Cell Physiology, 2009
193.
194.
195.
196.
197.
198.
199.
200.
201.
202.
203.
204.
205.
206.
207.
208.
209.
210.
211.
212.
213.
214.
215.
216.
Y. Chiu, et al., AtAPY1 and AtAPY2 function as Golgi-localized nucleoside diphosphatases in
Arabidopsis thaliana, Plant Cell Physiol, 2012
O.P. Cetinkol, et al., Understanding the impact of ionic liquid pretreatment on eucalyptus, Biofuels,
2010
Shepherd, et al., Eucalypts as a biofuel feedstock, Biofuels, 2011
B.A. Simmons, Opportunities and challenges in advanced biofuel production: the importance of
synthetic biology and combustion science, Biofuels, 2011
B.A. Simmons, Rethinking renewable energy in Japan, Biofuels, 2011
Jian Shi, et al., Impact of mixed feedstocks and feedstock densification on ionic liquid pretreatment
efficiency, Biofuels, 2013
Ronald, et al., Plant genetics, sustainable agriculture and global food security, Genetics, 2011
Ghosh, et al., A peptide-based method for 13C Metabolic Flux Analysis in microbial communities, PLoS
Comput Biol, 2014
Rotavera, et al., Photoionization mass spectrometric measurements of initial reaction pathways in lowtemperature oxidation of 2,5-dimethylhexane, J Phys Chem A, 2014
Loque, et al., Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium
transport activity, Journal of Biological Chemistry, 2009
H. R. Beller, et al., Definitive alkene identification needed for in vitro studies with ole (olefin
biosynthesis) proteins, Journal of Biological Chemistry, 2011
Casler, et al., The Switchgrass Genome: Tools and Strategies, Plant Genome, 2011
Z. Chen, et al., Tracing determinants of dual substrate specificity in glycoside hydrolase family 5, J Biol
Chem, 2012
P. McAndrew, et al., From soil to structure, a novel dimeric beta-glucosidase belonging to glycoside
hydrolase family 3 isolated from compost using metagenomic analysis, J Biol Chem, 2013
H. J. Joshi, et al., 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis
thaliana accessions, Bioinformatics, 2012
Kristen M. DeAngelis, et al., Changes in microbial dynamics during long-term decomposition in tropical
forests, Soil Biology and Biochemistry, 2013
Y. B. Melnichenko, et al., Monitoring Phase Behavior of Sub- and Supercritical CO2 Confined in Porous
Fractal Silica with 85% Porosity, Langmuir, 2010
G. Cheng, et al., Interactions of endoglucanases with amorphous cellulose films resolved by neutron
reflectometry and quartz crystal microbalance with dissipation monitoring, Langmuir, 2012
G. Cheng, et al., Effect of ionic liquid treatment on the structures of lignins in solutions: molecular
subunits released from lignin, Langmuir, 2012
Ronald, and R. Adamchak, The future of sustainable food production, Annals of the New York Academy
of Sciences, 2010
S. Scullin and L. D. Partridge, Modulation by pregnenolone sulfate of filtering properties in the
hippocampal trisynaptic circuit, Hippocampus, 2012
Klein-Marcuschamer, et al., Techno-economic analysis of a lignocellulosic ethanol biorefinery with ionic
liquid pre-treatment, Biofuels, Bioproducts and Biorefining, 2011
Goldberg, et al., Proposed design of distributed macroalgal biorefineries: thermodynamics,
bioconversion technology, and sustainability implications for developing economies, biofuels,
Bioproducts and Biorefining, 2013
Daniel Klein-Marcuschamer, et al., Technoeconomic analysis of renewable aviation fuel from
microalgae,Pongamia pinnata, and sugarcane, Biofuels, Bioproducts and Biorefining, 2013
217.
218.
219.
220.
221.
222.
223.
224.
225.
226.
227.
228.
229.
230.
231.
232.
233.
234.
235.
236.
237.
238.
Golberg, et al., Proposed design of distributed macroalgal biorefineries: thermodynamics,
bioconversion technology, and sustainability implications for developing economies, Biofuels
Bioproducts & Biorefining, et al., Biofpr, 2014
K. Cox, et al., Environmental life cycle assessment (LCA) of aviation biofuel from microalgae, Pongamia
pinnata, and sugarcane molasses, Biofuels Bioproducts & Biorefining, et al., Biofpr, 2014
J. Morgan, et al., Estimating molecular masses of petroleum-derived fractions: High mass (> 2000 u)
materials in maltenes and asphaltenes from Maya crude oil, Journal of Chromatography A, 2010
E. McKee, et al., Manipulation of the carbon storage regulator system for metabolite remodeling and
biofuel production in Escherichia coli, Microb Cell Fact, 2012
Eudes, et al., Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli, Microb
Cell Fact, 2013
Bi, et al., Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its
application to engineering hydrocarbon biofuel production, Microbial Cell Factories, 2013
O. Welz, et al., Low-temperature combustion chemistry of biofuels: pathways in the initial lowtemperature (550 K-750 K) oxidation chemistry of isopentanol, Physical Chemistry Chemical Physics,
2012
J. H. Mack, et al., Investigation of biofuels from microorganism metabolism for use as anti-knock
additives, Fuel, 2014
Singh, et al., Visualization of biomass solubilization and cellulose regeneration during ionic liquid
pretreatment of switchgrass, Biotechnology and Bioengineering, 2009
Y. J. Tang, et al., Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central
carbon metabolism, Biotechnology and Bioengineering, 2009
Y. J. Tang, et al., Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and
ethanol-tolerant Geobacillus strain, Biotechnology and Bioengineering, 2009
P. Reddy, et al., Bioenergy feedstock-specific enrichment of microbial populations during high-solids
thermophilic deconstruction, Biotechnology and Bioengineering, 2011
Sun, et al., Understanding tissue specific compositions of bioenergy feedstocks through hyperspectral
Raman imaging, Biotechnology and Bioengineering , 2011
J. M. Gladden, et al., Substrate perturbation alters the glycoside hydrolase activities and community
composition of switchgrass-adapted bacterial consortia, Biotechnol Bioeng, 2012
L. Sun, et al., Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy, Biotechnol
Bioeng, 2012
J. Zendejas, et al., Characterization of the acylglycerols and resulting biodiesel derived from vegetable
oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum), Biotechnol Bioeng,
2012
Klein-Marcuschamer, et al., The challenge of enzyme cost in the production of lignocellulosic biofuels,
Biotechnology and Bioengineering, 2012
Klein-Marcuschamer, et al., A matter of detail: Assessing the true potential of microalgal biofuels,
Biotechnol Bioeng, 2013
L. J. Weaver, et al., A kinetic-based approach to understanding heterologous mevalonate pathway
function in E. coli., Biotechnology and Bioengineering, 2014
K. W. George, et al., Correlation analysis of targeted proteins and metabolites to assess and engineer
microbial isopentenol production, Biotechnology and Bioengineering, 2014
Sharma, et al., Transcriptional dynamics during cell wall removal and regeneration reveals key genes
involved in cell wall development in rice, Plant Molecular Biology, 2011
J. Ito, et al., A survey of the Arabidopsis thaliana mitochondrial phosphoproteome, Proteomics, 2009
239.
240.
241.
242.
243.
244.
245.
246.
247.
248.
249.
250.
251.
252.
253.
254.
255.
256.
257.
258.
259.
260.
261.
262.
263.
N.L. Taylor, et al., The Arabidopsis thaliana 2-D gel mitochondrial proteome: Refining the value of
reference maps for assessing protein abundance, contaminants and post-translational modifications,
Proteomics, 2011
K. Agrawal, et al., Boosting the globalization of plant proteomics through INPPO: current
developments and future prospects, Proteomics, 2012
M. Jones, et al., The HUPO initiative on Model Organism Proteomes, iMOP, Proteomics, 2012
P. Schrimpf, et al., The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011,
Geneva, Switzerland, Proteomics, 2012
P. Singh, et al., Application of targeted proteomics to metabolically engineered Escherichia coli,
Proteomics, 2012
E. K. Baidoo and J. D. Keasling, Microbial metabolomics: welcome to the real world!, Metabolomics,
2013
R. Beller, et al., Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus, Applied and
Environmental Microbiology, 2010
J. Rutherford, et al., Functional genomic study of exogenous n-butanol stress in Escherichia coli,
Applied and Environmental Microbiology, 2010
R. Chhabra, et al., Generalized Schemes for High-Throughput Manipulation of the Desulfovibrio
vulgaris Genome, Applied and Environmental Microbiology, 2011
K. M. DeAngelis, et al., PCR amplification-independent methods for detection of microbial
communities by the high-density microarray PhyloChip, Applied and Environmental Microbiology, 2011
M. Gladden, et al., Glycoside hydrolase activities of thermophilic bacterial consortia adapted to
switchgrass, Applied and Environmental Microbiology, 2011
Rezaei, et al., Selection of Conditions for Cellulase and Xylanase Extraction from Switchgrass Colonized
by Acidothermus cellulolyticus, Applied Biochemistry and Biotechnology, 2011
Eudes, et al., Production of tranilast [N-(3',4'-dimethoxycinnamoyl)-anthranilic acid] and its analogs in
yeast Saccharomyces cerevisiae, Applied Microbiology and Biotechnology, 2011
Jeffrey A. Dietrich, et al., Transcription Factor-Based Screens and Synthetic Selections for Microbial
Small-Molecule Biosynthesis, ACS Synthetic Biology, 2012
J. Hillson, et al., j5 DNA Assembly Design Automation Software, ACS Synthetic Biology, 2012
H. Chou and J. D. Keasling, Synthetic pathway for production of five-carbon alcohols from isopentenyl
diphosphate, Appl Environ Microbiol, 2012
Groff, et al., Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars, Appl
Environ Microbiol, 2012
B. Goh, et al., Engineering of bacterial methyl ketone synthesis for biofuels, Applied and Environmental
Microbiology, 2012
Juminaga, et al., Modular Engineering of L-Tyrosine Production in Escherichia coli, Applied and
Environmental Microbiology, 2012
Y. Kung, et al., From fields to fuels: recent advances in the microbial production of biofuels, ACS Synth
Biol, 2013
Linshiz, et al., PaR-PaR laboratory automation platform, ACS Synth Biol, 2013
Muller, et al., Engineering of Ralstonia eutropha H16 for Autotrophic and Heterotrophic Production of
Methyl Ketones, Appl Environ Microbiol, 2013
J. Hillson, j5 DNA assembly design automation, ACS Synthetic Biology, 2013
Sarria, et al., Microbial Synthesis of Pinene, ACS Synthetic Biology, 2014
R. M. Phelan, Engineering Terpene Biosynthesis in Streptomyces for Production of the Advanced
Biofuel Precursor Bisabolene, ACS Synthetic Biology, 2014
264.
265.
266.
267.
268.
269.
270.
271.
272.
273.
274.
275.
276.
277.
278.
279.
280.
281.
282.
283.
284.
285.
286.
Linshiz, et al., PR-PR: Cross-Platform Laboratory Automation System, ACS Synthetic Biology, 2014
Javidpour, et al., Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the
Bacterial Production of Fatty Acids under Anaerobic Conditions, Applied and Environmental
Microbiology, 2014
L. Cote, et al., Gene family structure, expression and functional analysis of HD-Zip III genes in
angiosperm and gymnosperm forest trees, BMC Plant Biology, 2010
M. DeAngelis, et al., Evidence supporting dissimilatory and assimilatory lignin degradation in
Enterobacter lignolyticus SCF1, Frontiers in Microbial Physiology and Metabolism, 2013
Nyyssoenen, et al., Coupled high-throughput functional screening and next generation sequencing for
identification of plant polymer decomposing enzymes in metagenomic libraries, Frontiers in
Microbiology, 2013
X. Cheng, et al., High throughput nanostructure-initiator mass spectrometry screening of microbial
growth conditions for maximal beta-glucosidase production, Frontiers in Microbiology, 2013
S. A. Eichorst, et al., Substrate-Specific Development of Thermophilic Bacterial Consortia Using
Chemically Pretreated Switchgrass, Appl Environ Microbiol, 2014
J. Kirby, et al., Use of non-ionic surfactants for improvement of terpene production in Saccharomyces
cerevisiae, Appl Environ Microbiol, 2014
J. Ito, et al., Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and
tandem mass spectrometry, Analytical Biochemistry, 2014
Greving, et al., Acoustic deposition with NIMS as a high-throughput enzyme activity assay, Analytical
and Bioanalytical Chemistry, 2012
de Rond, et al., Versatile synthesis of probes for high-throughput enzyme activity screening, Anal
Bioanal Chem, 2013
M. Smith, et al., Fluorescent Lifetime Imaging of Lignin in the Plant Cell Wall, Biophysical Journal, 2010
Liu, et al., The N-Terminal Ig Domain of Endoglucanase Cel9A from the Thermoacidophilic
Alicyclobacillus Acidocaldarius Enhances Protein Stability, Biophysical Journal, 2010
Knierim, et al., TEM/FISH Imaging of Microbial Communities, Biophysical Journal, 2010
M. Smith-Moritz, et al., Dependence of Plant Cell Wall Composition and Structure on Cellulose
Synthase-Like Knock Out Mutant, Biophysical Journal, 2012
F. Nowroozi, et al., Metabolic pathway optimization using ribosome binding site variants and
combinatorial gene assembly, Applied Microbial Biotechnology, 2014
M.-K. Kang, et al., Synthetic biology platform of CoryneBrick vectors for gene expression in
Corynebacterium glutamicum and its application to xylose utilization, Applied Microbiology and
Biotechnology, 2014
C.-J. Park, et al., The endoplasmic reticulum-quality control component SDF2 is essential for XA21mediated immunity in rice, Plant Science, 2013
Geshi, et al., Glycosyltranfserases Involved in the Plant Cell Wall Polysaccharides Biosynthesis,
Glycobiology, 2008
S. F. Hansen, et al., Structural Comparison of Plant Glycosyltransferases, Glycobiology, 2011
K. H. Jung, et al., Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays:
Evaluation of Gene-Redundancy, Plos One, 2008
Shui, et al., Membrane proteomics of phagosomes suggests a connection to autophagy, Proceedings of
the National Academy of Sciences, 2008
M. Allgaier, et al., Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost
Community, Plos One, 2010
287.
288.
289.
290.
291.
292.
293.
294.
295.
296.
297.
298.
299.
300.
301.
302.
303.
304.
305.
306.
307.
Oikawa, et al., An integrative approach to the identification of Arabidopsis and rice genes involved in
xylan and secondary wall development, PLoS One, 2010
Christen, et al., High-throughput identification of protein localization dependency networks,
Proceedings of the National Academy of Sciences, 2010
Y. Cong, et al., 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its
unique subunit arrangement, Proceedings of the National Academy of Sciences, 2010
S. R. Chhabra, et al., Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate
Reducer Desulfovibrio vulgaris Hildenborough, PLoS One, 2011
K. M. DeAngelis, et al., Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil,
PLoS ONE , 2011
S. Chuck, et al., Overexpression of the maize Corngrass1 microRNA prevents flowering, improves
digestibility, and increases starch content of switchgrass, Proceedings of National Academy of
Sciences, 2011
Lee, et al., Genetic dissection of the biotic stress response using a genome-scale gene network for rice,
Proceedings of National Academy of Sciences, 2011
M. A. Atmodjo, et al., Galacturonosyltransferase (GAUT)1 and GAUT7 are the core of a plant cell wall
pectin biosynthetic homogalacturonan:galacturonosyltransferase complex, Proceedings of the
National Academy of Sciences, 2011
Bokinsky, et al., Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using
engineered Escherichia coli, Proceedings of the National Academy of Sciences, 2011
P. Cetinkol, et al., Structural and chemical characterization of hardwood from tree species with
applications as bioenergy feedstocks, PLoS One, 2012
Harholt, et al., The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a
comparative study of its cell wall, PLoS One, 2012
I. Park, et al., A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic
biofuels, PLoS One, 2012
J. Perez-Gil, et al., Mutations in Escherichia coli aceE and ribB genes allow survival of strains defective in
the first step of the isoprenoid biosynthesis pathway, PLoS One, 2012
K. Sharma, et al., A genome-wide survey of switchgrass genome structure and organization, PLoS One,
2012
Sogaard, et al., GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic
enzymes in the Golgi apparatus of living tissues, PLoS One, 2012
Chiniquy, et al., XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan, Proc
Natl Acad Sci U S A, 2012
J. Khudyakov, et al., Global transcriptome response to ionic liquid by a tropical rain forest soil
bacterium, Enterobacter lignolyticus SCF1, Proceedings of National Academy of Sciences, 2012
Ying Xu, et al., Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to
Deconstruct Switchgrass, PLoS One, 2013
J. A. Rodrigues, et al., Imprinted expression of genes and small RNA is associated with localized
hypomethylation of the maternal genome in rice endosperm, Proceedings of the National Academy of
Sciences of the United States of America, 2013
P. Reddy, et al., Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of
Rice Straw Using Metagenomic Analyses, PLoS One, 2013
T. Parsons, et al., Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by freeflow electrophoresis, PLoS One, 2013
308.
309.
310.
311.
312.
313.
314.
315.
316.
317.
318.
319.
320.
321.
322.
323.
324.
325.
326.
327.
328.
329.
330.
J. Joshua, et al., Functional characterization of the origin of replication of pRN1 from Sulfolobus
islandicus REN1H1, PLoS One, 2013
Z. Chen, et al., Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic
liquid pretreated switchgrass, PLoS One, 2013
Golberg, et al., Cloud-enabled microscopy and droplet microfluidic platform for specific detection of
Escherichia coli in water, PLoS One, 2014
E. Garcia and J. D. Keasling, Kinetics of Phosphomevalonate Kinase from Saccharomyces cerevisiae,
PLoS One, 2014
Frederix, et al., Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance,
PLoS One, 2014
J. Dougherty, et al., Cellulosic Biomass Pretreatment and Sugar Yields as a Function Of Biomass
Particle Size, PLoS One, 2014
P. Peralta-Yahya, et al., Advanced biofuel production in microbes, Biotechnology Journal, 2010
W. Blanch, et al., Biomass deconstruction to sugars, Biotechnology Journal, 2011
L. Sun, et al., Unveiling high-resolution, tissue specific dynamic changes in corn stover during ionic
liquid pretreatment, Rsc Advances, 2013
M. Rhee, et al., Versatile on-demand droplet generation for controlled encapsulation, Biomicrofluidics,
2014
De Michele, et al., Ammonium and urea transporter inventory of the selaginella and physcomitrella
genomes, Front Plant Sci, 2012
F. Hansen, et al., Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families, Front Plant
Sci, 2012
T. Parsons, et al., Proteomic dissection of the Arabidopsis Golgi and trans-Golgi network, Front Plant
Sci, 2012
L. Heazlewood, et al., The Green proteome: challenges in plant proteomics, Frontiers in Plant
Proteomics, 2011
Wipf, et al., Amino acid transporter inventory of the Selaginella genome, Frontiers in Plant Science,
2012
Chiniquy, et al., Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes
and their roles in xylan biosynthesis, Frontiers in Plant Science, 2013
Rita Sharma, et al., Construction of a rice glycoside hydrolase phylogenomic database and
identification of targets for biofuel research, Frontiers in Plant Science, 2013
W. Mann, et al., MASCP gator: an overview of the Arabidopsis proteomic aggregation portal, Frontiers
in Plant Science, 2013
W. Carroll, et al., Managing the green proteomes for the next decade of plant research, Frontiers in
Plant Science, 2013
Ito, et al., The Arabidopsis cytosolic proteome: the metabolic heart of the cell, Frontiers in Plant
Science, 2014
Lee, et al., Characterization of wastewater treatment plant microbial communities and the effects of
carbon sources on diversity in laboratory models, PLoS One, 2014
S. Parreiras, et al., Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant
Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn
Stover, PLoS One, 2014
Y. Ren, et al., Site-directed mutagenesis of IRX9, IRX9L and IRX14 proteins involved in xylan
biosynthesis: glycosyltransferase activity is not required for IRX9 function in Arabidopsis, PLoS One,
2014
331.
332.
333.
334.
335.
336.
337.
338.
339.
340.
341.
342.
343.
344.
345.
346.
347.
348.
349.
350.
351.
352.
353.
T. Yu, et al., Bioinformatic processing to identify single nucleotide polymorphism that potentially affect
Ape1 function, Mutation Research, 2010
L. Woo, et al., Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest
soils, Systematic and applied microbiology, 2014
Barcon, J. Alonso-Gutierrez, et al., Molecular and physiological approaches to understand the ecology
of methanol degradation during the biofiltration of air streams, Chemosphere, 2012
Liu, et al., Molecular simulations provide new insights into the role of the accessory immunoglobulinlike domain of Cel9A, FEBS Letters, 2010
Y. B. Melnichenko, et al., Accessibility of pores in coal to methane and carbon dioxide, Fuel, 2012
R. Arora, et al., Monitoring and Analyzing Process Streams Towards Understanding Ionic Liquid
Pretreatment of Switchgrass (Panicum virgatum L.), Bioenergy Research, 2010
C. R. Brennan, et al., Recovery of Sugars from Ionic Liquid Biomass Liquor by Solvent Extraction,
Bioenergy Research, 2010
J. Cao, et al., A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes, Bioenergy
Research, 2010
M. DeAngelis, et al., Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme
Discovery in Lignocellulolytic Microbial Communities, Bioenergy Research, 2010
Rautengarten, et al., A Simple Method for Enzymatic Synthesis of Unlabeled and Radiolabeled
Hydroxycinnamate-CoA, BioEnergy Research, 2010
V. Scheller, et al., The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming
Biomass Recalcitrance, BioEnergy Research, 2010
Chenlin Li, et al., Comparing the Recalcitrance of Eucalyptus, Pine, and Switchgrass Using Ionic Liquid
and Dilute Acid Pretreatments, Bioenergy Research, 2012
Jason S. Lupoi, et al., Assessment of Lignocellulosic Biomass Using Analytical Spectroscopy: an
Evolution to High-Throughput Techniques, Bioenergy Research, 2013
S. Lupoi, et al., Assessment of Lignocellulosic Biomass Using Analytical Spectroscopy: an Evolution to
High-Throughput Techniques, Bioenergy Research, 2014
H. Liu, et al., Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study,
Journal of Physical Chemistry B, 2010
H. Liu, et al., Molecular Dynamics Study of Polysaccharides in Binary Solvent Mixtures of an Ionic Liquid
and Water, Journal of Physical Chemistry B, 2011
H. Liu, et al., Simulations Reveal Conformational Changes of Methylhydroxyl Groups during Dissolution
of Cellulose I(beta) in Ionic Liquid 1-Ethyl-3-methylimidazolium Acetate, J Phys Chem B, 2012
Cheng, et al., Impact of Ionic Liquid Pretreatment Conditions on Cellulose Crystalline Structure Using 1Ethyl-3-methylimidazolium Acetate, Journal of Physical Chemistry B, 2012
Harholt, et al., ARAD proteins associated with pectic Arabinan biosynthesis form complexes when
transiently overexpressed in planta, Planta, 2012
Orfila, et al., Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of
cell wall polymers and tuber mechanical properties, Planta, 2012
Stoppel and J. Meurer, Complex RNA metabolism in the chloroplast: an update on the psbB operon,
Planta, 2013
N. Mac Dowell, et al., New Experimental Density Data and Soft-SAFT Models of Alkylimidazolium
([CnC1im](+)) Chloride (Cl(-)), Methylsulfate ([MeSO4](-)), and Dimethylphosphate ([Me2PO4](-))
Based Ionic Liquids, Journal of Physical Chemistry: B, 2014
H. Pereira, et al., Biochemical characterization and crystal structure of endoglucanase Cel5A from the
hyperthermophilic Thermotoga maritima, Journal of Structural Biology, 2010
354.
355.
356.
357.
358.
359.
360.
361.
362.
363.
364.
365.
366.
367.
368.
369.
370.
371.
372.
373.
374.
375.
376.
J. Steen, et al., Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol,
Microbial Cell Factories, 2008
A. Simmons, Synthetic enzymes: catalysis on demand, Microbial Biotechnology, 2011
Yu, et al., Probing conformational changes in Ape1 during the progression of base excision repair,
Biochemistry, 2010
Yuzawa, et al., Construction of a part of a 3-hydroxypropionate cycle for heterologous polyketide
biosynthesis in Escherichia coli, Biochemistry, 2012
Yuzawa, et al., Broad substrate specificity of the loading didomain of the lipomycin polyketide
synthase, Biochemistry, 2013
Hagen, S., et al., In Vitro Analysis of Carboxyacyl Substrate Tolerance in the Loading and First
Extension Modules of Borrelidin Polyketide Synthase, Biochemistry, 2014
Muyzer, et al., Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7, Standards in
Genomic Sciences, 2011
Chertkov, et al., Complete genome sequence of Tolumonas auensis type strain (TA 4T), Standards in
Genomic Sciences, 2011
DeAngelis, et al., Complete genome sequence of Enterobacter lignolyticus SCF1, Standards in Genomic
Sciences, 2011
DeAngelis, et al., Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with
and without iron, Standards in Genomic Sciences, 2013
Y. Satoh, et al., Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central
metabolic tyrosine, in Escherichia coli, J Agric Food Chem, 2012
M. Lafreniere, et al., Multiplexed extraction and quantitative analysis of pharmaceuticals from DBS
samples using digital microfluidics, Bioanalysis, 2014
Sarkar, et al., Plant cell walls throughout evolution: towards a molecular understanding of their design
principles, Journal of Experimental Botany, 2009
Simmons, Characterization of bacterial communities in solarized soil amended with lignocellulosic
organic matter, Applied Soil Ecology, 2013
C. S. Hastrup, et al., Differences in crystalline cellulose modification due to degradation by brown and
white rot fungi, Fungal Biology, 2012
M. Winger, et al., Secretome analysis of the thermophilic xylanase hyper-producer Thermomyces
lanuginosus SSBP cultivated on corn cobs, J Ind Microbiol Biotechnol, 2014
S. Kumar, et al., Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans,
BMC Systems Biology, 2011
Y. Lee, et al., Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and
imaging, Biotechniques, 2010
Woo, et al., Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated
from Wet Tropical Forest Soil, Genome Announcements, 2014
J. C. Bergmann, et al., Discovery of two novel beta-glucosidases from an Amazon soil metagenomic
library, FEMS Microbiology Letters, 2014
Y. J. Tang, et al., Investigation of carbon metabolism in "Dehalococcoides ethenogenes" strain 195 by
use of isotopomer and transcriptomic analyses, Journal of Bacteriology, 2009
Young, et al., Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living
actinobacterium, Journal of Bacteriology, 2010
J. Joshua, et al., Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by
Sulfolobus acidocaldarius, Journal of Bacteriology, 2011
377.
378.
379.
380.
381.
382.
383.
384.
385.
386.
387.
388.
389.
390.
391.
392.
393.
394.
395.
396.
397.
398.
399.
Bokinsky, et al., HipA-Triggered Growth Arrest and beta-Lactam Tolerance in Escherichia coli Are
Mediated by RelA-Dependent ppGpp Synthesis, J Bacteriol, 2013
H. Chou, et al., Direct calibration of PICKY-designed microarrays, BMC Bioinformatics, 2009
Ouellet, et al., A rapid and inexpensive labeling method for microarray gene expression analysis, BMC
Biotechnology, 2009
J. Dougherty, et al., Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening
and functional characterization, BMC Biotechnol, 2012
Deng, et al., Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme,
Rapid Commun Mass Spectrom, 2012
A.M. Smith-Moritz, et al., Combining multivariate analysis and monosaccharide composition modeling
to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy, Plant Methods,
2011
Klein-Marcuschamer and H. W. Blanch, Survival of the Fittest: An Economic Perspective on the
Production of Novel Biofuels, AiChe Journal, 2013
Frear, et al., Biogas potential and microbial population distributions in flushed dairy manure and
implications on anaerobic digestion technology, Journal of Chemical Technology and Biotechnology,
2011
Sathitsuksanoh, et al., New lignocellulose pretreatments using cellulose solvents: a review, Journal of
Chemical Technology and Biotechnology, 2013
E. Achyuthan, et al., Spectroscopic High Throughput Screening of Laccase-Catalyzed p-Cresol
Oxidation, Combinatorial Chemistry & High Throughput Screening, 2009
H. Jung, et al., Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data, Rice, 2009
Peijian Cao, et al., The Rice Oligonucleotide Array Database: an atlas of rice gene expression, Rice, 2012
Yang, et al., Monolignol Transporters and Cell Wall Oxidases Screens, Plant Biology, 2009
Eudes, et al., Synthesis of phenylpropanoid-esters and -amides in Arabidopsis thaliana to engineer a
cleavable lignin, Plant Biology, 2009
W. Singer, et al., Enrichment, Isolation and Characterization of Fungi Tolerant to 1-Ethyl-3Methylimadazolium Acetate, Journal of Applied Microbiology, 2011
P. Reddy, et al., Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1ethyl-3-methylimidazolium acetate, J Appl Microbiol, 2012
W. Simmons, et al., , Effect of inoculum source on the enrichment of microbial communities on two
lignocellulosic bioenergy crops under thermophilic and high-solids conditions, Journal of Applied
Microbiology, 2014
K. E. Achyuthan, et al., Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol
and Its Enzyme-Catalyzed Oxidation Products, Molecules, 2009
K. E. Achyuthan, et al., Supramolecular Self-Assembled Chaos: Polyphenolic Lignin's Barrier to CostEffective Lignocellulosic Biofuels, Molecules, 2010
K. E. Achyuthan, et al., Hitherto Unrecognized Fluorescence Properties of Coniferyl Alcohol, Molecules,
2010
Yuzawa, et al., Enzyme analysis of the polyketide synthase leads to the discovery of a novel analog of
the antibiotic alpha-lipomycin, Journal of Antibiotics, 2014
Y. Verhertbruggen, et al., Mannan synthase activity in the CSLD family, Plant Signaling & Behavior,
2011
Vega-Sanchez, et al., Abundance of mixed linkage glucan in mature tissues and secondary cell walls of
grasses, Plant Signal Behav, 2013
400.
401.
402.
403.
404.
405.
406.
407.
408.
409.
410.
411.
412.
413.
414.
415.
416.
417.
418.
419.
420.
421.
422.
L. Petersen, et al., Assay and heterologous expression in Pichia pastoris of plant cell wall type-II
membrane anchored glycosyltransferases, Glycoconjugate Journal , 2009
K. L. Keller, et al., Methods for engineering sulfate reducing bacteria of the genus desulfovibrio,
Methods in Enzymology, 2011
Y. J. Tang, et al., Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under
environmental or genetic perturbations, Biotechnol Prog, 2009
D. Marner, 2nd, et al., Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica
support, Biotechnology Progress, 2009
S. Shaikh, et al., Study of stationary phase metabolism via isotopomer analysis of amino acids from an
isolated protein, Biotechnology Progress, 2010
W. Simmons, et al., Bacillus coagulans tolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in
aqueous and solid-state thermophilic culture, Biotechnology Progress, 2014
Heather L. Szmidt-Middleton, et al., Utilizing a highly responsive gene, yhjX, in E. coli based production
of 1,4-butanediol, chemical engineering science, 2013
Han Min Woo, et al., Application of targeted proteomics and biological parts assembly in E. coli to
optimize the biosynthesis of an anti-malarial drug precursor, amorpha-4,11-diene, chemical
engineering science, 2013
Klein-Marcuschamer, et al., Technoeconomic analysis of biofuels: A wiki-based platform for
lignocellulosic biorefineries, Biomass & Bioenergy, 2010
M. Paap, et al., Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: A
comparative analysis of environmental and economic performance, Biomass & Bioenergy, 2013
Seema Singh, et al., Understanding the impact of ionic liquid pretreatment on cellulose and lignin via
thermochemical analysis, Biomass and Bioenergy, 2013
E. Vickers, et al., D. Klein-Marcuschamer, et al., J. O. Kromer, Examining the feasibility of bulk
commodity production in Escherichia coli, Biotechnology Letters, 2012
Galdzicki, K. P., et al., The Synthetic Biology Open Language (SBOL) provides a community standard
for communicating designs in synthetic biology, Computational Biology, 2014
Christensen, et al., Characterization of the primary cell walls of seedlings of Brachypodium distachyon A potential model plant for temperate grasses, Phytochemistry, 2010
Xie, J. Kirby and J. D. Keasling, Functional characterization of four sesquiterpene synthases from
Ricinus communis (Castor bean), Phytochemistry, 2012
W. Simmons, et al., Characterization of bacterial communities in solarized soil amended with
lignocellulosic organic matter, Applied Soil Ecology, 2014
Christensen, et al., Regulation of (1,3, et al., 1,4)-β-D-glucan synthesis in developing endosperm of
barley lys mutants, Journal of Cereal Science, 2012
Linshiz, et al., The fusion of biology, computer science, and engineering: towards efficient and
successful synthetic biology, Perspect Biol Med, 2012
Sharma, tools for developing glycosyl-transferase assays and methods for xylan profiling in plants,
pharmaceutical biology, 2012
McInerney, et al., Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase, Mol
Biol Int, 2014
E. Baidoo, et al., Mass spectrometry-based microbial metabolomics, Methods Mol Biol, 2012
S. Batth, et al., Targeted proteomics for metabolic pathway optimization, Methods Mol Biol, 2012
R. Beller, et al., Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus
denitrificans, Methods Mol Biol, 2012
423.
424.
425.
426.
427.
428.
429.
430.
431.
432.
433.
434.
435.
436.
437.
438.
439.
440.
441.
442.
443.
444.
445.
T. Parsons, et al., Separation of the plant golgi apparatus and endoplasmic reticulum by free-flow
electrophoresis, Methods in Molecular Biology, 2014
M. Estavillo, et al., Isolation of the plant cytosolic fraction for proteomic analysis, Plant Proteomics:
Methods and Protocols, 2014
K.-H. Jung, et al., Genome-wide Identification and Analysis of Early Heat Stress Responsive Genes in
Rice, Journal of Plant Biology, 2012
Pradhan Mitra, et al., Histochemical Staining of Arabidopsis thaliana Secondary Cell Wall Elements,
Journal of Visualized Experiments, JOVE, 2014
Keasling, Engineering Microorganisms with Plant-derived Genes to Produce Drugs and Fuels, In Vitro
Cellular & Developmental Biology Animal, 2010
W. Mann, et al., Proteome coverage of the model plant Arabidopsis thaliana: implications for shotgun
proteomic studies, J Proteomics, 2013
Ito, et al., The Role of Proteomics in the Development of Cellulosic Biofuels, Current Proteomics, 2010
E. Bartley, et al., Plant and microbial research seeks biofuel production from lignocellulose, California
Agriculture, 2009
B.A. Simmons, et al., Ionic liquid pretreatment, Chemical Engineering Progress, 2010
M.S. Kent, et al., Effect of Agitation/Flow on the Enzymatic Digestion of Cellulose: a Structural Study by
SANS, Polymer Preprints, ACS-PMSE symposium on Small Angle Neutron Scattering from Polymers
and Complex Fluids, 238th ACS National Meeting, Washington DC, Aug 16-20, 2009. , 2009
Geshi, et al., Toward tailored synthesis of functional polysaccharides in plants, Foods for Health in the
21st Century: A Road Map for the Future, 2010
S. Lalonde, et al., A membrane protein/signaling protein interaction network for Arabidopsis version
AMPv2, Frontiers in Physiology, 2010
J. Han, et al., Chemical profiling of the plant cell wall through Raman microspectroscopy in 2010 IEEE
International Symposium on Biomedical Imaging: From Nano to Macro, IEEE ISBI, 2010
Yang, et al., Characteristics of Isopentanol as a Fuel for HCCI Engines, Society of Automobile Engineers
International Journal of Fuels and Lubricants, 2010
M.J. Dunlop, et al., A model for improving microbial biofuel production using a synthetic feedback loop,
Synthetic and Systems Biology, 2010
C.J. Petzold, et al., Metabolic engineering of E.coli for the production of a precursor to artemisinin, an
anti-malarial drug, The Manual of Industrial Microbiology and Biotechnology, 2010
Anil Wipat, et al., Synthetic Biology Open Language (SBOL) Version 1.0.0, BioBricks Foundation
Request for Comments, 2011
Varanasi, et al., Quantifying Bio-Engineering: The Importance of Biophysics in Biofuel Research,
Biofuel's Engineering Process Technology, 2011
Datta, et al., Cellulases and Hemicellulases for Biomass Degradation: An Introduction, Chemical and
Biochemical Catalysis for Next Generation Biofuels, 2011
Loque, et al., Biomass Availability and Sustainability for BioFuels, Chemical and Biochemical Catalysis
for Next Generation Biofuels, 2011
B.A. Simmons, Introduction to Catalysis for Biofuels, Chemical and Biochemical Catalysis for Next
Generation Biofuels, 2011
S.R. Chhabra, et al., The Biological Basis | Metabolic Design and Control for Production in Prokaryotes,
Comprehensive Biotechnology, 2011
N.J. Hillson, DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems,
Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic
Biology, 2011
446.
447.
448.
449.
450.
451.
452.
453.
454.
455.
456.
457.
458.
459.
460.
461.
462.
J. D. Keasling, Joint BioEnergy Institute, Industrial Biotechnology, 2011
S. Lee, et al., BglBrick vectors and datasheets, et al., a synthetic biology platform for gene expression,
Journal of Biological Engineering , 2011
Klein-Marcuschamer, et al., Biofuel Economics, Plant Biomass Conversion, 2011
B.A. Simmons, Bioenergy from Plants and Plant Residues, Plant Biotechnology and Agriculture Prospects for the 21st Century, 2011
Sakuragi, et al., Visual mapping of cell wall biosynthesis, The Plant Cell Wall: Methods and Protocols,
2011
Reindl, et al., Nanostructure-initiator mass spectrometry (NIMS) for the analysis of enzyme activities,
Curr protoc chem biol, 2012
Patanjali Varanasi, et al., Mechanical Stress Analysis as a Method to Understand the Impact of
Genetically Engineered Rice and Arabidopsis Plants, Industrial Biotechnology, 2012
B.J Rutherford, et al., Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels,
Microbial Biotechnology: Energy and Environment, 2012
Mukhopadhyay, et al., Control of Stress Tolerance in Bacterial Host Organisms for Bioproduction of
Fuels, Microbial Stress Tolerance: From Genomics to Biofuels, 2012
T. Parsons, et al., The current state of the Golgi proteomes, Proteomics - Applications in Biology, 2012
Bokinsky, et al., Synthetic biology of microbial biofuel production: From enzymes to pathways to
organisms, Synthetic Biologu: Tools and Applications, 2012
Goldberg, et al., Distributed marine biorefineries for developing economies., , 2012
L. Heazlewood, et al., Proteomics - Applications in Biology, , 2012
Seema Singh, et al., Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges, Aqueous
Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013
R. E. Paull, et al., Lotus Cell Walls and the Genes Involved in its Synthesis and Modification, Tropical
Plant Biology, 2013
N.J. Hillson, J5 DNA Closing and Assembly Methods, Methods and Protocols, 2014
Chandrasekaran and A. K. Singh, One-Pot, Microscale Cell-Free Enzyme Expression and Screening,
Cell-Free Protein Synthesis: Methods and Protocols, 2014
Download