Bio
Dr. Zhang is Associate Professor
Research in the Center for Ecogenomics of Biodesign Institute and
affiliate Professor of Microbiology in the School of Life Science at
ASU. Prior to joining ASU in 2007, Prof. Zhang was a Senior Research
Scientist II and Senior Principal Investigator at Microbiology
Department of the Pacific Northwest National Laboratory of the U.S.
Department of Energy (DOE).
He has broad research experience in
microbial genetics, physiology and ecology, has authored more than
60 peer-reviewed papers and 8 pending US patent applications. His
recent research focuses on microbial metabolic engineering, applying
metatranscriptomics and single-cell transcriptomics for complex
microbial community, and developing computational tools for
integrating various post-genomic datasets. He has served as a
frequent reviewer for about a dozen journals including Genome
Biology, BMC Bioinformatics and Proteomics, and also served as a
reviewer for grant proposals to the Department of Energy (DOE) and
the National Science Foundation (NSF) in recent years.
At ASU Prof. Zhang also serves as
program faculty for the Biological Design (BD); Civil
and Environmental Engineering (CEE); Environmental Life
Science (ELS); Microbiology (MIO); Molecular and
Cellular Biology (MCB) Ph.D. graduate programs: and
serves as a member of the Executive Committee for Environmental
Life Science (ELS) graduate program.
Research Expertise
Systems Microbiology; Environmental
Microbiology; Metabolic Engineering and Synthetic Biology; Biofuels Research
Recent Publication
L. Chen, D.
Shu, W. Wang, J. Chen, Y. Jiang, W.W. Zhang, W.H. Jiang, and Y.H.
Lu. (2009) Global transcriptomics analysis reveals roles of the
negative regulator AveI for avermectin biosynthesis in
Streptomyces avermitilis. FMES Microbiological
Letter. 298 (2): 199-207.
W.
Torres-Garcia, W.W. Zhang *, R. Johnson, G. Runger, and D.R.
Meldrum. (2009) Integrative analysis of transcriptomic and proteomic
data of Desulfovibrio vulgaris: a nonlinear model to
predict abundance of undetected proteins. Bioinformatics.
25 (15): 1905-1914.
Y.H. Cai, P.
Trodler, S.M. Jiang, W.W.Zhang, Y. Wu, Y.H. Lu, S. Yang, and W.H.
Jiang. (2009) Identification and characterization of a novel
D-hydantoinase from Jannaschia sp. CCS1. FEBS Journal. 276
(13): 3575-3588.
D. Shu, L.
Chen, W.H. Wang, W.W. Zhang, S. Yang, Y.H. Lu, and W.H. Jiang.
(2009) afsQ1-Q2-sigQ is a pleiotropic but conditionally required
signal transduction system for both secondary metabolism and
morphological development in Streptomyces coelicolor.
Applied Microbiology and Biotechnology. 81 (6): 1149-1160.
L. Nie, G.
Wu, and W.W. Zhang *. (2008) Statistic application and challenges in
global proteomic analysis by mass spectrometry.
Critical Review in Biotechnology. 28 (4): 297-307.
L. Chen, Y.
Lu, J. Chen, W.W. Zhang, D. Shu, S. Yang, Z. Qin, W. Jiang. (2008)
Characterization of a negative regulator AveI for avermectin
biosynthesis in Streptomyces avermitilis NRRL8165.
Applied Microbiology and Biotechnology. 80 (2): 277-286.
L. Nie, G.
Wu, and W.W. Zhang *. (2008) Integrative Analyses of
Post-transcriptional Regulation in the Yeast Saccharomyces
cerevisiae Using Transcriptomic and Proteomic Data. Current
Microbiology. 57 (1): 18-22.
Y.H Lu, W.H.
Wang, D. Shu, W.W. Zhang, L. Chen, Z.J. Qin, S. Yang, and W.H.
Jiang. (2007) Genetic and proteomic analyses of a novel
two-component regulatory system JyhA1/A2 in Streptomyces
coelicolor: involvement in the regulation of biosynthesis of
both type II actinorhodin and an uncharacterized type I polyketide.
Applied Microbiology and Biotechnology. 77 (3): 625-635.
J.C.
Scholten, L. Nie, D.E. Culley, K.J. Munn, L. Chow, F.J. Brockman,
and W.W. Zhang*. (2007) Development and assessment of whole-genome
oligonucleotide microarrays to analyze a mixed-cultural anaerobic
microbial community and its response to oxidative stress.
Biochemical Biophysical Research Communications. 358 (2):
571-577.
W.W. Zhang *,
D.E. Culley, L. Nie., and J.C. Scholten. (2007) Comparative
transcriptome analysis of Desulfovibrio vulgaris planktonic
culture and mature biofilm grown on iron surface. Applied
Microbiology and Biotechnology. 76 (2): 447–457.
L. Nie, G.
Wu, D.E. Culley, J.C. Scholten, and W.W. Zhang *. (2007) Integrated
analysis of transcriptomic and proteomic data: challenges, solution
and new applications. Critical Reviews in Biotechnology. 27 (2): 63-75.
S.M Jiang,
C.H. Li, W.W. Zhang, Y.H. Cai, Y.L. Yang, S. Yang, and W.H. Jiang.
(2007) Directed evolution and structural analysis of
N-carbamoyl-D-amino acid amidohydrolase provide insights on
recombinant protein solubility in Escherichia coli.
Biochemical Journal. 402 (3): 429-437.
J.C.
Scholten, D.E. Culley, F. J. Brockman, G. Wu, and W.W. Zhang *.
(2007) Evolution of syntrophic interaction between Desulfovibrio
vulgaris and Methanosarcina barkeri: an ancient
horizontal gene transfer event involved. Biochemical Biophysical
Research Communications. 352 (1): 48-54.
L. Nie, G.
Wu, W.W. Zhang *. (2006) Correlation of mRNA expression and protein
abundance affected by multiple sequence features related to
translational efficiency in Desulfovibrio vulgaris: A
quantitative analysis. Genetics. 174 (4): 2229–2243.
W.W. Zhang *,
M.A. Gritsenko, R.J. Moore, D.E. Culley, L. Nie, D. G. Camp II, R.D.
Smith, and F.J. Brockman. (2006) LC-MS/MS based proteomic analysis
and functional inference of a large set of hypothetical proteins in
Desulfovibrio vulgaris. Biochemical Biophysical Research
Communications. 349 (4): 1412-1419.
W.W. Zhang *,
M.A. Gritsenko, R.J. Moore, D.E. Culley, L. Nie, K. Petritis, E.F.
Strittmatter, D. G. Camp II, R.D. Smith, and F.J. Brockman. (2006)
Proteomic view of the cellular metabolism in Desulfovibrio
vulgaris determined by liquid chromatography coupled with
tandem mass spectrometry. Proteomics. 6 (15): 4286-4299.
W.W. Zhang *,
D.E. Culley, L. Nie, and F.J. Brockman. (2006) DNA microarray
analysis of anaerobic Methanosarcina barkeri reveals
responses to heat shock and air exposure. Journal of Industrial
Microbiology and Biotechnology. 33 (9): 784-790.
W.W. Zhang *,
D.E. Culley, M. Hogan, L. Vitiritti, and F.J. Brockman. (2006)
Oxidative stress and heat-shock responses in Desulfovibrio
vulgaris by genome-wide transcriptomic analysis. Antonie
van Leeuwenhoek. 90 (1): 41-55.
L. Nie, G.
Wu, F. J. Brockman, and W.W. Zhang *. (2006) Integrated analysis of
transcriptomic and proteomic data of Desulfovibrio
vulgaris: zero-inflated Poisson regression models to
integrate and interpret microarray and proteomic data.
Bioinformatics. 22 (13): 1641-1647.
D.E. Culley,
W.P. Kovacik, F. J. Brockman, and W.W. Zhang *. (2006) Evaluation
and optimization of RNA isolation from Methanosarcina
barkeri for oligonucleotide microarray analysis. Journal of
Microbiological Methods. 67 (1): 36-43.
W.W. Zhang *,
D.E. Culley, J.C. Scholten, M. Hogan, L. Vitiritti, and F.J.
Brockman. (2006) Global transcriptomic analysis of Desulfovibrio
vulgaris grown on different electron donors. Antonie van
Leeuwenhoek. 89 (2): 221-237.
G. Wu, L.
Nie, and W.W. Zhang *. (2006) Relation between
mRNA expression and sequence information in Desulfovibrio
vulgaris: Combinatorial contributions of upstream motifs and
coding sequences to the variation in mRNA abundance. Biochemical
Biophysical Research Communications. 344 (1): 114-121.
W.W. Zhang *,
D.E. Culley, G. Wu, and F.J. Brockman. (2006) Two-component signal
transduction systems of Desulfovibrio vulgaris: structural
and phylogenetic analysis and deduction of cognate pairs.
Journal of Molecular Evolution. 62 (4): 473-487.
G. Wu, L.
Nie, and W.W. Zhang *. (2006) Predicted highly expressed genes in
Nocardia farcinica and the implication to its primary
metabolism and nocardial virulence. Antonie van
Leeuwenhoek. 89 (1): 135-146.
L. Nie, G.
Wu, and W.W. Zhang *. (2006) Correlation between mRNA and protein
abundance in Desulfovibrio vulgaris: A multiple regression
to identify sources of variations. Biochemical Biophysical
Research Communications. 339 (2): 603-610.
G. Wu, D.E.
Culley, and W.W. Zhang *. (2005) Predicted highly expressed genes in
two Streptomyces genomes and the implications for primary
and secondary metabolisms. Microbiology. 151 (7): 2175-2187.
W.W. Zhang *,
and L. Shi. (2005) Distribution and evolution of multiple-step
phosphorelay in prokaryotes: lateral domain recruitment involved in
the formation of hybrid-type histidine kinases.
Microbiology. 151 (7): 2159-2173. (Paper commented and
recommended by the Faculty 1000 Biology)
W.W. Zhang *,
and L. Shi. (2004) Evolution of Mg (II) or Mn (II)-dependent protein
phosphatases in Streptomyces: early diverge of the
catalytic domains and lateral recruitment of additional sensory
domains. Microbiology. 150 (12): 4189-4197.
L. Shi, and
W.W. Zhang *. (2004) Comparative analysis of eukaryotic-type protein
phosphatases in two Streptomyces genomes.
Microbiology. 150 (7): 2247-2256.
W.W. Zhang *,
D.L. Needham, M. Coffin, A. Rooker, P. Hurban, M.M. Tanzer,
and J.R. Shuster. (2003) Microarray analyses of
the metabolic responses of Saccharomyces cerevisiae to
organic solvent dimethyl sulphoxide (DMSO). Journal of
Industrial Microbiology and Biotechnology. 30 (1): 57-69.
W.W. Zhang,
(2003) “Molecular regulation of secondary metabolism in
Actinomycetes”, in: Z.H. Liu and C.L. Jiang (Eds.),
“Modern Molecular Biology and Biotechnology of
Actinomycetes”, Science Press of China, Beijing, pp118-160
(Invited Book Chapter)
K. Zerbe, O.
Pylypenko, F. Vitali, W.W. Zhang, S. Rousett, M. Heck, J.W.
Vrijbloed, D. Bischoff, R.D. Süssmuth, W. Wohlleben, J.A.
Robinson, and I. Schlichting. (2002) Crystal structure of OxyB, a
cytochrome P450 implicated in an oxidative phenol coupling reaction
during vancomycin biosynthesis. Journal of Biological
Chemistry. 277 (49): 47476-47485.
W. Wang, W.W.
Zhang, H. Chen, J.S. Chiao, G.P. Zhao, and W.H. Jiang. (2002)
Molecular and biochemical characterization of a novel two-component
signal transduction system amrA-amkA involved in the
secondary metabolism in rifamycin SV-producing Amycolatopsis
mediterranei U32. Archives of Microbiology. 178 (5): 376-386.
W. Wang, W.W.
Zhang, J. Gao, J.S. Chiao, G.P. Zhao, and W.H. Jiang. (2002) MoeA,
an enzyme in molybdopterin synthesis pathway, is required for the
rifamycin SV production in Amycolatopsis mediterranei U32.
Applied Microbiology and Biotechnology. 60 (1-2): 139-146.
Y. Yao, W. W.
Zhang, J.S. Chiao, W.H. Jiang, and G.P. Zhao. (2002) Efficient
isolation of total RNA from antibiotic-producing bacterium
Amycolatopsis mediterranei. Journal of
Microbiological Methods. 51 (2): 191-195.
T.A.Cropp, S.
Chen, H.B. Liu, W.W. Zhang, K.A. Reynolds. (2001) Genetic approaches
for controlling ratios of related polyketide products in
fermentation processes. Journal of Industrial Microbiology and
Biotechnology. 27 (6): 368-377.
L. Yang, W.W.
Zhang, J.S. Chiao, G.P. Zhao, and W.H. Jiang. (2001) A
eukaryotic-like serine/threonine protein kinase involved in the
carbon-dependent pigment formation in rifamycin SV producing
Amycolatopsis mediterranei U32. Biochemical
Biophysical Research Communications. 284 (2):
357-362.
W.W. Zhang
and K.A. Reynolds. (2001) MeaA, a putative B12 dependent mutase,
provides methylmalonyl-CoA for monensin A production in
Streptomyces cinnamonesis. Journal of
Bacteriology. 183 (6): 2071-2080.
W.W. Zhang *,
L. Li, W.H. Jiang, G.P. Zhao, Y.L. Yang, and J.S. Chiao. (2000) A
novel transmembrane serine/threonine protein kinase from a rifamycin
SV-producing Amycolatopsis mediterranei U32. European
Journal of Biochemistry. 267 (12): 3744-3752.
W.W. Zhang *,
W.H. Jiang, G.P. Zhao, Y.L. Yang, and J.S. Chiao.
(2000) Expression, purification and kinetic analysing of
aspartokinase and asparate semialdehyde dehydrogenase of
Amycolatopsis mediterranei in Escherichia coli.
Applied Microbiology and Biotechnology. 54 (1): 52-58.
W.W. Zhang *,
W.H. Jiang, G.P. Zhao, Y.L. Yang, and J.S. Chiao. (1999) Sequence
analysis and expression of aspartokinase and asparate semialdehyde
dehydrogenase operon from rifamycin SV-producing Amycolatopsis
mediterranei U32. Gene. 237 (2): 413-419.
W.W. Zhang *,
L. Yang, W.H. Jiang, G.P. Zhao, Y.L. Yang, and J.S. Chiao. (1999)
Molecular analysis and heterologous expression of the gene encoding
methylmalonyl-CoA mutase from a rifamycin SV-producing
Amycolatopsis mediterranei U32. Applied Biochemistry
and Biotechnology. 82 (3): 209-225.
(* As corresponding author)
Microbial Systems Biology
Metabolic Engineering and Synthetic Biology
Biofuels Research
Environmental Biotechnology
