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Weiwei Zhong
Assistant Professor
Assistant Professor of Biochemistry and Cell
Biology
e-mail:[email protected]
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B.S. Biology (1997) University of Science and
Technology of China, Hefei, China
Ph.D. Cell Biology (2002) University of Georgia, Athens,
GA
M.S. Computer Science (2003) University of Georgia,
Athens, GA
Primary Department
Department of BioSciences
Department Affiliations
 Department of Computer Science
 Institute of Biosciences and Bioengineering
 Systems, Synthetic, and Physical Biology
Websites
Personal page
Research Areas
Genetic interaction networks, computer vision system for animal development and behavioral
analysis
Research Statement 2010
Our research goal is to decipher the gene networks behind complex traits such as
development and behavior. We apply a suite of technologies in genetics, computer science,
and engineering in our approach. We are interested in both developing new technologies for
genetic studies and applying these tools to conduct large-scale genetic screens in the
nematode C. elegans. We first develop tools to build a highthroughput research pipeline. Hypothesis-driven research is a
process of two steps: hypothesis generation and experimental
verification. Accordingly, our pipeline is composed of a
bioinformatic system that predicts gene networks, and a computer
vision system that facilitates high-speed experimental testing of
C. elegans genetic interactions. We then apply this research
pipeline to conduct genome-scale, quantitative genetic screens in
C. elegans to discover the gene networks regulating development,
behavior, and physiology. With the systems biology approach, we
expect to bring our understanding of genome function to a new
level.
Teaching Areas
genetics, bioinformatics, systems biology
Selected Publications
Refereed articles
Aleman-Meza, B., Loeza-Cabrera, M., Peña-Ramos, O., and Zhong, W. "High-content
behavioral profiling reveals neuronal genetic network modulating Drosophila larval locomotor
program." Submitted
Fan, Y., Guo, Y.R., Yuan, W., Zhong, W.* and Tao, Y.J "Structure of a pentameric fiber reveals
the mechanism of Orsay virus attachment to host cells." PLoS PathogenIn Revision
Labocha, M. K., Aleman-Meza, B., Rocha-Villarreal, R., Nguyen, J. K., and Zhong, W.
"Quantitative epistasis mapping of genetic interaction networks reveals network structures
determining trait robustness." Submitted
Labocha, M. K., Yuan, W., Aleman-Meza, B., and Zhong, W. "A strategy of applying
quantitative epistasis analysis on developmental traits.." Submitted
Yuan, W., Zhou, Y., Fan, Y., Guo, Y.R., Tao, Y.J., and Zhong, W. "Orsay δ protein interacts
with host cytoskeleton to mediate polarized viral exit from C. elegans intestine." In Progress
Zhou, Y., Loeza-Cabrera, M., Liu, Z., Aleman-Meza,B., Nguyen, J. K., Jung, S.K., Choi, Y.,
Shou, Q., Butcher, R.A., and Zhong, W "Nematode alarm pheromone induces a fear-like
response in C. elegans." GeneticsIn Revision
Aleman-Meza B., Jung S.K., Zhong W. (2015). An automated system for quantitative analysis
of Drosophila larval locomotion. BMC Developmental Biology, 15:11. DOI: 10.1186/s12861015-0062-0
Jung S.K., Qu X., Aleman-Meza B., Wang T., Riepe C., Liu Z., Li Q., Zhong W. (2015). A multiendpoint, high-throughput study of nanomaterial toxicity in Caenorhabditis elegans. Environ
Sci Technol DOI: 10.1021/es5056462
Labocha, K. M., Liu, Z., Aleman-Meza, B., and Zhong, W. Different genetic interaction network
structures determine phenotypic robustness. In preparation
Labocha, M.K., Jung S.K., Aleman-Meza B., Liu Z., Zhong W. (2015). WormGender - OpenSource Software for Automatic Caenorhabditis elegans Sex Ratio Measurement. PLoS ONE,
10(9):e0139724. DOI: 10.1371/journal.pone.0139724
Liu, Z., Nguyen, J., Aleman-Meza, B., Jung, S.K., and Zhong, W. Existence of a nematode
alarm pheromone. In preparation.
Contreras, E.Q., Puppala, H.L., Escalera, G., Zhong, W., and Colvin, V.L. Size-dependent
impacts of silver nanoparticles on the lifespan, fertility, growth, and locomotion of
Caenorhabditis elegans. Environ Toxicol Chem. 33(12):2716-2123. doi:
10.1002/etc.2705.(2014).
Guo, Y.R., Hryc, C.F., Jakana, J., Jiang, H., Wang, D., Chiu, W., Zhong, W., and Tao, Y.J., The
crystal structure of a nematode-infecting virus. Proc Natl Acad Sci U S A. 11(35):12781-6.
doi: 10.1073/pnas.1407122111.(2014)
Jung, S., Aleman-Meza, B., Riepe, C. , Zhong, W. QuantWorm: A Comprehensive Software
Package for Caenorhabditis elegans Phenotypic Assays. PLoS ONE 9(1): e84830. DOI:
10.1371/journal.pone.0084830 (2014)
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0084830
Contreras, E.Q., Cho, M., Zhu, H., Puppala, H.L., Zhong, W., and Colvin, V.L. Toxicity of
Quantum Dots and Cadmium Salt to Caenorhabditis elegans after Multigenerational Exposure.
Environ Sci Technol. 47: 1148-1154. (2013)
Yu, H., Aleman-Meza, B., Gharib, S., Labocha, K. M., Sternberg, P. W. and Zhong, W.
Systematic profiling of Caenorhabditis elegans locomotive behaviors reveals additional
components in G-protein Gαq signaling. Proc Natl Acad Sci U S A. 110:11940-11945. (2013)
Cantacessi, C., Campbell, B. E., Young, N. D., Jex, A. R., Hall, R. S., Presidente, P. J.,
Zawadzki, J. L., Zhong, W., Aleman, B., Loukas, A., Sternberg, P. W., Gasser, R. B.
"Differences in transcription between free-living and CO2-activated third-stage larvae of
Haemonchus contortus." BMC Genomics, 11 (2010) : 266.
Hu, M., He. L., Campbell. B. E., Zhong, W., Sternberg, P. W., Gasser, R. B. "A vacuolar-type
proton (H(+)) translocating ATPase alpha subunit encoded by the Hc-vha-6 gene of
Haemonchus contortus." Mol Cell Probes, 24 (2010) : 196-203.
Hu, M., Zhong, W., Campbell, B.E., Sternberg, P.W., Pellegrino, M.W., Gasser, R.B.
"Elucidating ANTs in worms using genomic and bioinformatic tools--biotechnological
prospects?." Biotechnol Adv., 28 (2010) : 49-60.
Cantacessi, C., Loukas, A., Campbell, B. E., Mulvenna, J., Ong, E. K., Zhong, W., Sternberg,
P. W., Otranto, D., and Gasser, R. B. "Exploring transcriptional conservation between
Ancylostoma caninum and Haemonchus contortus by oligonucleotide microarray and
bioinformatic analyses.." Mol Cell Probes, 23 (2009) : 1-9.
Cantacessi, C., Zou, F. C., Hall, R. S., Zhong, W., Campbell, B. E., Ranganathan, S.,
Sternberg, P. W., Zhu, X. Q., and Gasser, R. B. "Bioinformatic analysis of abundant genderenriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow
platform." Mol Cell Probes, 23 (2009) : 205-217.
Campbell, B. E., Nagaraj, S. H., Hu, M., Zhong, W., Sternberg, P. W., Ong, E. K., Loukas, A.,
Ranganathan, S., Beveridge, I., McInnes, R. L., Hutchinson, G. W., and Gasser, R. B.
"Gender-enriched transcripts in Haemonchus contortus - predicted functions and genetic
interactions based on comparative analyses with Caenorhabditis elegans.." Int J Parasitol, 38
(2008) : 65-83.
Cui, X., Lee, L., Heng, X., Zhong, W., Sternberg, P. W., Psaltis, D., and Yang, C. "Lensless
high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell
imaging." Proc Natl Acad Sci U S A, 105 (2008) : 10670-10675.
Huang, C. Q., Gasser, R. B., Cantacessi, C., Nisbet, A. J., Zhong, W., Sternberg, P. W.,
Loukas, A., Mulvenna, J., Lin, R. Q., Chen, N., and Zhu, X. Q. "Genomic-bioinformatic analysis
of transcripts enriched in the third-stage larva of the parasitic nematode Ascaris suum." PLoS
Negl Trop Dis. , 2 (2008) : e246.
Zhong, W. and Sternberg, P. W. "Automated data integration for developmental biological
research." Development, 134 (2007) : 3227-3238.
Zhong, W. and Sternberg, P. W. "Genome-wide prediction of C. elegans genetic
interactions." Science, 311 (2006) : 1481-1484.
Zhong, W., Feng, H., Santiago, F. E., and Kipreos, E. T. "CUL-4 ubiquitin ligase maintains
genome stability by restraining DNA replication licensing." Nature, 423 (2003) : 885-889.
Feng, H.*, Zhong, W.*, Punkosdy, G., Gu, S., Zhou, L., Seabolt, E. K., and Kipreos, E. T.
(*co-first authors), "CUL-2 is required for the G1-to-S-phase transition and mitotic
chromosome condensation in Caenorhabditis elegans." Nat Cell Biol., 1 (1999) : 486-491.
Presentations
Conference Paper
Talk, The Orsay virus Delta protein mediates viral exit, C. elegans topical meeting: Aging,
Metabolism, Stress, Pathgenesis and Small RNAs. Madison, WI
Invited Talks
Genetic interaction networks and phenotypic robustness, Research Exchange Seminar,
University
of Texas M.D. Anderson Cancer Center, Houston, TX
Genetic interaction networks and phenotypic variability. Huazhong Agricultural University,
Wuhan, China
Genetic interaction networks and trait robustness. Paul W. Sternberg Symposium, California
Institute of Technology, Pasadena, CA
Genetic interaction networks and trait robustness. Texas A&M University, College station, TX,
2016
Genetic interaction networks and trait robustness. Texas Woman’s University, Denton, TX
2016
Genetic interaction networks and trait robustness. University of California at Los Angeles, Los
Angeles, CA
"Genetic interaction map of development genes." Searle Scholars Meeting, Chicago, IL. (April,
2012)
"C. elegans genetic interaction networks." University of Melbourne, Melbourne, Australia.
(2009)
Posters
Sponsor. "Existence of a nematode alarm pheromone." 20th International C. elegans
Meeting, Los Angeles, CA. (June 2015)
"Poster presented by Sang-Kyu Jung, Development of a comprehensive image analysis
software package for the analysis of lifespan, locomotion, body length, and egg laying of C.
elegans. 19th International C. elegans Meeting, Los Angeles, CA." (June, 2013)
"Towards a global quantitative epistasis map." 17th International C. elegans meeting, Los
Angeles, CA. (2009)
Seminar Speaker
"High-throughput mapping of C. elegans genetic interaction networks." University of Houston,
Houston, TX. (Octorber, 2012)
Session Chair
"Gene Expression ." 17th International C. elegans meeting, Los Angeles, CA. (2009)
Editorial Positions
Other, Various Periodicals. (2007 - 2016)
Member of the Editorial Board, Scientific Reports. (2016 - 2017)
Supervised Theses & Dissertations
Elizabeth Contreras, PhD Investigating the biological impacts of nanoengineered materials in
Caenorhabditis elegans and in vitro. (2012) (Committee Member)
Xiaolei Qu, PhD Impact of Sunlight and Natural Organic Matter on the Fate, Transport, and
Toxicity of Carbon Based Nanomaterials. (2013) (Committee Member)
Yanru Dou, MS Rbt1 is required for Nitric Oxide Stress Resistance in the Human Commensal
Fungus Candida albicans . (Committee Member)
Yu-Yu Cheng, PhD Characterization of transcriptional delay by synthetic biology approach.
(Committee Member)
Yanlin Fan, PhD Structure and function studies of Orsay virus. (Committee Member)
Zheng Liu, PhD TBD. (Thesis or Dissertation Director)
Yusong Guo, PhD TBD. (Co-Director)
Awards, Prizes, & Fellowships
Hamill Award, (2013)
Searle Scholars Award, Kinship Foundation (07/01/09 )
Australian Research Council (ARC) International Fellow, Australian Research Council (01/01/09
)
Positions Held
Honorary Appointment, University of Melbourne. (2009 - 2009)
Joint Appointment, Computer Science Department, Rice University. (2009 - 2009)