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Scholarly Interest Report
         
Weiwei Zhong
Assistant Professor
Assistant Professor of Biochemistry and Cell Biology
 
e-mail:Weiwei.Zhong@rice.edu
 
  • 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
Picture
 
Department Affiliations
 
  • Department of Computer Science
  • Institute of Biosciences and Bioengineering
  • Systems, Synthetic, and Physical Biology
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    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 high-throughput 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., Peņa-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/s12861-015-0062-0

     
     

    Jung S.K., Qu X., Aleman-Meza B., Wang T., Riepe C., Liu Z., Li Q., Zhong W. (2015). A multi-endpoint, 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 - Open-Source 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 gender-enriched 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) (Thesis Committee Member)

     Xiaolei Qu, PhD Impact of Sunlight and Natural Organic Matter on the Fate, Transport, and Toxicity of Carbon Based Nanomaterials. (2013) (Thesis Committee Member)

     Yanru Dou, MS Rbt1 is required for Nitric Oxide Stress Resistance in the Human Commensal Fungus Candida albicans . (Thesis Committee Member)

     Yu-Yu Cheng, PhD Characterization of transcriptional delay by synthetic biology approach. (Thesis Committee Member)

     Yanlin Fan, PhD Structure and function studies of Orsay virus. (Thesis Committee Member)

     Zheng Liu, PhD TBD. (Thesis Director)

     Yusong Guo, PhD TBD. (Thesis 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)