Ma, J., and Ptashne, M. (1987).  Deletion analysis of GAL4 defines two transcriptional activating segments.  Cell 48, 847-853.  PMID: 3028647


Ma, J., and Ptashne, M. (1987).  The carboxy terminal 30 amino acids of GAL4 are recognized by GAL80.  Cell 50, 137-142.  PMID: 3297349


Ma, J., and Ptashne, M. (1987).  A new class of yeast transcriptional activators.  Cell 51, 113-119.  PMID: 3115591


Ruden, D., Ma, J., and Ptashne, M. (1988).  No strict alignment is required between a transcriptional activator binding site and the "TATA box" of a yeast gene.  Proc. Natl. Acad. Sci. USA 85, 4262-4266.   PMID: 3132708; PMCID: PMC280407


Ma, J., Przibilla, E., Hu, J., Bogorad, L., and Ptashne, M. (1988).  Yeast activators stimulate plant gene expression.  Nature 334, 631-633.   PMID: 3165494


Sadowski, I., Ma, J., Triezenberg, S., and Ptashne, M. (1988).  GAL4-VP16 is an unusually potent transcriptional activator.  Nature 335, 563-564.  PMID: 3047590


Ma, J., and Ptashne, M. (1988). Converting a eukaryotic transcriptional inhibitor into an activator.  Cell 55, 443-446.  PMID: 3180218


Driever, W., Ma, J., Nusslein-Volhard, C., and Ptashne, M. (1989).  Rescue of bicoid mutant Drosophila embryos by Bicoid fusion proteins containing heterologous activating sequences.  Nature 342, 149-154.  PMID: 2509940


Ruden, D., Ma, J., Li, Y., Wood, K., and Ptashne, M. (1991).  Generating yeast transcriptional activators containing no yeast protein sequences.  Nature 350, 250-252.  PMID: 2005981


Dasmahapatra, B., DiDomenico, B., Dwyer, S., Ma, J.,  Sadowski, I., and Schwartz, J. (1992).  A novel genetic system to study a proteolytic enzyme.  Proc. Natl. Acad. Sci. USA 89, 4159-4162.  PMID: 1570342; PMCID: PMC525652


Ma, J. (1992).  Detecting interactions between eukaryotic proteins in bacteria. Gene Expression 2, 139-146.  PMID: 1633437


Lehming, N., Thanos, D., Brickman, J., Ma, J.,  Maniatis, M., and Ptashne, M. (1994).  A HMG-like protein that can switch a transcriptional activator to a repressor.  Nature 371, 175-179.  PMID: 8072548


Ma, X., Yuan, D., Diepold, K., Scarborough, T., and Ma, J. (1996).  The Drosophila morphogenetic protein Bicoid binds DNA cooperatively.  Development 122, 1195-1206.  PMID: 8620846


Shaw, S. P., Wingfield, J., Dorsey, M. J., and Ma, J.  (1996). Identifying a species-specific region of yeast TFIIB in vivo.  Molecular and Cellular Biology 16, 3651-3657.  PMID: 8668181; PMCID: PMC231360


Yuan, D., Ma, X., and Ma, J. (1996).  Sequences outside the homeodomain of Bicoid are required for protein-protein interaction. J. Biol. Chem. 271, 21660-21665.  PMID: 8702955


Shaw, S. P., Carson, D. J., Dorsey, M. J., and Ma, J.  (1997).  Mutational studies of yeast TFIIB in vivo reveal a functional surface important for gene activation. Proc. Natl. Acad. Sci. USA 94, 2427-2432.  PMID: 9122211; PMCID: PMC20104


Ma, X., Yuan, D., Scarborough, T., and Ma, J. (1999).  Contribution to gene activation by multiple functions of Bicoid. Biochem. J. 338, 447-455.  PMID: 10024522; PMCID: PMC1220072


Yuan, D., Ma, X., and Ma, J. (1999).  Recognition of multiple patterns of DNA sites by the Drosophila homeodomain protein Bicoid.  J. Biochem. 125, 809-817.  PMID: 10101296


Zhang, D., Dorsey, M. J., Voth, W. P., Carson, D. J., Zeng, X., Stillman, D. J., and Ma, J. (2000).  Intramolecular interaction of yeast TFIIB in transcriptional Control.  Nucl. Acids Res.  28, 1913-1920.  PMID: 10756191; PMCID: PMC103289


Dave, V., Zhao, C., Yang, F., Tung, C.-S., and Ma, J. (2000).  Reprogrammable recognition codes in Bicoid homeodomain-DNA interaction.  Mol. Cell. Biol. 20, 7673-7684.  PMID: 11003663; PMCID: PMC86337


Zhao, C., Dave, V., Yang, F. Scarborough, T., and Ma, J. (2000).  Target selectivity of Bicoid is dependent on non-consensus site recognition and protein-protein interaction. Mol. Cell. Biol. 20, 8112-8123.  PMID: 11027281; PMCID: PMC86421


Zhao, C., York, A., Yang, F., Forsthoefel, D. J., Dave, V., Fu, D., Zhang, D., Corado, M. S., Small, S., Seeger, M. A., and Ma, J. (2002).  The activity of the Drosophila morphogenetic protein Bicoid is inhibited by a domain located outside its homeodomain.  Development 129, 1669-1680.  PMID: 11923203


Zhang, D., Carson, D. J., and Ma, J.  (2002).  The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells.  Nucl. Acids Res. 30, 3078-3085.  PMID: 12136090; PMCID: PMC135743


Zeng, X., Zhang, D, Dorsey, M, and Ma, J. (2003).  Hypomutable regions of yeast TFIIB in a unigenic evolution test represent structural domains.  Gene 309, 49-56.  PMID: 12727357


Leung, T.C., Bischof, J., Soll, I., Niessing, D., Zhang, D., Ma, J., Jackle, H., and Driever, W.  (2003).  bozozok directly represses bmp2b transcription and mediates the earliest dorsoventral asymmetry of bmp2b expression in zebrafish. Development 130, 3639-3649.  PMID: 12835381


Fu, D., Zhao, C., and Ma, J. (2003).  Enhancer sequences influence the role of the amino terminal domain of Bicoid in transcription. Mol. Cell. Biol. 23, 4439-4448.  PMID: 12808087; PMCID: PMC164838


Zhao, C., Fu, D., Dave, V., and Ma, J.  (2003).  A composite motif of the Drosophila morphogenetic protein Bicoid critical to transcription control and pattern formation. J. Biol. Chem. 278, 43901-43909.  PMID: 12939280           


Fu, D., Wen, Y., and Ma, J. (2004).  The co-activator  CREB-binding protein participates in enhancer-dependent activities of Bicoid.  J. Biol. Chem. 279, 48725-48733.  PMID: 15358774


Chaney, B. A., Clark-Baldwin, K., Dave, V., Ma, J., and Rance, M. (2005).  Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome.  Biochemistry 44, 7497-7511.  PMID: 15895993


Fu, D., and Ma, J. (2005).  Interplay between positive and negative activities that influence the role of Bicoid in transcription.  Nucl. Acids Res. 33, 3985-3993.  PMID: 16030350; PMCID: PMC1178001


Baird-Titus, J., Clark-Baldwin, K., Dave, V., Caperelli, C. A., Ma, J., and Rance, M. (2006).  The solution structure of the native K50 Bicoid homeodomain to the consensus TAATCC DNA-binding site.  J. Mol. Biol. 356, 1137-1151.  PMID: 16406070


Song, Y., He, F., Xie, G., Guo, X., Xu, Y., Chen, Y., Liang, X., Stagljar, I., Egli, D., Ma, J., and Jiao, R. (2007).  CAF-1 is essential for Drosophila development and involved in the maintenance of epigenetic memory.  Dev. Biol. 311, 213-222.  PMID: 17916346


He, F., Wen, Y., Deng, J., Lin, X., Lu, J., Jiao, R., and Ma, J. (2008).  Probing intrinsic properties of a robust morphogen gradient in Drosophila.  Dev. Cell 15, 558-567.  PMID: 18854140; PMCID: PMC2629455


Xu, Y., Lei, Z., Huang, H., Dui, W., Ma, J., and Jiao, R. (2009).  dRecQ4 is required for DNA synthesis and essential for cell proliferation in Drosophila.  PLoS One 4(7), e6107.  PMID: 19572017; PMCID: PMC2700968


Deng, J., Wang, W., Lu, J. L., and Ma, J. (2010).  A two-dimensional simulation model of the Bicoid gradient in Drosophila.  PLoS ONE 5(4), e10275.  PMID: 20422054; PMCID: PMC2858077


Chen, Y., Dui, W., Yu, Z., Li, C., Ma, J., and Jiao, R. (2010).  Drosophila RecQ5 is required for efficient SSA repair and suppression of LOH in vivo.  Protein & Cell 1(5), 478-490.  PMID: 21203963


He, F., Sounders, T., E., Wen, Y., Cheung, D., Jiao, R., Ten Wolde, P. R., Howard, M., and Ma, J. (2010).  Shaping a morphogen gradient for positional precision.  Biophy. J.  99, 697-707.  PMID: 20682246; PMCID: PMC2913175


Huang, H., Yu, Z., Zhang, S., Liang, X., Chen, J., Li, C., Ma, J., and Jiao, R. (2010).  Drosophila CAF-1 regulates HP1-mediated epigenetic silencing and pericentric heterochromatin stability.  J. Cell Sci. 123, 2853-2861.  PMID: 20663913


He, F., Wen, Y., Cheung, D., Deng, J., Lu, L. J., Jiao, R., and Ma, J. (2010).  Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos.  BMC Dev. Biol. 10, 80.  PMID: 20678215; PMCID: PMC2919471


Liu, J. and Ma, J. (2011).  Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos.  Nature Cell Biol. 13, 22-29.  PMID: 21170036; PMCID: PMC3074934


He, F., Ren, J., Wang, W., and Ma, J. (2011).  A multiscale investigation of Bicoid-dependent transcriptional events in Drosophila embryos.  PLoS ONE 6, e19122.  PMID: 21544208 PMCID: PMC3081338


Huang, H., Chen, H., Liang, X., Li C., Xue, L., Ma, J., and Jiao, R. (2011).  Drosophila Smt3 negatively regulates JNK signaling through sequestering Hipk in the nucleus.  Development 138, 2477-2485.  PMID: 21561986


Cheung, D., Miles, C., Kreitman, M., and Ma, J. (2011).  Scaling of the Bicoid morphogen gradient by a volume-dependent production rate.  Development 138, 2741-2749.  PMID: 21613328; PMCID: PMC3109599


Ren, J., Jegga, A., Zhang, M., Deng, J., Liu, J., Gordon, C. B., Aronow, B. J., Lu, L. J., Zhang, B., and Ma, J. (2011).  A Drosophila model of the neurodegenerative disease SCA17 reveals a role of RBP-J/Su(H) in modulating the pathological outcome.  Human Mol. Genetics 20, 3424-3436.  PMID: 21653638; PMCID: PMC3153307


He, F., Ren, J., Wang, W., and Ma, J. (2012).  Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts.  Bioinformatics 28, 970-975.  PMID: 22302571; PMCID: PMC3315720


Xie, G., Zhang, H., Du, G., Huang, Q., Liang, X., Ma, J., and Jiao, R.  (2012).  Uif, a large transmembrane protein with EGF-like repeats, can antagonize Notch signaling in Drosophila.  PLoS ONE 7: e36362.  PMID: 22558447; PMCID: PMC3340373


Liu, J. and Ma, J. (2012). Drosophila Bicoid is a substrate of sumoylation and its activator function is subject to inhibition by this post-translational modification.  FEBS Letters 586, 1719-1723.  PMID: 22584054; PMCID: PMC3372618


Dui, W., Lu, W., Ma, J., and Jiao, R. (2012).  A systematic phenotypic screen of F-box genes through a tissue-specific RNAi-based approach in Drosophila. Journal of Genetics and Genomics 39, 397-413.  PMID: 22884096


Dui, W., Wei, B., He, F., Lu, W., Li, C., Liang, X., Ma, J., and Jiao, R. (2013).  The Drosophila F-box protein dSkp2 regulates cell proliferation through targeting Dacapo for degradation.  Mol. Biol. Cell 24, 1676-1687.  PMID: 23552694; PMCID: PMC3667721


He, F. and Ma, J. (2013). A spatial point pattern analysis in Drosophila blastoderm embryos evaluating the potential inheritance of transcriptional states.  PLoS ONE 8(4), e60876.  PMID: 23593336; PMCID: PMC3621909


Liu, J. and Ma, J. (2013).  Uncovering a dynamic feature of the transcriptional regulatory network for anterior-posterior patterning in the Drosophila embryo. PLoS ONE 8(4), e62641.  PMID: 23646132; PMCID: PMC3639989


Liu, J. and Ma, J.  (2013).  Dampened regulates the activating potency of Bicoid and the embryonic patterning outcome in Drosophila.  Nature Communications 4, 2968.  PMID: 24336107; PMCID: PMC3902774


Cheung, D., Miles, C., Kreitman, M., and Ma, J. (2014).  Adaptation of length scale and amplitude of the Bicoid gradient profile to achieve robust patterning in abnormally large Drosophila melanogaster embryos.  Development 141, 122-135.  PMID: 24284208; PMCID: PMC3865754


He, F., Wei, C., Wu, H., Cheung, D., Jiao, R., and Ma, J. (2015).  Fundamental origins and limits for scaling a maternal morphogen gradient.  Nature Communications 6, 6679.  PMID: 25809405; PMCID: PMC4375784


Cheung, D. and Ma, J. (2015).  Probing the impact of temperature on molecular events in a developmental system.  Scientific Reports 5, 13124.  PMID: 26286011; PMCID: PMC4541335


Liu, J., and Ma, J. (2015).  Modulation of temporal dynamics of gene transcription by activator potency in the Drosophila embryo.   Development 142, 3781-3790. PMID: 26395487; PMCID: PMC4647213


Wu, H., Manu, Jiao, R., and Ma, J. (2015).  Temporal and spatial dynamics of scaling-specific features of a gene regulatory network in Drosophila.  Nature Communications 6, 10031.  PMID: 26644070; PMCID: PMC4686680


Liu, J., Xiao, Y., Zhang, T., and Ma, J. (2016).  Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control.  FLY (Austin) 10, 101-107.  PMID: 27172244