Department of MBS

Phone: (512) 471-5105
Fax: (512) 471-1218

NHB 2.606, Stop A5000
100 East 24th St.
Austin TX 78712

Publications from 2016-17

To download the complete 2016-17 list, please click here.


  1. Yuan, J., Jiao, W., Wang, L., Ma, Y., Ye, W., Jin, Z., Lu, J., Hong, D., You, S., Cheng, Z., and Chen, Z. J. (2017) Both maternally and paternally imprinted genes regulate seed development in rice. New PhytologistPubMed>>
  1. Song, Q., Zhang, T., Stelly, D. M., and Chen, Z. J. (2017) Epigenomic and functional analyses reveal roles for epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biology 18:99. Genome Biology 18:99. PubMed>>
  1. G. Malyutin, S. Musalgaonkar. S. Patchett, J. Frank and A.W. Johnson (2017) Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. EMBO J. 2017 Apr 3;36(7):854-868. doi: 10.15252/embj.201696012. PubMed>>
  1. Amarnath, L.M. Stevens and D.S. Stein (2017) Reconstitution of Torso signaling in cultured cells suggests a role for both Trunk and Torso-like in receptor activation. Development 144(4):677-686. PubMed>>
  1. Wang L., Zhang F., Rode S., Ko E., Kim J., Lyer V and Qiao H* (2017) Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis. BMC genomics 18:538. PubMed>>
  1. Zhang, F., Wang, L., Qi, B., Zhao, B., Ko E., Riggan, ND., Kevin C and Qiao H* (2017) Ethylene mediates direct regulation of histone acetylation in the ethylene. Proceedings of the national Academy of Science USA. PNAS>>
  1. S. Abell, M. Mercado, T. Caneque, R. Rodriguez and B. Xhemalce (2017) Click-Quantitative Mass Spectrometry Identifies PIWIL3 as a Mechanistic Target of RNA Interference Activator Enoxacin in Cancer Cells. J Am Chem Soc.139(4):1400-1403. PubMed>>
  1. W. Leung, N. Makharashvili, P. Agarwal,  L-Y. Chiu, R. Pourpre, M.B. Cammarata, J.R. Cannon, A. Sherker, D. Durocher, J.S. Brodbelt, T.T. Paull and K.M.Miller (2017) ZMYM3 regulates BRCA1 localization at damaged chromatin to promote DNA repair. Genes & Development 31(3):260-274. PubMed>>
  1. Kim, S.J., Schätzle, Sohail, S.A., Haap, W., Jang, s.-H., Gregersen, P.K. Georgiou, G. and B. Diamond (2017) “Increased Cathepsin S in Prdm1-/-Dendritic Cells Alters TFH Repertoire and Contributes to Lupus,” Nature Immunology doi: 1038/ni.3793 [Epub ahead of print] PMID: 28692065. PubMed>>
  1. Lee, C.-H., Romain, G., Yan, W., Watanabe, W., Charab,, Todorova, B., Lee, Y., Triplett, K., Donkor, M., Lungu, O.I., Lux, A., Marshall, N., Lindorfer, M.A., Richard-Le Goff, O., Balbino, B., Kang, T.H., Tanno, H., Delidakis, G., Alford, C., Taylor, R.P., Nimmerjahn, F., Varadarajan, N., Bruhns, P. Zhang, Y.J.  and G. Georgiou (2017) “IgG Fc Domains that Bind C1q but not Effector Fcγ Receptors Delineate the Significance of Complement-Dependent Cell-Mediated Cytotoxicity and Phagocytosis in Antibody Function” Nature Immunology doi: 10.1038/ni.3770. [Epub ahead of print] MID: 28604720. PubMed>>
  1. Williams, L.D., Ofek, G., Schatzle, S., McDaniel, J.R., Lu, X., Nicely, N.I., Wu, L., Lougheed, C.S., Bradley, T., Louder, M.K., McKee, K., Bailer, R.T., O’Dell, S., Georgiev, I.S., Seaman, M., Parks, R., Marshall, D., Anasti, K., Yang, G., Nie, X., Tumab, N., Wiehe, K., Wagh, K., Korber, B., Kepler, T., Alam, S.M., Morris, L., Kamanga, G., Choen, M.S., Bonsignori, M., Xia, S., Montefiori, D., Kelsoe, G., Gao, F., Mascola, J.R., Moody, M.A., Saunders, K.O., Liao, H., Tomaras, G.D., Georgiou, G.and B.F. Haynes (2017) “Potent and broad HIV-neutralizing antibodies in memory B cells and plasma”, Science Immunology 2, Issue 7,  doi: 10.1126/sciimmunol.aal2200. PubMed>>
  1. Cramer, S.L., Saha, A., Liu, J., Tadi, S., Tiziani, S., Yan, W., Triplett, K., Lamb, C., Alters, S.E., Rowlinson, S., Zhang, Y., Keating, M.J., Huang, P., DiGiovanni, J., Georgiou, G., and E. Stone (2017) “Systemic Depletion of Serum L-Cyst(e)ine with an Engineering Human Enzyme Mediates Potent Induction of ROS Leading to Selective Cancer Ablation,” Nature Medicine 23:120-127doi: 10.1038/nm.4232PMID: 27869804. AACR>>
  1. Ko, D. K., Rohozinski, D., Song, Q., Taylor, S. H., Juenger, T. E., Harmon, F. G., Chen, Z. J. (2016) Temporal shift of circadian-mediated gene expression and carbon fixation contributes to biomass heterosis in maize hybrids. PLoS Genetics12(7):e1006197. PubMed>>
  1. Lee, J., Boutz, D.R., Chromikova, V., Joyce, M.G., Vollmers, C., Leung, K., Horton, A.P., DeKosky, B.J., Lee, C.H., Lavinder, J.J., Murrin, E.M., Chrysostomou, C., Hoi, K.H., Tsybovsky, Y., Thomas, P.T., Druz, A., Zhang, B., Zhang, Y., Wang, L., Kong, W.P., Park, D., Popova, L.I., Dekker, C.L., Davis, M.M., Bloom, C.E., Ross, T.M., Ellington, A.D., Wilson, P.C., Marcotte, E.M., Mascola, J.R., Ippolito, G.C., Krammer, F., Quake, S.R., Kwong, P.D. and Georgiou, G. (2016) “Quantitative, Molecular-Level Analysis of the Serum Antibody Repertoire Reveals Unanticipated Features of the Response to Influenza Vaccine,” Nature Medicine 22:1456-64PMID: 27820605. PubMed>>
  1. J Xia, L.T. Chen, Q. Mei. H. Ma, J.A. Halliday, H.Y. Lin, D. Magnan, J.P. Pribis, D. M., Fitzgerald, H.M. Hamilton, M. Richters, R.B. Nehring, X. Shen, L. Li, D. Bates, P.J. Hastings, C. Herman, M. Jayaram and S.M. Rosenberg (2016) Holliday junction trap shows how cells use recombination and a junction guardian role of RecQ helicase. Sci Adv18;2(11):e1601605. SciAdv>>
  1. Zhang, F., Qi, B., Wang, L., Zhao, B., Rode, S., Riggan, ND., Ecker JR and Qiao H* (2016) EIN2- dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signaling. Nature communications. doi:10.1038/ncomms13018. Nature>>
  1. Zhang F., Wang L., Lim J., Kim T., Pyo Y., Sung S., Shin C and Qiao H* (2016). Phosphorylation of CBP20 links microRNA to root growth in the ethylene response. PLOS Genetics, doi: 10.1371. PubMed>>

Publications from 2015-16

To download the complete 2015-16 list, please click here.


  1. P.MMacdonald, M. Kanke, A. Kenny (2016) Community effects in regulation of translation. eLife2016;5:e10965. View>>
  1. Nath, L. Christian, S. Youngsun Tan, S. Ki, L. I. R. Ehrlich, and M. Poenie(2016) Dynein separately partners with NDE1 and dynactin to orchestrate T cell focused secretion. Journal of Immunology (in press). View Abstract>>
  1. A. Triplett, K. T. Cardenas, J. N. Lancaster, Z. Hu, H. J. Selden, G. Jasso, S. Balasubramanyam, K. Chan, L. Li, X. Chen, A. M. Marcogliese, U. P. Dave, P. E. Love, and L. I. R. Ehrlich(2016) Dendritic cells in the tumor microenvironment directly support T-All growth through IGF1R activation. Proc. Natl. Acad. Sci. USA. 113(8): E1016-25. PMID 26862168. View Abstract>>
  1. Qin, J. Yao, D.C. Wu, R. Nottingham, S. Mohr, S. Hunicke-Smith, A.M. Lambowitz (2016) High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases. RNA22(1): 111-128. View Abstract>>
  1. M. Nottingham, D.C. Wu, Y. Qin, J. Yao, S. Hunicke-Smith, A.M. Lambowitz(2016) RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase. RNA 22(4): 597-613. View Abstract>>
  1. Silas#, G. Mohr#, D.J. Sidote, L.M. Markham, A. Sanchez-Amat, D. Bhaya, A.M. Lambowitz*, A.Z. Fire* (2016) Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science351(6276): aad4234. #Co-first authors, *Co-corresponding authors. [Commentaries Sontheimer, E.J. and Marraffini, L.A. CRISPR goes retro, Science 351, 920-921, 2016; Waldron, D. CRISPR memories of RNA, Nature Reviews Genetics, 2016; Calkins, K. CRISPR serves up more than DNA, Biomedical Beat Blog, NIGMS, 2016.] View Abstract>>
  1. Lamech, M. Sanoji, P.J. Paukstelis, A.M. Lambowitz(2016) Structural divergence of the group I intron-binding surface in fungal mitochondrial tyrosyl-tRNA synthetases that function in RNA splicing. Journal of Biological Chemistry 291(22): 11911-11927. View Abstract>>
  1. Lee, S. S. Stevens(2016) Spliceosomal intronogenesis. Proceedings of the National Academy of Sciences 113(23); 6514-6519. View Abstract>>
  1. H. Liu, L. Zhou, G. Chen, R. M. Krug (2015) Battle between influenza A virus and a newly identified antiviral activity of the PARP-containg ZAPL protein. Proceedings of the National Academy of Sciences USA 112(45): 14048-14053. View Abstract>>
  1. Wan, B. Borgeson, S. Phanse, F. Tu, K. Drew, G. Clark, X. Xiong, O. Kagan, J. Kwan, A. Bezginov, K. Chessman, S. Pal, G. Cromar, O. Papoulas, Z. Ni, D. R. Boutz, S. Stoilova, P. C. Havugimana, X. Guo, R. H. Malty, M. Sarov, J. Greenblatt, M. Babu, W. B. Derry, E. R. Tillier, J. B. Wallingford, J. Parkinson,E. M. Marcotte, A. Emili (2015) Panorama of ancient metazoan macromolecular complexes. Nature, 525:339–344. View Abstract>>
  1. Zheng #, Q. Qin #, W.C. Clark, C. Yi, C. He, A.M. Lambowitz*,T. Pan* (2015) Efficient and quantitative high-throughput transfer RNA sequencing. NatureMethods 12(9): 835-837. #Co-first authors, *Co-corresponding authors. View>>
  1. Zhang, Y. Hu, W. Jiang, L. Fang, X. Guan, J. Chen, J. Zhang, C. A. Saski, B. E. Scheffler, D. M. Stelly, A. M. Hulse-Kemp, Q. Wan, B. Liu, C. Liu, S. Wang, M. Pan, Y. Wang, D. Wang, W. Ye, L. Chang, W. Zhang, Q. Song, R. C. Kirkbride, X. Chen, E. Dennis, D. J. Llewellyn, D. G. Peterson, P. Thaxton, D. C. Jones, Q. Wang, X. Xu, H. Zhang, H. Wu, L. Zhou, G. Mei, S. Chen, Y. Tian, D. Xiang, X. Li, J. Ding, Q. Zuo, L. Tao, Y. Liu, J. Li, Y. Lin, Y. Hui, Z. Cao, C. Cai, X. Zhu, Z. Jiang, B. Zhou, W. Guo, R. Li, and Z. J. Chen(2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33:531-537. View>>
  1. Miller, Q. Song, X. Shi, T. E. Juenger, and Z. J. Chen (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of ArabidopsisNature Communications 6:7453. View>>
  1. Shi, C. Zhang, D. -K. Ko, and Z. J. Chen(2015) Genome-wide dosage-dependent and -independent regulation contributes to gene expression and evolutionary novelty in plant polyploids. Molecular Biology and Evolution 32:2351-2366. View Abstract>>
  1. Song, and Z. J. Chen (2015) Epigenetic and developmental regulation in plant polyploids. Current Opinions in Plant Biology24:101–109. View Abstract>>
  1. Song, X. Guan, Z. J. Chen (2015) Dynamic roles for small RNAs and DNA methylation during ovule and fiber development in allotetraploid cotton. PLoS Genetics11(12):e1005724. View>>
  1. Li, H. Huang, G. Gropp, B. Gjetvaj, D. Lindsay, S. Wei, C. Coutu, Z. Chen, X. -C. Wan, A. Hannoufa, M. Gruber, D. Lydiate, Z. J.Chen,D. Hegedus, and M. -J. Gao (2015) SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation program. Nature Communications 6:7243. View Abstract>>
  1. Hu, J. N. Lancaster, C. Sasiponganan, L. I. R. Ehrlich(2015) CCR4 promotes medullary entry and thymocyte-dendritic cell interactions required for central tolerance. Journal of Experimental Medicine. 212 (11):1947-1965. PMID 26417005. View>>
  1. M.  Harshey, J. D. Partridge (2015) Shelter in a swarm. J. Mol. Biol.427:3683-3694. View Abstract>>
  1. Ariel, A. Rabani, S. Benisty, J. D. Partridge, R. M. Harshey, A. Be'er00 (2015) Swarming bacteria migrate by Lévy walk. Nature Communications 6:8396. doi: 10.1038/ncomms9396. View Abstract>>