Recent Publications

2014

Wong, X*., Luperchio, TR.* and Reddy, KL., 2014, "NET gains and losses: the role of changing nuclear envelope proteomes in genome regulation," Curr Opin Cell Biol. 28C:105-120.  Review.​ *equal contribution PubMed
Colis, L., Peltonen, K., Sirajuddin, P., Liu, H., Sanders, S., Ernst, G., Barrow, JC. and Laiho, M., 2014, "DNA intercalator BMH-21 inhibits RNA polymerase I independent of DNA damage response," Oncotarget, 5(12):4361-4369. PMCID: PMC4147329 PubMed
Davis, CH.*, Kim, KY., Bushong, EA., Mills, EA.*, Boassa, D., Shih, T., Kinebuchi, M., Phan, S., Zhou, Y., Bihlmeyer, NA., Nguyen, JV.*, Jin, Y., Ellisman, MH. and Marsh-Armstrong, N., 2014, "Transcellular degradation of axonal mitochondria," Proc Natl Acad Sci U S A. 111(26):9633-8.  PMCID: PMC4084443 *equal contribution​ PubMed
Guzzo, CM., Ringel, A., Cox, E., Uzoma, I., Zhu, H., Blackshaw, S., Wolberger, C. and Matunis, MJ., 2014, "Characterization of the SUMO-Binding Activity of the Myeloproliferative and Mental Retardation (MYM)-Type Zinc Fingers in ZNF261 and ZNF198," PLoS One. 9(8):e105271. PMCID: PMC4136804​ PubMed
Kuang, Z., Cai, L., Zhang, X., Ji, H., Tu, BP. and Boeke, JD., 2014, "High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast," Nat Struct Mol Biol. 21(10):854-63  PMCID: PMC4190017 ​ PubMed
Papazyan, R., Voronina, E., Chapman, JR., Luperchio, TR., Gilbert, TM., Meier, E., Mackintosh, SG., Shabanowitz, J., Tackett, AJ., Reddy, KL., Coyne, RS., Hunt, DF., Liu, Y. and Taverna, SD., 2014, "Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis," Elife. 3:e02996. PMCID: PMC4141274 PubMed
Cieniewicz, AM.*, Moreland, L., Ringel, AE., Mackintosh, SG., Raman, A*., Gilbert, TM.*, Wolberger, C., Tackett, AJ. and Taverna, SD., 2014, "The bromodomain of Gcn5 regulates site-specificity of lysine acetylation on histone H3," Mol Cell Proteomics,13(11):2896-910.  PMCID: PMC4223480 *equal contribution​ PubMed
Gilbert, TM., McDaniel, SL., Byrum, SD., Cades, JA., Dancy, BC., Wade, H., Tackett, AJ., Strahl, BD. and Taverna, SD., 2014, "An H3K36me3 binding PWWP protein targets the NuA3 acetyltransferase complex to coordinate transcriptional elongation at coding regions," Mol Cell Proteomics, 13(11):2883-95. PMCID: PMC4223479​ PubMed
Li, Y.*, Ma, Q.*, Cherry, CM.* and Matunis, EL., 2014, "Steroid signaling promotes stem cell maintenance in the Drosophila testis," Dev Biol. 394(1):129-41.  PMCID: PMC4165524 *equal contribution​ PubMed
Kim, YJ., Lim, H., Li, Z., Oh, Y., Kovlyagina, I., Choi, IY., Dong, X. and Lee, G., 2014, "Generation of Multipotent Induced Neural Crest by Direct Reprogramming of Human Postnatal Fibroblasts with a Single Transcription Factor," Cell Stem Cell, 15(4):497-506 ​ PubMed
Debeljak, M., Freed, DN., Welch, JA., Haley, L., Beierl, K., Iglehart, BS., Pallavajjala, A., Gocke, CD., Leffell, MS., Lin, MT., Pevsner, J., Wheelan, SJ and Eshleman, JR., 2014, "Haplotype counting by next-generation sequencing for ultrasensitive human DNA detection," J Mol Diagn. 16(5):495-503.      PubMed 
Colis, L., Ernst, G., Sanders, S., Liu, H., Sirajuddin, P., Peltonen, K., DePasquale, M., Barrow, JC. and Laiho, M., 2014, "Design, synthesis, and structure-activity relationships of pyridoquinazolinecarboxamides as RNA polymerase I inhibitors," J Med Chem 57(11):4950-61.​ PMCID: PMC4059246​ PubMed 
Prendergast, J., Umanah, GK., Yoo, SW., Lagerlöf, O., Motari, MG., Cole, RN., Huganir, RL., Dawson, TM., Dawson, VL. and Schnaar, RL., 2014, "Ganglioside regulation of AMPA receptor trafficking," J Neurosci. 34(39):13246-58. PMCID: PMC4172811  PubMed
Chung, S., Hanlon, CD. and Andrew, DJ., 2014, "Building and specializing epithelial tubular organs: the Drosophila salivary gland as a model system for revealing how epithelial organs are specified, form and specialize," Wiley Interdiscip Rev Dev Biol. 3(4):281-300. PMCID: PMC4448711 PubMed
Deng, K. and Siliciano, RF., 2014, "HIV: Early treatment may not be early enough," Nature.  PubMed
Fan, L., Guan, X., Wang, W., Zhao, JY., Zhang, H., Tiwari, V., Hoffman, PN., Li, M. and Tao, YX., 2014, "Impaired neuropathic pain and preserved acute pain in rats overexpressing voltage-gated potassium channel subunit Kv1.2 in primary afferent neurons," Mol Pain. 10(1):8.  PMCID: PMC3909300 ​ PubMed
Paix, A.*, Wang, Y.*, Smith, H., Lee, CY*., Calidas, D.*, Lu, T*., Smith, J.*, Schmidt, H.*, Krause, M. and Seydoux, G., 2014, "Scalable and Versatile Genome Editing Using Linear DNAs with Micro-homology to Cas9 Sites in Caenorhabditis elegans," Genetics, 198(4):1347-56.  PMCID: PMC4256755 *equal contribution​ PubMed
Li, Z., He, SQ., Xu, Q., Yang, F., Tiwari, V., Liu, Q., Tang, Z., Han, L., Chu, YX., Wang, Y., Hin, N., Tsukamoto, T., Slusher, B., Guan, X., Wei, F., Raja, SN., Dong, X. and Guan, Y., 2014, "Activation of MrgC receptor inhibits N-type calcium channels in small-diameter primary sensory neurons in mice," Pain, 155(8):1613-21. PMCID: PMC4104261  PubMed
Kim, YS.*, Chu, Y., Han, L*., Li, M., Li, Z.*, Lavinka, PC.*, Sun, S*., Tang, Z., Park, K.*, Caterina, MJ., Ren, K., Dubner, R., Wei, F. and Dong, X., 2014, "Central Terminal Sensitization of TRPV1 by Descending Serotonergic Facilitation Modulates Chronic Pain," Neuron, 81(4):873-87.  PMCID: PMC3943838 *equal contribution PubMed
Gilbert, CE., Zuckerman, DM., Currier, PL. and Machamer, CE., 2014, "Three basic residues of intracellular loop 3 of the Beta-1 adrenergic receptor are required for golgin-160-dependent trafficking," Int J Mol Sci. 15(2):2929-45. PMCID: PMC3958891 PubMed
Brubaker, SW., Gauthier, AE., Mills, EW., Ingolia, NT. and Kagan, JC.,  2014, "A Bicistronic MAVS Transcript Highlights a Class of Truncated Variants in Antiviral Immunity," Cell. 2014 Feb 13;156(4):800-11. doi: 10.1016/j.cell.2014.01.021. PMCID: PMC3959641 PubMed
Meier, EL. and Goley, ED., 2014, "Form and function of the bacterial cytokinetic ring," Curr Opin Cell Biol. 26C:19-27.  PubMed
Oldach, L. and Zhang, J., 2014, "Genetically Encoded Fluorescent Biosensors for Live-Cell Visualization of Protein Phosphorylation," Chem Biol. 21(2):186-197. PMCID: PMC4050661  PubMed
Luperchio, TR., Wong, X. and Reddy, KL., 2014, "Genome regulation at the peripheral zone: lamina associated domains in development and disease," Curr Opin Genet Dev. 25C:50-61.  Review. PubMed
Huebner, RJ., Lechler, T. and Ewald, AJ., 2014, "Developmental stratification of the mammary epithelium occurs through symmetry-breaking vertical divisions of apically positioned luminal cells," Development. 141(5):1085-94. PMCID: PMC3929409 PubMed
Annaluru, N., Muller, H., Mitchell, LA., Ramalingam, S., Stracquadanio, G., Richardson, SM., Dymond, JS., Kuang, Z., Scheifele, LZ., Cooper, EM., Cai, Y., Zeller, K., Agmon, N., Han, JS., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., London, V., Yeluru, A., Murugan, S., Kandavelou, K., Agier, N., Fischer, G., Yang, K., Martin, JA., Bilgel, M., Bohutski, P., Boulier, KM., Capaldo, BJ., Chang, J., Charoen, K., Choi, WJ., Deng, P., DiCarlo, JE., Doong, J., Dunn, J., Feinberg, JI., Fernandez, C., Floria, CE., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, CY., Lee, PA., Li, S., Lin, D., Linder, ME., Ling, J., Liu, J., Liu, J., London, M., Ma, H., Mao, J., McDade, JE., McMillan, A., Moore, AM., Oh, WC., Ouyang, Y., Patel, R., Paul, M., Paulsen, LC., Qiu, J., Rhee, A., Rubashkin, MG., Soh, IY., Sotuyo, NE., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, WR., Xu, Y., Yu, AT., Koszul, R., Bader, JS., Boeke, JD. and Chandrasegaran, S., 2014, "Total synthesis of a functional designer eukaryotic chromosome," Science. 344(6179):55-8. . Erratum in: Science. 2014 May 23;344(6186):816. PMCID: PMC4033833 PubMed
Hodge, DL., Berthet, C., Coppola, V., Kastenmüller, W., Buschman, MD., Schaughency, PM., Shirota, H., Scarzello, AJ., Subleski, JJ., Anver, MR., Ortaldo, JR., Lin, F., Reynolds, DA., Sanford, ME., Kaldis, P., Tessarollo, L., Klinman, DM. and Young, HA., 2014, "IFN-gamma AU-rich element removal promotes chronic IFN-gamma expression and autoimmunity in mice," J Autoimmun. 53:33-45. PMCID: PMC4148478 PubMed
Shamir, ER., Pappalardo, E., Jorgens, DM., Coutinho, K., Tsai, WT., Aziz, K., Auer, M., Tran, PT., Bader, JS. and Ewald, AJ., 2014, "Twist1-induced dissemination preserves epithelial identity and requires E-cadherin," J Cell Biol. 204(5):839-56. PMCID: PMC3941052 PubMed
Huebner, RJ. and Ewald, AJ., 2014, "Cellular foundations of mammary tubulogenesis," Semin Cell Dev Biol, 31:124-31. Review.​ PMCID: PMC4116098 PubMed
Sluch, VM. and Zack, DJ. 2014, "Stem cells, retinal ganglion cells and glaucoma," Dev Ophthalmol. 53:111-21. PMCID: PMC4547935  PubMed
Kim, MS., Pinto, SM., Getnet, D., Nirujogi, RS., Manda, SS., Chaerkady, R., Madugundu, AK., Kelkar, DS., Isserlin, R., Jain, S., Thomas, JK., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, NA., Balakrishnan, L., Advani, J., George, B., Renuse, S., Selvan, LD., Patil, AH., Nanjappa, V., Radhakrishnan, A., Prasad, S., Subbannayya, T., Raju, R., Kumar, M., Sreenivasamurthy, SK., Marimuthu, A., Sathe, GJ., Chavan, S., Datta, KK., Subbannayya, Y., Sahu, A., Yelamanchi, SD., Jayaram, S., Rajagopalan, P., Sharma, J., Murthy, KR., Syed, N., Goel, R., Khan, AA., Ahmad, S., Dey, G., Mudgal, K., Chatterjee, A., Huang, TC., Zhong, J., Wu, X., Shaw, PG., Freed, D., Zahari, MS., Mukherjee, KK., Shankar, S., Mahadevan, A., Lam, H., Mitchell, CJ., Shankar, SK., Satishchandra, P., Schroeder, JT., Sirdeshmukh, R., Maitra, A., Leach, SD., Drake, CG., Halushka, MK., Prasad, TS., Hruban, RH., Kerr, CL., Bader, GD., Iacobuzio-Donahue, CA., Gowda, H. and Pandey, A., 2014, "A draft map of the human proteome, "Nature. 509(7502):575-81. PMCID: PMC4403737 PubMed
Chivukula, RR., Shi, G., Acharya, A., Mills, EW., Zeitels, LR., Anandam, JL., Abdelnaby, AA., Balch, GC., Mansour, JC., Yopp, AC., Maitra, A. and Mendell, JT., 2014, "An Essential Mesenchymal Function for miR-143/145 in Intestinal Epithelial Regeneration," Cell.157(5):1104-16. PMCID: PMC4175516​ PubMed
Salgado, M., Swanson, MD., Pohlmeyer, CW., Buckheit, RW 3rd., Wu, J., Archin, NM., Williams, TM., Margolis, DM., Siliciano, RF., Garcia, JV. and Blankson,  JN., 2014, "HLA-B*57 Elite Suppressor and Chronic Progressor HIV-1 Isolates Replicate Vigorously and Cause CD4+ T cell Depletion in Humanized BLT Mice," J Virol. 88:3340-3352  PMCID: PMC3957943 PubMed

2013

Patenaude, C., Zhang, Y., Cormack, B., Koehler, J. and Rao, R., 2013, "Essential Role for Vacuolar Acidification in Candida albicans Virulence," J Biol Chem. 288(36):26256-64.  PMCID: PMC3764829PubMed
Frueh, DP., Goodrich, AC., Mishra, SH. and Nichols, SR., 2013, "NMR methods for structural studies of large monomeric and multimeric proteins," Curr Opin Struct Biol., 23, 734-9. PMCID: PMC3805735PubMed
Eyler, DE., Wehner, KA. and Green, R., 2013, "Eukaryotic release factor 3 is required for multiple turnovers of peptide release catalysis by eukaryotic release factor 1," J Biol Chem., 288(41):29530-8. PMCID: PMC3795251  PubMed
Yu, H., Lin, Z., Mattmann, ME., Zou, B., Terrenoire, C., Zhang, H., Wu, M., McManus, OB., Kass, RS., Lindsley, CW., Hopkins, CR. and Li, M., 2013, "Dynamic subunit stoichiometry confers a progressive continuum of pharmacological sensitivity by KCNQ potassium channels," Proc Natl Acad Sci U S A. 110(21):8732-7. PMCID: PMC3666726 PubMed
Shirley, MD, 2013, "Concerns regarding "Whole exome sequencing reveals minimal differences between cell line and whole blood derived DNA", Genomics. 102(4):430.  PubMed
Tu-Sekine, B., Goldschmidt, H., Petro, E. and Raben, DM., 2013, "Diacylglycerol kinase θ: regulation and stability," Adv Biol Regul. 53(1):118-26. PMCID: PMC3992713PubMed
Berk, JM., Maitra, S., Dawdy, AW., Shabanowitz, J., Hunt, DF. and Wilson, KL., 2013, "O-GlcNAc regulates emerin binding to BAF in a chromatin- and lamin B-enriched 'niche'," J Biol Chem. 288(42):30192-209. PMCID: PMC3798487  PubMed
Hu, S., Wan, J., Su, Y., Song, Q., Zeng, Y., Nguyen, HN., Shin, J., Cox, E., Rho, HS., Woodard, C., Xia, S., Liu, S., Lyu, H., Ming, GL., Wade, H., Song, H., Qian, J. and Zhu, H., 2013, "DNA methylation presents distinct binding sites for human transcription factors," Elife. 2:e00726. PMCID: PMC3762332 PubMed​
Zhang, X., Visser, B., Tschurl, M., Collins, E., Wang, Y., Wang, Q., Li, Y., Sun, Q., Jena, P., Gantefoer, G., Boesl, U., Heiz, U., Bowen, K., 2013, "Communication: In search of four-atom chiral metal clusters," J Chem Phys.139(11):111101. PMID: 24070270 PubMed
Newman, RH., Hu, J., Rho, HS., Xie, Z., Woodard, C., Neiswinger, J., Cooper, C., Shirley, M., Clark, HM., Hu, S., Hwang, W., Jeong, JS., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Xia, S., Ji, H., Dalby, KN., Birnbaum, MJ., Cole, PA., Knapp, S., Ryazanov, AG., Zack, DJ., Blackshaw, S., Pawson, T., Gingras, AC., Desiderio, S., Pandey, A., Turk, BE., Zhang, J., Zhu, H. and Qian, J., 2013, "Construction of human activity-based phosphorylation networks," Mol Syst Biol. 9:655. PMCID: PMC3658267  PubMed
Teng, X., Dayhoff-Brannigan, M., Cheng, WC., Gilbert, CE., Sing, CN., Diny, N.L., Wheelan, SJ., Dunham, MJ., Boeke, JD., Pineda, FJ. and Hardwick, JM., 2013, "Genome-wide Consequences of Deleting Any Single Gene," Mol Cell. 52(4):485-94. PMCID: PMC3975072     PubMed
Dickey,. SW., Baker, RP., Cho, S. and Urban, S.., 2013, "Proteolysis inside the membrane is a rate-governed reaction not driven by substrate affinity," Cell. 2013 Dec 5;155(6):1270-81.  PMCID: PMC3917317 PubMed
He, SQ., Han, L., Li, Z., Xu, Q., Tiwari, V., Yang, F., Guan, X., Wang, Y., Raja, SN., Dong, X. and Guan, Y., 2013, "Temporal changes in MrgC expression after spinal nerve injur," Neuroscience. pii: S0306-4522(13)01065-8. PMCID: PMC3945476 PubMed
He, SQ., Li, Z., Chu, YX., Han, L., Xu, Q., Li, M., Yang, F., Liu, Q., Tang, Z., Wang, Y., Hin, N., Tsukamoto, T., Slusher, B., Tiwari, V., Shechter, R., Wei, F., Raja, SN., Dong, X. and Guan, Y., 2013, "MrgC agonism at central terminals of primary sensory neurons inhibits neuropathic pain," Pain, 155(3):534-44.  PMCID: PMC3945061 PubMed
Hua, ZL., Smallwood, PM. and Nathans, J., 2013, "Frizzled3 controls axonal development in distinct populations of cranial and spinal motor neurons," Elife. 2:e01482.  PMCID: PMC3865743  PubMed
Pohlmeyer, CW., Buckheit, RW 3rd., Siliciano, RF. and Blankson, JN., 2013, "CD8+ T cells from HLA-B*57 elite suppressors effectively suppress replication of HIV-1 escape mutants," Retrovirology. 10:152. PMCID: PMC3878989 PubMed
Zhou, Y. and Wang, X., 2013, "Spatially extended forward suppression in primate auditory cortex," Eur J Neurosci. PMID 24372934 PubMed

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