Basic Sciences Division

Basic Sciences Publications Archive

2014

Daugherty, M.D., Malik, H.S. (2014). How a Virus Blocks a Cellular Emergency Access Lane to the Nucleus, STAT! Cell Host Microbe, 16(2), 150-2.
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Engel, G.A., Small, C.T., Soliven, K., Feeroz, M.M., Wang, X., Hasan, M.K., Oh, G., Alam, S.M.R., Craig, K.L., Jackson, D.L., Matsen, F.A., Linial, M.L., Jones-Engel, L. (2013). Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection. Emerg Microbes Infec, 2.

Skene, P.J., Henikoff, S. (2014). Histones push the envelope. Nat Struct Mol Biol, 21(8), 651-2.
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Taylor, A.F., Amundsen, S.K., Guttman, M., Lee, K.K., Luo, J., Ranish, J., Smith, G.R. (2014). Control of RecBCD Enzyme Activity by DNA Binding- and Chi Hotspot-dependent Conformational Changes. J Mol Biol.
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Bloom, J.D. (2014). An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol.
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Fowler, K.R., Sasaki, M., Milman, N., Keeney, S., Smith, G.R. (2014). Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome. Genome Res.
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Bachtrog, D., Mank, J.E., Peichel, C.L., Kirkpatrick, M., Otto, S.P., Ashman, T.-L., Hahn, M.W., Kitano, J., Mayrose, I., Ming, R., Perrin, N., Ross, L., Valenzuela, N., Vamosi, J.C., Tree of Sex, C. (2014). Sex determination: why so many ways of doing it? PLoS Biol, 12(7), e1001899. PMCID: PMC4077654.
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Thyagarajan B., Bloom, JD. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. eLife 2014;10.7554/eLife.03300
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Zanders, S.E., Eickbush, M.T., Yu, J.S., Kang, J.-W., Fowler, K.R., Smith, G.R., Malik, H.S. (2014). Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. Elife, 3, e02630. PMCID: PMC4066438.
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Machkovech, H., Bloom, J.D. (2014). Generation Of a Human T-Cell Receptor Cell Line to Evaluate Influenza Peptide Presentation. J Invest Med, 62(1), 279-.

Procko, E., Berguig, G.Y., Shen, B.W., Song, Y., Frayo, S., Convertine, A.J., Margineantu, D., Booth, G., Correia, B.E., Cheng, Y., Schief, W.R., Hockenbery, D.M., Press, O.W., Stoddard, B.L., Stayton, P.S., Baker, D. (2014). A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells. Cell, 157(7), 1644-56.
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Belfort, M., Marraffini, L., Macfarlan, T., Boeke, J., Slotkin, K., Malik, H., Maquat, L. (2014). Mobile DNA: an evolving field. Mobile DNA, 5, 16. PMCID: PMC4046146.
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Galizi, R., Doyle, L.A., Menichelli, M., Bernardini, F., Deredec, A., Burt, A., Stoddard, B.L., Windbichler, N., Crisanti, A. (2014). A synthetic sex ratio distortion system for the control of the human malaria mosquito. Nat Commun, 5, 3977. PMCID: PMC4057611.
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Daugherty, M.D., Young, J.M., Kerns, J.A., Malik, H.S. (2014). Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts. PLoS Genet, 10(5), e1004403.
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Diolaiti, D., McFerrin, L., Carroll, P., Eisenman, R.N. (2014). Functional interactions among members of the MAX and MLX transcriptional network during oncogenesis. Biochim Biophys Acta.
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Kamenova, I., Warfield, L., Hahn, S. (2014). Mutations on the DNA binding surface of TBP discriminate between yeast TATA and TATA-less gene transcription. Mol Cell Biol.
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Green, R., Shou, W. (2014). Modeling community population dynamics with the open-source language R. Methods in molecular biology, 1151, 209-31.
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Waite, A.J., Shou, W. (2014). Constructing synthetic microbial communities to explore the ecology and evolution of symbiosis. Methods in molecular biology, 1151, 27-38.
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Sinnar, S.A., Antoku, S., Saffin, J.-M., Cooper, J.A., Halpain, S. (2014). Capping Protein Is Essential for Cell Migration in Vivo and for Filopodial Morphology and Dynamics. Mol Biol Cell.
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Villamaria, C.Y., Fries, C.A., Spencer, J.R., Roth, M.B., Davis, M.R. (2014). Hydrogen sulfide mitigates reperfusion injury in a porcine model of vascularized composite autotransplantation. Annals of plastic surgery, 72(5), 594-8.
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Bloom, J. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol first published online May 24, 2014 doi:10.1093/molbev/msu173
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Gong LI, Bloom JD (2014) Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution. PLoS Genet 10(5): e1004328. doi:10.1371/journal.pgen.1004328.
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Conacci-Sorrell, M., Ngouenet, C., Anderson, S., Brabletz, T., Eisenman, R.N. (2014). Stress-induced cleavage of Myc promotes cancer cell survival. Genes Dev, 28(7), 689-707.
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Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, T.D., Codomo, C.A., Brogaard, K., Widom, J., Wang, J.-P., Henikoff, J.G. (2014). The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. Elife, 3, e01861.
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Skene, P.J., Hernandez, A.E., Groudine, M., Henikoff, S. (2014). The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. Elife, 3, e02042.
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Ye, X., Linton, J.M., Schork, N.J., Buck, L.B., Petrascheck, M. (2014). A pharmacological network for lifespan extension in Caenorhabditis elegans. Aging Cell, 13(2), 206-15. PMCID: PMC3955372.
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Steiner, F.A., Henikoff, S. (2014). Holocentromeres are dispersed point centromeres localized at transcription factor hotspots. Elife, 3, e02025.
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Orsi, G.A., Kasinathan, S., Hughes, K.T., Saminadin-Peter, S., Henikoff, S., Ahmad, K. (2014). High-resolution mapping defines the cooperative architecture of Polycomb response elements. Genome Res.
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Tenthorey, J.L., Kofoed, E.M., Daugherty, M.D., Malik, H.S., Vance, R.E. (2014). Molecular Basis for Specific Recognition of Bacterial Ligands by NAIP/NLRC4 Inflammasomes. Mol Cell.
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Butler, J., Hooper, K.A., Petrie, S., Lee, R., Maurer-Stroh, S., Reh, L., Guarnaccia, T., Baas, C., Xue, L., Vitesnik, S., Leang, S.-K., McVernon, J., Kelso, A., Barr, I.G., McCaw, J.M., Bloom, J.D., Hurt, A.C. (2014). Estimating the Fitness Advantage Conferred by Permissive Neuraminidase Mutations in Recent Oseltamivir-Resistant A(H1N1)pdm09 Influenza Viruses. PLoS Pathog, 10(4), e1004065.
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Biggins S, Welch MD. (2014). Editorial overview: Cell architecture: Cellular organization and function. Current opinion in cell biology, 26, v-vii.
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Driver JW, Powers AF, Sarangapani KK, Biggins S, Asbury CL. (2014). Measuring kinetochore-microtubule interaction in vitro. Methods Enzymol, 540, 321-37.
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Miller CT, Glazer AM, Summers BR, Blackman BK, Norman AR, Shapiro MD, Cole BL, Peichel CL, Schluter D, Kingsley DM. (2014). Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci. Genetics.
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Quillien, A., Moore, J.C., Shin, M., Siekmann, A.F., Smith, T., Pan, L., Moens, C.B., Parsons, M.J., Lawson, N.D. (2014). Distinct Notch signaling outputs pattern the developing arterial system. Development.
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Stoddard, B.L. (2014). Homing endonucleases from mobile group I introns: discovery to genome engineering. Mobile DNA, 5(1), 7. PMCID: PMC3943268.
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Takeuchi, R., Choi, M., Stoddard, B.L. (2014). Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. Proc Natl Acad Sci U S A.
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Weber, C.M., Ramachandran, S., Henikoff, S. (2014). Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase. Mol Cell, 53(5), 819-30.
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Yoshida, K., Makino, T., Yamaguchi, K., Shigenobu, S., Hasebe, M., Kawata, M., Kume, M., Mori, S., Peichel, C.L., Toyoda, A., Fujiyama, A., Kitano, J. (2014). Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species. PLoS Genet, 10(3), e1004223.
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Dillin, A., Gottschling, D.E., Nystrom, T. (2014). The good and the bad of being connected: the integrons of aging. Current opinion in cell biology, 26C, 107-12. PMCID: PMC3927154.
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Poudel, K.R., Bai, J. (2014). Synaptic vesicle morphology: a case of protein sorting? Current opinion in cell biology, 26C, 28-33.
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Momeni, B., Waite, A.J., Shou, W. (2013). Spatial self-organization favors heterotypic cooperation over cheating. Elife, 2, e00960. PMCID: PMC3823188.
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Mills, M.G., Greenwood, A.K., Peichel, C.L. (2014). Pleiotropic effects of a single gene on skeletal development and sensory system patterning in sticklebacks. EvoDevo, 5(1), 5.
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Krassovsky, K., Henikoff, S. (2014). Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster. BMC Genomics, 15(1), 105.
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Correia, B.E., Bates, J.T., Loomis, R.J., Baneyx, G., Carrico, C., Jardine, J.G., Rupert, P., Correnti, C., Kalyuzhniy, O., Vittal, V., Connell, M.J., Stevens, E., Schroeter, A., Chen, M., Macpherson, S., Serra, A.M., Adachi, Y., Holmes, M.A., Li, Y., Klevit, R.E., Graham, B.S., Wyatt, R.T., Baker, D., Strong, R.K., Crowe, J.E., Johnson, P.R., Schief, W.R. (2014). Proof of principle for epitope-focused vaccine design. Nature.
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Qin L-X, Breeden L, Self SG. (2014). Finding gene clusters for a replicated time course study. BMC research notes, 7(1), 60.
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Lopez-Yglesias, A.H., Zhao, X., Quarles, E.K., Lai, M.A., Vandenbos, T., Strong, R.K., Smith, K.D. (2014). Flagellin Induces Antibody Responses through a TLR5- and Inflammasome-Independent Pathway. Journal of immunology.|
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Zigman, M., Laumann-Lipp, N., Titus, T., Postlethwait, J., Moens, C.B. (2014). Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis. Development, 141(3), 639-49.
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Klein, B.J., Piao, L., Xi, Y., Rincon-Arano, H., Rothbart, S.B., Peng, D., Wen, H., Larson, C., Zhang, X., Zheng, X., Cortazar, M.A., Pena, P.V., Mangan, A., Bentley, D.L., Strahl, B.D., Groudine, M., Li, W., Shi, X., Kutateladze, T.G. (2014). The Histone-H3K4-Specific Demethylase KDM5B Binds to Its Substrate and Product through Distinct PHD Fingers. Cell Rep.
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Abreu-Blanco, M.T., Verboon, J.M., Parkhurst, S.M. (2013). Coordination of Rho Family GTPase Activities to Orchestrate Cytoskeleton Responses during Cell Wound Repair. Curr Biol.
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Codomo, C.A., Furuyama, T., Henikoff, S. (2014). CENP-A octamers do not confer a reduction in nucleosome height by AFM. Nat Struct Mol Biol, 21(1), 4-5.
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London, N., Biggins, S. (2014). Mad1 kinetochore recruitment by Mps1-mediated phosphorylation of Bub1 signals the spindle checkpoint. Genes Dev.
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Cipak, L., Polakova, S., Hyppa, R.W., Smith, G.R., Gregan, J. (2014). Synchronized fission yeast meiosis using an ATP analog-sensitive Pat1 protein kinase. Nature protocols, 9(1), 223-31.
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Conacci-Sorrell, M., McFerrin, L., Eisenman, R.N. (2014). An Overview of MYC and Its Interactome. Cold Spring Harb Perspect Med, 4(1).
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Dynan, W., Fox, K., Stoddard, B. (2014). Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases. Nucleic Acids Res, 42(1), 1-2. PMCID: PMC3874147.
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2013

Ruiz M, Ganfornina MD, Correnti C, Strong RK, Sanchez D. (2013). Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila. FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
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Yang F, Teves SS, Kemp CJ, Henikoff S. (2013). Doxorubicin, DNA torsion, and chromatin dynamics. Biochim Biophys Acta.
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Ardekani, R., Greenwood, A.K., Peichel, C.L., Tavare, S. (2013). Automated quantification of the schooling behaviour of sticklebacks. Eurasip J Image Vide.

Blackledge, N.P., Thomson, J.P., Skene, P.J. (2013). CpG island chromatin is shaped by recruitment of ZF-CxxC proteins. Cold Spring Harbor perspectives in biology, 5(11), a018648.
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Kasinathan, S., Orsi, G.A., Zentner, G.E., Ahmad, K., Henikoff, S. (2013). High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods.
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Ashenberg, O., Gong, L.I., Bloom, J.D. (2013). Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci U S A.
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Hickman, J.W., Kotovic, K.M., Miller, C., Warrener, P., Kaiser, B., Jurista, T., Budde, M., Cross, F., Roberts, J.M., Carleton, M. (2013). Glycogen synthesis is a required component of the nitrogen stress response in Synechococcus elongatus PCC 7942. Algal Res, 2(2), 98-106.

Spragg, C.J., Emerman, M. (2013). Antagonism of SAMHD1 is actively maintained in natural infections of simian immunodeficiency virus. Proc Natl Acad Sci U S A.
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Teves, S.S., Henikoff, S. (2013). Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol.
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Finton K, Jaffe J, Larman B, Larimore K, Friend D, Correnti C, Stuart A, Vanden Bos T, Elledge S, Greenberg P, Stamatatos L, Strong RK. Characterizing the functional autoreactivity and polyspecificity of the MPER-specific bNAb 4E10 and an ensemble of its germline-encoded precursors. AIDS Res Hum Retroviruses. 2013 NOV 1; 29(11): A48-A48.

Wang Y, Pan L, Moens CB, Appel B. Notch3 establishes brain vascular integrity by regulating pericyte number. Development. 2013 Dec 4.
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Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. megaTALs: A rare-cleaving nuclease architecture for therapeutic genome engineering. Nucleic Acids Res. 2013 Nov 26.
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Delaurier A, Huycke TR, Nichols JT, Swartz ME, Larsen A, Walker C, Dowd J, Pan L, Moens CB, Kimmel CB. Role of mef2ca in developmental buffering of the zebrafish larval hyoid dermal skeleton. Dev Biol. 2013 Nov 21.
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Teckchandani A, Laszlo GS, Simo S, Shah K, Pilling C, Strait AA, Cooper JA. Cullin5 destabilizes cas to inhibit src-dependent cell transformation. J Cell Sci. 2013 Nov 27.
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Ashenberg O, Gong I, Bloom J. Mutational effects on stability are largely conserved during protein evolution. PNAS Early edition, Dec 2013.
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Nair RN, Bannister TD, Hodder P, Eberhart C, Vega VF, Spicer T, Mercer B, Amundsen SK, Karabulut A, Smith G. Inhibitors of AddAB and RecBCD bacterial DNA repair enzymes: A novel class of antibiotics identified through molecular probe development efforts. Abstr Pap Am Chem Soc. 2013 APR 7; 245.

Paudyal P, Shrestha S, Madanayake T, Shuster CB, Rohrschneider LR, Rowland A, Lyons BA. Grb7 and filamin-a associate and are colocalized to cell membrane ruffles upon EGF stimulation. J Mol Recognit. 2013 Nov; 26(11): 532-541.
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Miles S, Li L, Davison J, Breeden LL. Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state. PLoS Genet. 2013 Oct; 9(10): e1003854.
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Stenbak CR, Craig KL, Ivanov SB, Wang X, Soliven KC, Jackson DL, Gutierrez GA, Engel G, Jones-Wengel L, Linial ML. New world simian foamy virus infections in vivo and in vitro. J Virol. 2013 Nov 6.
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Su CY, Kemp HA, Moens CB. Cerebellar development in the absence of gbx function in zebrafish. Dev Biol. 2013 Oct 30.
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Simó S, Cooper JA. Rbx2 Regulates Neuronal Migration through Different Cullin 5-RING Ligase Adaptors. Dev Cell. 2013 Nov 6. pii: S1534-5807(13)00570-4. doi: 10.1016/j.devcel.2013.09.022. [Epub ahead of print]
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Li L, Anderson S, Secombe J, Eisenman RN. The drosophila ubiquitin-specific protease puffyeye regulates dMyc-mediated growth. Development. 2013 Oct 30.
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Malfavon-Borja R, Sawyer SL, Wu LI, Emerman M, Malik HS. An evolutionary screen highlights canonical and non-canonical candidate antiviral genes within the primate TRIM gene family. Genome Biol Evol. 2013 Oct 24.
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Zentner GE, Henikoff S. Mot1 redistributes TBP from TATA-containing to TATA-less promoters. Mol Cell Biol. 2013 Oct 21.
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Grunberg S, Hahn S. Structural insights into transcription initiation by RNA polymerase II. Trends Biochem Sci. 2013 Oct 11.
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Soliven K, Wang X, Small CT, Feeroz MM, Lee EG, Craig KL, Hasan K, Engel GA, Jones-Engel L, Matsen FA,4th, Linial ML. Simian foamy virus infection of rhesus macaques in bangladesh: Relationship of latent proviruses and transcriptionally active viruses. J Virol.2013 Oct 9.
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Bandura JL, Jiang H, Nickerson DW, Edgar BA. The molecular chaperone Hsp90 is required for cell cycle exit in. PLoS Genet. 2013 Sep; 9(9): e1003835.
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Hyppa RW, Fowler KR, Cipak L, Gregan J, Smith GR. DNA intermediates of meiotic recombination in synchronous S. pombe at optimal temperature. Nucleic Acids Res. 2013 Oct 1.
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Klezovitch O, Vasioukhin V. Your gut is right to turn left. Dev Cell. 2013 Sep 30; 26(6): 553-554.
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Kuo Y, Ren S, Lao U, Edgar BA, Wang T. Suppression of polyglutamine protein toxicity by co-expression of a heat-shock protein 40 and a heat-shock protein 110. Cell Death Dis. 2013 Oct 3; 4: e833.
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Li L, Miles S, Melville Z, Prasad A, Bradley G, Breeden LL. Key events during the transition from rapid growth to quiescence in budding yeast require posttranscriptional regulators. Mol Biol Cell. 2013 Oct 2.
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Talbert PB, Henikoff S. Phylogeny as the basis for naming histones. Trends Genet. 2013 Sep; 29(9): 499-500.
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Rasmussen JP, Feldman JL, Reddy SS, Priess JR. Cell interactions and patterned intercalations shape and link epithelial tubes in C. elegans. PLoS Genet. 2013 Sep; 9(9): e1003772.
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Ng TM, Lenstra TL, Duggan N, Jiang S, Ceto S, Holstege FC, Dai J, Boeke JD, Biggins S. Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics. 2013 Sep 20.
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Greenwood AK, Wark AR, Yoshida K, Peichel CL. Genetic and neural modularity underlie the evolution of schooling behavior in threespine sticklebacks. Curr Biol. 2013 Sep 10.
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Cheng C, Ansari MM, Cooper JA, Gong X. EphA2 and src regulate equatorial cell morphogenesis during lens development. Development. 2013 Sep 11.
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Cooper JA. Cell biology in neuroscience: Mechanisms of cell migration in the nervous system. J Cell Biol. 2013 Sep 2; 202(5): 725-734.
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Etienne L, Emerman M. The mongoose, the pheasant, the pox, and the retrovirus. PLoS Biol. 2013 Aug; 11(8): e1001641.
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Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 2013 Sep 12; 501(7466): 212-216.
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Hooper KA, Bloom JD. A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein. Published ahead of print 11 September 2013, doi: 10.1128/JVI.01889-13 JVI.01889-13.
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Hendry AP, Peichel CL, Matthews B, Boughman JW, Nosil P. Stickleback research: The now and the next. Evol Ecol Res. 2013 Feb; 15(2): 111-141.

Compton AA, Malik HS, Emerman M. Host gene evolution traces the evolutionary history of ancient primate lentiviruses. Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12; 368(1626): 20120496.
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Knutson BA. Emergence and expansion of TFIIB-like factors in the plant kingdom. Gene. 2013 Aug 15; 526(1): 30-38.
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Lenkowski JR, Qin Z, Sifuentes CJ, Thummel R, Soto CM, Moens CB, Raymond PA. Retinal regeneration in adult zebrafish requires regulation of TGFbeta signaling. Glia. 2013 Aug 5.
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Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J Am Chem Soc. 2013 Aug 7.
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Biggins S. The composition, functions, and regulation of the budding yeast kinetochore. Genetics. 2013 Aug; 194(4): 817-846.
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Rincon-Arano H, Parkhurst SM, Groudine M. UpSET-ing the balance: Modulating open chromatin features in metazoan genomes. Fly (Austin). 2013 May 6; 7(3).
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Alunni A, Krecsmarik M, Bosco A, Galant S, Pan L, Moens CB, Bally-Cuif L. Notch3 signaling gates cell cycle entry and limits neural stem cell amplification in the adult pallium. Development. 2013 Jul 17.
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O'Keefe DD, Thomas SR, Bolin K, Griggs E, Edgar BA, Buttitta LA. Combinatorial control of temporal gene expression in the drosophila wing by enhancers and core promoters. BMC Genomics. 2012 Sep 20; 13: 498-2164-13-498.
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Yadon AN, Tsukiyama T. DNA looping-dependent targeting of a chromatin remodeling factor. Cell Cycle. 2013 Jun 15; 12(12): 1809-1810.
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Carter JJ, Daugherty MD, Qi X, Bheda-Malge A, Wipf GC, Robinson K, Roman A, Malik HS, Galloway DA. Identification of an overprinting gene in merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. Proc Natl Acad Sci U S A. 2013 Jul 11.
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Gatchalian J, Futterer A, Rothbart SB, Tong Q, Rincon-Arano H, Sanchez de Diego A, Groudine M, Strahl BD, Martinez-A C, van Wely KH, Kutateladze TG. Dido3 PHD modulates cell differentiation and division. Cell Rep. 2013 Jul 11; 4(1): 148-158.
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Patel MR, Malik HS. Convergent evolution of escape from hepaciviral antagonism in primates. Am J Phys Anthropol. 2013; 150: 217-217.

Ritland Politz JC, Scalzo D, Groudine M. Something silent this way forms: The functional organization of the nuclear repressive compartment. Annu Rev Cell Dev Biol. 2013 Jul 5.
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Weber ND, Takeuchi R, Jarjour J, Stone D, Stoddard BL, Jerome KR. Enzyme engineering of homing endonucleases to target HBV cccDNA. Mol Ther. 2013 JUN; 21: S75-S76.

Wang Z, Halbert CL, Lee D, Butts T, Storb R, Tapscott SH, Miller D. Elimination of contaminating capsid-expressing genes in AAV vectors reduces immune responses to vector administration in a canine gene therapy model. Mol Ther. 2013 JUN; 21: S171-S171.

Wang Y, Jarjour J, Boissel S, Thyme S, Khan I, Pangallo J, Baker D, Stoddard B, Scharenberg AM, Rawlings DJ. Engineering an XID-site specific I-AniI homing endonuclease through combination of rational design and directed evolution. Mol Ther. 2013 JUN; 21: S122-S123.

Mintzer E, Jarjour J, Scharenberg A, Stoddard B, Baker D, Weber N, Stone D, Jerome KR. Development of designer homing endonucleases for inactivation of the HIV provirus. Mol Ther. 2013 JUN; 21: S73-S74.

Ali M, Rincon-Arano H, Zhao W, Rothbart SB, Tong Q, Parkhurst SM, Strahl BD, Deng LW, Groudine M, Kutateladze TG. Molecular basis for chromatin binding and regulation of MLL5. Proc Natl Acad Sci U S A. 2013 Jun 24.
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Allred BE, Correnti C, Clifton MC, Strong RK, Raymond KN. Siderocalin outwits the coordination chemistry of vibriobactin, a siderophore of vibrio cholerae. ACS Chem Biol. 2013 Jun 18.
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Duggal NK, Fu W, Akey JM, Emerman M. Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations. Virology. 2013 Jun 8.
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Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AF, Imhof A, Mellone BG, Malik HS. Stepwise evolution of essential centromere function in a drosophila neogene. Science. 2013 Jun 7; 340(6137): 1211-1214.
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Balazs AB, Bloom JD, Hong CM, Rao DS, Baltimore D. Broad protection against influenza infection by vectored immunoprophylaxis in mice. Nat Biotechnol. 2013 Jun 2.
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Mitchell PS, Emerman M, Malik HS. An evolutionary perspective on the broad antiviral specificity of MxA. Curr Opin Microbiol. 2013 May 28.
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Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AF, Imhof A, Mellone BG, Malik HS. Stepwise evolution of essential centromere function in a drosophila neogene. Science. 2013 Jun 7; 340(6137): 1211-1214.
Abstract »

Politz JC, Ragoczy T, Groudine M. When untethered, something silent inside comes. Nucleus. 2013 May 15; 4(3).
Abstract »

Skene PJ, Henikoff S. Histone variants in pluripotency and disease. Development. 2013 Jun; 140(12): 2513-2524.
Abstract »

Levine MT, Malik HS. A rapidly evolving genomic toolkit for drosophila heterochromatin. Fly (Austin). 2013 Mar 21; 7(3).
Abstract »

Metzger MJ, Stoddard BL, Monnat RJ,Jr. PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks. DNA Repair (Amst). 2013 May 16.
Abstract »

Hubert CG, Bradley RK, Ding Y, Toledo CM, Herman J, Skutt-Kakaria K, Girard EJ, Davison J, Berndt J, Corrin P, Hardcastle J, Basom R, Delrow JJ, Webb T, Pollard SM, Lee J, Olson JM, Paddison PJ. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes Dev. 2013 May 1; 27(9): 1032-1045.
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Akiyoshi B, Nelson CR, Biggins S. The aurora B kinase promotes inner and outer kinetochore interactions in budding yeast. Genetics. 2013 May 1.
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Lizhi Ian Gong, Marc A Suchard, Jesse D Bloom. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2013;2:e00631. May 14, 2013.
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Furuyama T, Codomo CA, Henikoff S. Reconstitution of hemisomes on budding yeast centromeric DNA. Nucleic Acids Res. 2013 Apr 24.
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Martin-Castellanos C, Fowler KR, Smith GR. Making chromosomes hot for breakage. Cell Cycle. 2013 Apr 11; 12(9).
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Sarangapani KK, Akiyoshi B, Duggan NM, Biggins S, Asbury CL. Phosphoregulation promotes release of kinetochores from dynamic microtubules via multiple mechanisms. Proc Natl Acad Sci U S A. 2013 Apr 15.
Abstract »

Lee EG, Stenbak CR, Linial ML. Foamy virus assembly with emphasis on pol encapsidationViruses. 2013 Mar 20; 5(3): 886-900.
Abstract »

Yadon AN, Singh BN, Hampsey M, Tsukiyama T. DNA looping facilitates targeting of a chromatin remodeling enzymeMol Cell. 2013 Mar 5
Abstract »

Nechiporuk T, Klezovitch O, Nguyen L, Vasioukhin V. Dlg5 maintains apical aPKC and regulates progenitor differentiation during lung morphogenesis. Dev Biol. 2013 Mar 2
Abstract »

Zentner GE, Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol. 2013 Mar 5; 20(3): 259-266.
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Teves SS, Henikoff S. The heat shock response: A case study of chromatin dynamics in gene regulationBiochem Cell Biol. 2013 Feb; 91(1): 42-48.
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Hewamadduma CA, Grierson AJ, Ma TP, Pan L, Moens CB, Ingham PW, Ramesh T, Shaw PJ. Tardbpl splicing rescues motor neuron and axonal development in a mutant tardbp zebrafish. Hum Mol Genet. 2013 Feb 19.
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Zentner GE, Tsukiyama T, Henikoff S (2013) ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies. PLoS Genet 9(2): e1003317.
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Akiyoshi B, Nelson CR, Duggan N, Ceto S, Ranish JA, Biggins S. The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein. PLoS Genet. 2013 Feb; 9(2): e1003216.
Abstract »

Fowler KR, Gutierrez-Velasco S, Martin-Castellanos C, Smith GR. Protein determinants of meiotic DNA break hot spots. Mol Cell. 2013 Feb 7.
Abstract »

Momeni B, Brileya KA, Fields MW, Shou W. Strong inter-population cooperation leads to partner intermixing in microbial communities. elife. 2013; 2: e00230.
Abstract »

Nakayama M, Nakayama A, van Lessen M, Yamamoto H, Hoffmann S, Drexler HC, Itoh N, Hirose T, Breier G, Vestweber D, Cooper JA, Ohno S, Kaibuchi K, Adams RH. Spatial regulation of VEGF receptor endocytosis in angiogenesis. Nat Cell Biol. 2013 Jan 27
Abstract »

Wragg RT, Snead D, Dong Y, Ramlall TF, Menon I, Bai J, Eliezer D, Dittman JS. Synaptic vesicles position complexin to block spontaneous fusion. Neuron. 2013 Jan 23; 77(2): 323-334.
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Malfavon-Borja R, Wu LI, Emerman M, Malik HS. Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomesProc Natl Acad Sci U S A. 2013 Jan 14.
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Sanchez-Arevalo Lobo VJ, Doni M, Verrecchia A, Sanulli S, Faga G, Piontini A, Bianchi M, Conacci-Sorrell M, Mazzarol G, Peg V, Losa JH, Ronchi P, Ponzoni M, Eisenman RN, Doglioni C, Amati B. Dual regulation of myc by ablOncogene. 2013 Jan 14.
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Hoot S, McGuire AT, Cohen KW, Strong RK, Hangartner L, Klein F, Diskin R, Scheid JF, Sather DN, Burton DR, Stamatatos L. Recombinant HIV envelope proteins fail to engage germline versions of anti-CD4bs bNAbsPLoS Pathog. 2013 Jan; 9(1): e1003106.
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Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB. RNA-seq based mapping and candidate identification of mutations from forward genetic screensGenome Res. 2013 Jan 8.
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2012

Wark AR, Mills MG, Dang LH, Chan YF, Jones FC, Brady SD, Absher DM, Grimwood J, Schmutz J, Myers RM, Kingsley DM, Peichel CL. Genetic architecture of variation in the lateral line sensory system of threespine sticklebacksG3 (Bethesda). 2012 Sep; 2(9): 1047-1056.
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Momeni B, Shou W. Cryosectioning yeast communities for examining fluorescence patterns. J Vis Exp. 2012 Dec 26; (70). pii: 50101. doi(70): 10.3791/50101.
Abstract »

Rodriguez J, Tsukiyama T. ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress. Genes Dev. 2013 27: 74-86.
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Talbert PB, Henikoff S. Chromatin: Packaging without nucleosomes. Curr Biol. 2012 Dec 18; 22(24): R1040-3.
Abstract »

Rincon-Arano H, Halow J, Delrow JJ, Parkhurst SM, Groudine M. UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. Cell. 2012 Nov 20.
Abstract »

Fior R, Maxwell AA, Ma TP, Vezzaro A, Moens CB, Amacher SL, Lewis J, Saude L. The differentiation and movement of presomitic mesoderm progenitor cells are controlled by mesogenin 1Development. 2012 Dec; 139(24): 4656-4665.
Abstract »

Hughes AL, Gottschling DE. An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast. Nature. 2012 Nov 21.
Abstract »
News Article »

Rodriguez-Mesa E, Abreu-Blanco MT, Rosales-Nieves AE, Parkhurst SM. Developmental expression of drosophila wiskott-aldrich syndrome family proteins. Dev Dyn. 2012 Dec; 241(12): C1.

Momeni B, Brileya KA, Fields MW, Shou W. Strong inter-population cooperation leads to partner intermixing in microbial communities. In press.

Waite AJ, Shou W. Feature Article: Adaptation to a new environment allows cooperators to purge cheaters stochastically. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19079-86. doi: 10.1073/pnas.1210190109. Epub 2012 Oct 22.
Abstract »

Abreu-Blanco MT, Verboon JM, Liu R, Watts JJ, Parkhurst SM. 2012. Drosophila embryos close epithelial wounds using a combination of cellular protrusions and an actomyosin purse string. J Cell Sci. Epub ahead of print, doi: 10.1242/​jcs.109066.
Article »
Abstract »

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