The Program in Molecular Medicine at the University of Massachusetts Medical School was established in a new research building in 1989. Faculty include both clinical investigators and basic scientists, many of whom focus their research on human disease processes. The laboratory groups and core facilities that compose Molecular Medicine represent many disciplines in the bio-medical sciences: biochemistry and molecular biology, cell biology, medicine, immunology, molecular genetics and microbiology, pediatrics, pharmacology, physiology, genomics, bioinformatics and proteomics. This diverse scientific environment makes the Program an exceptional training ground for graduate students and postdoctoral fellows, who in turn contribute much to its vitality and excitement. This collection showcases publications and presentations written by faculty and researchers of the Program in Molecular Medicine.

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Publications from 2010

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A novel pleckstrin homology domain-containing protein enhances insulin-stimulated Akt phosphorylation and GLUT4 translocation in adipocytes, Qiong L. Zhou, Zhen Y. Jiang, Allan S. Mabardy, Claudia M. Del Campo, David G. Lambright, John Holik, Kevin E. Fogarty, Juerg R. Straubhaar, Sarah M. Nicoloro, Anil Chawla, and Michael P. Czech

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ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data, Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Herve Pages, Simon M. Lin, David S. Lapointe, and Michael R. Green

Publications from 2009

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Identification of flavopiridol analogues that selectively inhibit positive transcription elongation factor (P-TEFb) and block HIV-1 replication, Akbar Ali, Animesh Ghosh, Robin S. Nathans, Natalia Sharova, Siobhan O'Brien, Hong Cao, Mario Stevenson, and Tariq M. Rana

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pRB/CKI pathways at the interface of cell cycle and development, Victor R. Ambros

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Tissue damage-induced intestinal stem cell division in Drosophila, Alla Amcheslavsky, Jin Jiang, and Y. Tony Ip

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An essential role for the RNA-binding protein Smaug during the Drosophila maternal-to-zygotic transition, Beatrice Benoit, Chun Hua He, Fan Zhang, Sarah M. Votruba, Wael Tadros, J. Timothy Westwood, Craig A. Smibert, Howard D. Lipshitz, and William E. Theurkauf

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Depletion of the programmed death-1 receptor completely reverses established clonal anergy in CD4(+) T lymphocytes via an interleukin-2-dependent mechanism, Kenneth D. Bishop, John E. Harris, John P. Mordes, Dale L. Greiner, Aldo A. Rossini, Michael P. Czech, and Nancy E. Phillips

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CPEB regulation of human cellular senescence, energy metabolism, and p53 mRNA translation, David M. Burns and Joel D. Richter

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Defining the Importance of Fatty Acid Metabolism in Maintaining Adipocyte Function: A Dissertation, Jennifer L. Christianson

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Ceramide kinase regulates phospholipase C and phosphatidylinositol 4, 5, bisphosphate in phototransduction, Ujjaini Dasgupta, Takeshi Bamba, Salvatore Chiantia, Pusha Karim, Ahmad N. Abou Tayoun, Ikuko Yonamine, Satinder S. Rawat, Raghavendra Pralhada Rao, Kunio Nagashima, Eiichiro Fukusaki, Vishwajeet Puri, Patrick J. Dolph, Petra Schwille, Jairaj K. Acharya, and Usha Acharya

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Induction of hepatitis by JNK-mediated expression of TNF-alpha, Madhumita Das, Guadalupe Sabio, Feng Jiang, Mercedes Rincon, Richard Flavell, and Roger J. Davis

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Protein kinase D1-mediated phosphorylation and subcellular localization of beta-catenin, Cheng Du, Meena Jaggi, Chuanyou Zhang, and Kethandapatti Balaji

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Determinants flanking the CD4 binding loop modulate macrophage tropism of human immunodeficiency virus type 1 R5 envelopes, Maria J. Duenas-Decamp, Paul J. Peters, Dennis R. Burton, and Paul R. Clapham

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Characterization of mouse IFT complex B, John A. Follit, Fenghui Xu, Brian T. Keady, and Gregory J. Pazour

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Role of WFS1 in Regulating Endoplasmic Reticulum Stress Signaling: A Dissertation, Sonya G. Fonseca

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Endoplasmic reticulum stress in beta-cells and development of diabetes, Sonya G. Fonseca, Mark Burcin, Jesper Gromada, and Fumihiko Urano

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CD4+ regulatory T cells require CTLA-4 for the maintenance of systemic tolerance, Randall H. Friedline, David S. Brown, Hai Nguyen, Hardy Kornfeld, Jinhee Lee, Yi Zhang, Mark Appleby, Sandy D. Der, Joonsoo Kang, and Cynthia A. Chambers

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A Multiparameter Network Reveals Extensive Divergence Between C. elegans bHLH Transcription Factors: A Dissertation, Christian A. Grove

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A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors, Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, and Albertha J. M. Walhout

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A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans, Christopher M. Hammell, Xantha Karp, and Victor R. Ambros

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nhl-2 Modulates microRNA activity in Caenorhabditis elegans, Christopher M. Hammell, Isabella Lubin, Peter R. Boag, T. Keith Blackwell, and Victor R. Ambros

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Selective interaction between Trf3 and Taf3 required for early development and hematopoiesis, Daniel O. Hart, Manas K. Santra, Tamal Raha, and Michael R. Green

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Transmembrane passage of hydrophobic compounds through a protein channel wall, Elizabeth M. Hearn, Dimki R. Patel, Bryan W. Lepore, Mridhu Indic, and Bert Van den Berg

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Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets, Xin Hong, Molly Hammell, Victor R. Ambros, and Stephen M. Cohen

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Distinct patterns of dendritic cell cytokine release stimulated by fungal beta-glucans and toll-like receptor agonists, Haibin Huang, Gary R. Ostroff, Chrono K. Lee, Jennifer P. Wang, Charles A. Specht, and Stuart M. Levitz

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Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer, Steven A. Johnsen, Cenap Gungor, Tanja Prenzel, Sabine Riethdorf, Lutz Riethdorf, Naoko Taniguchi-Ishigaki, Thomas Rau, Baris Tursun, J. David Furlow, Guido Sauter, Martin Scheffner, Klaus Pantel, Frank Gannon, and Ingolf Bach

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Valproate, a mood stabilizer, induces WFS1 expression and modulates its interaction with ER stress protein GRP94, Chihiro Kakiuchi, Shinsuke Ishigaki, Christine M. Oslowski, Sonya G. Fonseca, Tadafumi Kato, and Fumihiko Urano

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The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters, Carla Andrea Klattenhoff, Hualin Xi, Chengjian Li, Soohyun Lee, Jia Xu, Jaspreet S. Khurana, Fan Zhang, Nadine Schultz, Birgit S. Koppetsch, Anetta Nowosielska, Herve Seitz, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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Phosphorylation of Ewing's sarcoma protein (EWS) and EWS-Fli1 in response to DNA damage, Iva V. Klevernic, Simon Morton, Roger J. Davis, and Philip Cohen

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Nutrient stress activates inflammation and reduces glucose metabolism by suppressing AMP-activated protein kinase in the heart, Hwi Jin Ko, Zhiyou Zhang, Dae Young Jung, John Y. Jun, Zhexi Ma, Kelly E. Jones, Sook Y. Chan, and Jason K. Kim

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The Chlamydomonas reinhardtii BBSome is an IFT cargo required for export of specific signaling proteins from flagella, Karl-Ferdinand Lechtreck, Eric C. Johnson, Tsuyoshi Sakai, Deborah A. Cochran, Bryan A. Ballif, John Rush, Gregory J. Pazour, Mitsuo Ikebe, and George B. Witman (The Journal of cell biology)

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Suppression of Ca2+ syntillas increases spontaneous exocytosis in mouse adrenal chromaffin cells, Jason J. Lefkowitz, Kevin E. Fogarty, Lawrence M. Lifshitz, Karl D. Bellve, Richard A. Tuft, Ronghua ZhuGe, John V. Walsh Jr., and Valerie De Crescenzo

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Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies, Chengjian Li, Vasily V. Vagin, Soohyun Lee, Jia Xu, Shengmei Ma, Hualin Xi, Herve Seitz, Michael D. Horwich, Monika Syrzycka, Barry M. Honda, Ellen L. W. Kittler, Maria L. Zapp, Carla Andrea Klattenhoff, Nadine Schultz, William E. Theurkauf, Zhiping Weng, and Phillip D. Zamore

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Role of MKK3-p38 MAPK signalling in the development of type 2 diabetes and renal injury in obese db/db mice, A. K. H. Lim, David J. Nikolic-Paterson, F. Y. Ma, E. Ozols, M. C. Thomas, Richard Flavell, Roger J. Davis, and Greg H. Tesch

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Cytoplasmic polyadenylation and cytoplasmic polyadenylation element-dependent mRNA regulation are involved in Xenopus retinal axon development, Andrew C. Lin, Chin Lik Tan, Chien-Ling Lin, Laure Strochlic, Yi-Shuian Huang, Joel D. Richter, and Christine E. Holt

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Delineating the C. elegans MicroRNA Regulatory Network: A Dissertation, Natalia Julia Martinez

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The interplay between transcription factors and microRNAs in genome-scale regulatory networks, Natalia Julia Martinez and Albertha J. M. Walhout

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p53-independent apoptosis limits DNA damage-induced aneuploidy, Laura M. McNamee and Michael H. Brodsky

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Low-cost HIV-1 diagnosis and quantification in dried blood spots by real time PCR, Nishaki Mehta, Sonia Trzmielina, Bareng A. S. Nonyane, Melissa N. Eliot, Rongheng Lin, Andrea S. Foulkes, Kristina McNeal, Arthur Ammann, Vindu Eulalievyolo, John L. Sullivan, Katherine Luzuriaga, and Mohan Somasundaran

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TLR agonists prevent the establishment of allogeneic hematopoietic chimerism in mice treated with costimulation blockade, David M. Miller, Thomas B. Thornley, Todd Pearson, Annie J. Kruger, Masahiro Yamazaki, Leonard D. Shultz, Raymond M. Welsh, Michael A. Brehm, Aldo A. Rossini, and Dale L. Greiner

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Mcl-1 integrates the opposing actions of signaling pathways that mediate survival and apoptosis, Caroline Morel, Scott M. Carlson, Forest M. White, and Roger J. Davis

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Converging pathways in lifespan regulation., Sri Devi Narasimhan, Kelvin Yen, and Heidi A. Tissenbaum

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Annotating the human genome with Disease Ontology, John D. Osborne, Jared M. Flatow, Michelle Holko, Simon M. Lin, Warren A. Kibbe, Lihua Julie Zhu, Maria I. Danila, Gang Feng, and Rex L. Chisholm

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Nuclear Dynamics of a Broken Chromosome: A Dissertation, Pranav O. Oza

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Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery, Pranav O. Oza, Sue L. Jaspersen, Adriana Miele, Job Dekker, and Craig L. Peterson

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A PP2A regulatory subunit regulates C. elegans insulin/IGF-1 signaling by modulating AKT-1 phosphorylation., Srivatsan Padmanabhan, Arnab Mukhopadhyay, Sri Devi Narasimhan, Gregory J. Tesz, Michael P. Czech, and Heidi A. Tissenbaum

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Epigenetic silencing of the RASSF1A tumor suppressor gene through HOXB3-mediated induction of DNMT3B expression, Rajendra Kumar Palakurthy, Narendra Wajapeyee, Manas K. Santra, Claude Gazin, Ling Lin, Stephane Gobeil, and Michael R. Green

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The Chlamydomonas Flagellum as a Model for Human Ciliary Disease, Gregory J. Pazour and George B. Witman (The Chlamydomonas Sourcebook)

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The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors, John S. Reece-Hoyes, Bart Deplancke, M. Inmaculada Barrasa, Julia Hatzold, Ryan B. Smit, H. Efsun Arda, Patricia A. Pope, Jeb Gaudet, Barbara Conradt, and Albertha J. M. Walhout

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Making synaptic plasticity and memory last: mechanisms of translational regulation, Joel D. Richter and Eric Klann

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Regulation of the immune response by stress-activated protein kinases, Mercedes Rincon and Roger J. Davis

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Prevention of steatosis by hepatic JNK1, Guadalupe Sabio, Julie Cavanagh-Kyros, Hwi Jin Ko, Dae Young Jung, Susan Gray, John Y. Jun, Tamera Barrett, Alfonso Mora, Jason K. Kim, and Roger J. Davis

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F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage, Manas K. Santra, Narendra Wajapeyee, and Michael R. Green

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Transcription and signalling pathways involved in BCR-ABL-mediated misregulation of 24p3 and 24p3R, Zhi Sheng, Shu-Zong Wang, and Michael R. Green

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Chemokine signaling guides regional patterning of the first embryonic artery, Arndt F. Siekmann, Clive Standley, Kevin E. Fogarty, Scot A. Wolfe, and Nathan D. Lawson

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Recombinational Repair of a Chromosomal DNA Double Strand Break: A Dissertation, Manisha Sinha

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Dynein light intermediate chain 1 is required for progress through the spindle assembly checkpoint, Mylavarapu V. S. Sivaram, Thomas Wadzinski, Sambra D. Redick, Tapas K. Manna, and Stephen J. Doxsey

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Signal transduction cross talk mediated by Jun N-terminal kinase-interacting protein and insulin receptor substrate scaffold protein complexes, Claire L. Standen, Norman J. Kennedy, Richard A. Flavell, and Roger J. Davis

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Basic science summary, Mario Stevenson

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The osteogenic transcription factor runx2 controls genes involved in sterol/steroid metabolism, including CYP11A1 in osteoblasts, Nadiya M. Teplyuk, Ying Zhang, Yang Lou, John R. Hawse, Mohammad Q. Hassan, Viktor Teplyuk, Jitesh Pratap, Mario Galindo, Janet L. Stein, Gary S. Stein, Jane B. Lian, and Andre J. Van Wijnen (Molecular endocrinology (Baltimore, Md.))

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The tail binds to the head-neck domain, inhibiting ATPase activity of myosin VIIA, Nobuhisa Umeki, HyunSuk Jung, Shinya Watanabe, Tsuyoshi Sakai, Xiang-Dong Li, Reiko Ikebe, Roger W. Craig, and Mitsuo Ikebe

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DNA damage-induced cell death is enhanced by progression through mitosis, Hanne Varmark, Cynthia A. Sparks, Joshua J. Nordberg, Birgit S. Koppetsch, and William E. Theurkauf

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Efficacy of IGFBP7 for treatment of metastatic melanoma and other cancers in mouse models and human cell lines, Narendra Wajapeyee, Varun Kapoor, Meera Mahalingam, and Michael R. Green

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Getting an edge on human disease, Albertha J. M. Walhout

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Identification of a protein, G0S2, that lacks Bcl-2 homology domains and interacts with and antagonizes Bcl-2, Christian Welch, Manas K. Santra, Wissal El-Assaad, Xiaochun Zhu, Wade E. Huber, Richard A. Keys, Jose G. Teodoro, and Michael R. Green

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Nuclear localization of p38 MAPK in response to DNA damage, C. David Wood, Tina Thornton, Guadalupe Sabio, Roger J. Davis, and Mercedes Rincon

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Systematic analysis of dynamic miRNA-target interactions during C. elegans development, Liang Zhang, Molly Hammell, Brian A. Kudlow, Victor R. Ambros, and Min Han

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Nuclear factor-kappaB-mediated transforming growth factor-beta-induced expression of vimentin is an independent predictor of biochemical recurrence after radical prostatectomy, Qiang Zhang, Brian T. Helfand, Thomas L. Jang, Lihua Julie Zhu, Lin Chen, Ximing J. Yang, James Kozlowski, Norm Smith, Shilajit Kundu, Guangyu Yang, Adekunle A. Raji, Borko Javonovic, Michael Pins, Paul Lindholm, Yinglu Guo, William J. Catalona, and Chung Lee

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Identification of the Function of the Vpx Protein of Primate Lentiviruses: A Dissertation, Xiaonan Zhu

Publications from 2008

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Cell-nonautonomous function of ceramidase in photoreceptor homeostasis, Jairaj K. Acharya, Ujjaini Dasgupta, Satinder S. Rawat, Changqing Yuan, Parthena D. Sanxaridis, Ikuko Yonamine, Pusha Karim, Kunio Nagashima, Michael H. Brodsky, Susan Tsunoda, and Usha Acharya

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Jun N-terminal kinase 1 regulates epithelial-to-mesenchymal transition induced by TGF-beta1, John F. Alcorn, Amy S. Guala, Jos van der Velden, Brian McElhinney, Charles G. Irvin, Roger J. Davis, and Yvonne M.W. Janssen-Heininger

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The evolution of our thinking about microRNAs, Victor R. Ambros

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PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans, Pedro J. Batista, J. Graham Ruby, Julie M. Claycomb, H. Rosaria Chiang, Noah Fahlgren, Kristin D. Kasschau, Daniel A. Chaves, Weifeng Gu, Jessica J. Vasale, Shenghua Duan, Darryl Conte, Shujun Luo, Gary P. Schroth, James C. Carrington, David P. Bartel, and Craig C. Mello

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Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes, Mugdha Bhati, Christopher Lee, Amy L. Nancarrow, Mihwa Lee, Vanessa J. Craig, Ingolf Bach, J. Mitchell Guss, Joel P. Mackay, and Jacqueline M. Matthews

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The role of nitric oxide and the unfolded protein response in cytokine-induced beta-cell death, Kari T. Chambers, Julie A. Unverferth, Sarah M. Weber, Ronald C. Wek, Fumihiko Urano, and John A. Corbett

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H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment, Menno P. Creyghton, Styliani Markoulaki, Stuart S. Levine, Jacob Hanna, Michael A. Lodato, Ky Sha, Richard A. Young, Rudolf Jaenisch, and Laurie A. Boyer

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Natural resistance of human immunodeficiency virus type 1 to the CD4bs antibody b12 conferred by a glycan and an arginine residue close to the CD4 binding loop, Maria J. Duenas-Decamp, Paul J. Peters, Dennis R. Burton, and Paul R. Clapham

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The DNA replication checkpoint directly regulates MBF-dependent G1/S transcription, Chaitali Dutta, Prasanta K. Patel, Adam Rosebrock, Anna Oliva, Janet K. Leatherwood, and Nicholas R. Rhind

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Targeting dendritic cell signaling to regulate the response to immunization, David Escors, Luciene Lopes, Rongtuan Lin, John Hiscott, Shizuo Akira, Roger J. Davis, and Mary K. Collins

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Prostate carcinoma and radiation therapy: therapeutic treatment resistance and strategies for targeted therapeutic intervention, Thomas J. Fitzgerald, Tao Wang, Hira Lal Goel, Jiayi Huang, Gary S. Stein, Jane B. Lian, Roger J. Davis, Stephen J. Doxsey, Kethandapatti C. Balaji, Jesse N. Aronowitz, and Lucia R. Languino

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Roles for Histones H4 Serine 1 Phosphorylation in DNA Double Strand Break Repair and Chromatin Compaction: A Dissertation, Melissa Anne Foley

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The Golgin GMAP210/TRIP11 anchors IFT20 to the Golgi complex, John A. Follit, Jovenal T. San Agustin, Fenghui Xu, Julie A. Jonassen, Rajeev Samtani, Cecilia W. Lo, and Gregory J. Pazour

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MKK3 signalling plays an essential role in leukocyte-mediated pancreatic injury in the multiple low-dose streptozotocin model, Kyoichi Fukuda, Greg H. Tesch, Felicia Y. Yap, Josephine M. Forbes, Richard Flavell, Roger J. Davis, and David J. Nikolic-Paterson

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The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome, Yutao Fu, Manisha Sinha, Craig L. Peterson, and Zhiping Weng

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Pruritus in polycythemia vera is associated with a lower risk of arterial thrombosis, Naseema Gangat, Jacob J. Strand, Terra L. Lasho, Chin-Yang Li, Animesh Dev Pardanani, and Ayalew Tefferi

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Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells, Megha Ghildiyal, Herve Seitz, Michael D. Horwich, Chengjian Li, Tingting Du, Soohyun Lee, Jia Xu, Ellen L. W. Kittler, Maria L. Zapp, Zhiping Weng, and Phillip D. Zamore

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Safety and immunogenicity of recombinant poxvirus HIV-1 vaccines in young adults on highly active antiretroviral therapy, Thomas C. Greenough, Coleen K. Cunningham, Petronella Muresan, Margaret M. McManus, Deborah Persaud, Terry Fenton, Piers Barker, Aditya Gaur, Dennis Panicali, John L. Sullivan, and Katherine Luzuriaga

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On the dynamics of acute EBV infection and the pathogenesis of infectious mononucleosis, Vey Hadinoto, Michael Shapiro, Thomas C. Greenough, John L. Sullivan, Katherine Luzuriaga, and David A. Thorley-Lawson

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Adipocyte Insulin-Mediated Glucose Transport: The Role of Myosin 1c, and a Method for in vivo Investigation: A Dissertation, G. Nana Hagan

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A Rictor-Myo1c complex participates in dynamic cortical actin events in 3T3-L1 adipocytes, G. Nana Hagan, Yenshou Lin, Mark A. Magnuson, Joseph Avruch, and Michael P. Czech

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mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts, Molly Hammell, Dang Long, Liang Zhang, Andrew Lee, C. Steven Carmack, Min Han, Ye Ding, and Victor R. Ambros

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A genetically encoded fluorescent sensor of ERK activity, Christopher D. Harvey, Anka G. Ehrhardt, Cristina Arrigo Cellurale, Haining Zhong, Ryohei Yasuda, Roger J. Davis, and Karel Svoboda

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Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation, Elizabeth M. Hearn, Dimki R. Patel, and Bert Van den Berg

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Risk factors for leukemic transformation in patients with primary myelofibrosis, Jocelin Huang, Chin-Yang Li, Ruben A. Mesa, Wentling Wu, Curtis A. Hanson, Animesh Dev Pardanani, and Ayalew Tefferi

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Multisite phosphorylation regulates Bim stability and apoptotic activity, Anette Hubner, Tamera Barrett, Richard Flavell, and Roger J. Davis

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c-Jun N-terminal kinase 1 interacts with and negatively regulates Wnt/beta-catenin signaling through GSK3beta pathway, Dong Hu, Wenfeng Fang, Anjia Han, Lindsay Gallagher, Roger J. Davis, Bin Xiong, and Wancai Yang

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Isolation of neuronal chromatin from brain tissue, Yan Jiang, Anouch Matevossian, Hsien-Sung Huang, Juerg R. Straubhaar, and Schahram Akbarian

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Deletion of IFT20 in the mouse kidney causes misorientation of the mitotic spindle and cystic kidney disease., Julie A. Jonassen, Jovenal T. San Agustin, John A. Follit, and Gregory J. Pazour

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Analysis of CPEB Family Protein Member CPEB4 Function in Mammalian Neurons: A Dissertation, Ming-Chung Kan

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Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast, Tommy Kaplan, Chih Long Liu, Judith A. Erkmann, John Holik, Michael Grunstein, Paul D. Kaufman, Nir Friedman, and Oliver J. Rando