The Program in Biochemistry & Molecular Pharmacology is an academic program of the Graduate School of Biomedical Sciences (GSBS) at the University of Massachusetts Medical School. The program offers graduate study and research focused in the areas of molecular, cellular and regulatory biochemistry; molecular biophysics; chemical biology; and structural biology. This collection showcases publications and presentations authored by students in this program.

Attention GSBS Biochemistry & Molecular Pharmacology students: To submit your publications, go to GSBS Student Publications and click on Submit Research in the left sidebar. You’ll need to log in or create a free account. If you have the article's PubMed ID, submission is very easy. Enter the PubMed ID and information from PubMed will be used to populate the submission form. Questions? Contact Lisa Palmer.

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Publications from 2009

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A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay, Sarah E. Cole, Frederick J. laRiviere, Christopher N. Merrikh, and Melissa J. Moore

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Cellular redistribution of Rad51 in response to DNA damage: novel role for Rad51C., Otto S. Gildemeister, Jay M. Sage, and Kendall L. Knight

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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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Discovery of a novel activator of KCNQ1-KCNE1 K channel complexes., Karen Mruk and William R. Kobertz

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InAKTivation of insulin/IGF-1 signaling by dephosphorylation., Sri Devi Narasimhan, Arnab Mukhopadhyay, and Heidi A. Tissenbaum

Publications from 2008

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Modulation of N-type Calcium Channel Activity by G-proteins and Protein Kinase C, Curtis F. Barrett and Ann R. Rittenhouse

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Amphetamine-induced decreases in dopamine transporter surface expression are protein kinase C-independent, Ekaterina Boudanova, Deanna M. Navaroli, and Haley E. Melikian

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IL-13 is required for eosinophil entry into the lung during respiratory syncytial virus vaccine-enhanced disease, Elaine M. Castilow, David K. Meyerholz, and Steven Michael Varga

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Thunderclap headache and normal computed tomographic results: value of cerebrospinal fluid analysis, Stefan A. Dupont, Eelco F. M. Wijdicks, Edward M. Manno, and Alejandro A. Rabinstein

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RNA target specificity of the embryonic cell fate determinant POS-1, Brian M. Farley, John M. Pagano, and Sean P. Ryder

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The Tec kinases Itk and Rlk regulate NKT cell maturation, cytokine production, and survival, Martin Felices and Leslie J. Berg

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A structured light-based system for scanning subcutaneous tumors in laboratory animals, Ibrahim Cem Girit, Maria Jure-Kunkel, and Kim W. McIntyre

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Transplantation survival is maintained by granzyme B+ regulatory cells and adaptive regulatory T cells, David C. Gondek, Victor Devries, Elizabeth C. Nowak, Li-Fan Lu, Kathryn A. Bennett, Zachary Aaron Scott, and Randolph J. Noelle

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Current in vitro kinase assay technologies: the quest for a universal format, Yong Jia, Christopher M. Quinn, Silvia Kwak, and Robert Vincent Talanian

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Zinc binding modulates the entire folding free energy surface of human Cu,Zn superoxide dismutase., Can Kayatekin, Jill A. Zitzewitz, and C. Robert Matthews

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The pluripotency regulator Oct4: a role in somatic stem cells, Christopher Joachim Lengner, G. Grant Welstead, and Rudolf Jaenisch

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Programmed death ligand 1 regulates a critical checkpoint for autoimmune myocarditis and pneumonitis in MRL mice, Julie Ann Lucas, Julia Menke, Whitney A. Rabacal, Frederick J. Schoen, Arlene H. Sharpe, and Vicki R. Kelley

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Immunogenicity of DNA vaccines in humans: it takes two to tango, Shan Lu

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Beyond IP3: roles for higher order inositol phosphates in immune cell signaling, Andrew Todd Miller, Philip P. Chamberlain, and Michael P. Cooke

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Role of innate immunity in transplantation tolerance., David M. Miller, Aldo A. Rossini, and Dale L. Greiner

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TLR agonists abrogate co-stimulation blockade-induced mixed chimerism and transplantation tolerance., David M. Miller, Thomas B. Thornley, Todd Pearson, Masahiro Yamazaki, Michael A. Brehm, Aldo A. Rossini, and Dale L. Greiner

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Defects in skin gamma delta T cell function contribute to delayed wound repair in rapamycin-treated mice, Robyn E. Mills, Kristen R. Taylor, Katie Podshivalova, Dianne B. McKay, and Julie Marie Jameson

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Vitamin D control of gene expression: temporal and spatial parameters for organization of the regulatory machinery, Martin A. Montecino, Gary S. Stein, Janet L. Stein, Jane B. Lian, Andre J. Van Wijnen, Loreto Carvallo, Sylvain Marcellini, Fernando Cruzat, and Gloria Arriagada

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The number of respiratory syncytial virus (RSV)-specific memory CD8 T cells in the lung is critical for their ability to inhibit RSV vaccine-enhanced pulmonary eosinophilia, Matthew R. Olson, Stacey M. Hartwig, and Steven Michael Varga

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Model for the peptide-free conformation of class II MHC proteins, Corrie A. Painter, Anthony Cruz, Gustavo E. Lopez, Lawrence J. Stern, and Zarixia Zavala-Ruiz

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Non-obese diabetic-recombination activating gene-1 (NOD-Rag1 null) interleukin (IL)-2 receptor common gamma chain (IL2r gamma null) null mice: a radioresistant model for human lymphohaematopoietic engraftment, Todd Pearson, Leonard D. Shultz, David M. Miller, Marie A. King, Joseph Laning, William Fodor, Amy Cuthbert, Lisa M. Burzenski, Bruce Gott, Bonnie L. Lyons, Oded Foreman, Aldo A. Rossini, and Dale L. Greiner

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A protocolized approach to identify and manage hyperglycemia in a pediatric critical care unit, Catherine M. Preissig, Inger Hansen, Pei-Ling Roerig, and Mark R. Rigby

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Utilization of Fc receptors as a mucosal vaccine strategy against an intracellular bacterium, Francisella tularensis, Deepak B. Rawool, Constantine Bitsaktsis, Ying Li, Diane R. Gosselin, Yili Lin, Nitin V. Kurkure, Dennis W. Metzger, and Edmund J. Gosselin

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High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection, Alleluiah Rutebemberwa, Stuart C. Ray, Jacqueline A. Astemborski, Jordana Levine, Lin Liu, Kimberly A. Dowd, Shalyn C. Clute, Changyu Wang, Alan J. Korman, Alessandro Sette, John Sidney, Drew M. Pardoll, and Andrea L. Cox

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Puromycin-sensitive aminopeptidase limits MHC class I presentation in dendritic cells but does not affect CD8 T cell responses during viral infections, Charles Fenton Towne, Ian A. York, Joost J. Neijssen, Margaret L. Karow, Andrew J. Murphy, David M. Valenzuela, George D. Yancopoulos, Jacques J. Neefjes, and Kenneth L. Rock

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Class II major histocompatibility complex tetramer staining: progress, problems, and prospects, Sabrina S. Vollers and Lawrence J. Stern

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Attenuated inflammatory responses in hemochromatosis reveal a role for iron in the regulation of macrophage cytokine translation, Lijian Wang, Erin E. Johnson, Hai Ning Shi, W. Allan Walker, Marianne Wessling-Resnick, and Bobby J. Cherayil

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Proliferative expansion and acquisition of effector activity by memory CD4+ T cells in the lungs following pulmonary virus infection, Erika L. Wissinger, Whitney W. Stevens, Steven Michael Varga, and Thomas J. Braciale

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A DNA vaccine prime followed by a liposome-encapsulated protein boost confers enhanced mucosal immune responses and protection, Kejian Yang, Barbara J. Whalen, Rebecca S Tirabassi, Liisa K. Selin, Tatyana S. Levchenko, Vladimir P. Torchilin, Edward H. Kislauskis, and Dennis L. Guberski

Publications from 2007

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Coordinated regulation of Toll-like receptor and NOD2 signaling by K63-linked polyubiquitin chains, Derek W. Abbott, Yibin Yang, Jessica E. Hutti, Swetha Madhavarapu, Michelle A. Kelliher, and Lewis C. Cantley

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Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein, Munehito Arai, Elena Kondrashkina, Can Kayatekin, C. Robert Matthews, Masahiro Iwakura, and Osman Bilsel

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Phosphorylation at serine 208 of the 1alpha,25-dihydroxy Vitamin D3 receptor modulates the interaction with transcriptional coactivators, Gloria Arriagada, Roberto Paredes, Juan Olate, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Janet L. Stein, Sergio Onate, and Martin A. Montecino

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Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity, Jared R. Auclair, Karin M. Green, Shivender Shandilya, James E. Evans, Mohan Somasundaran, and Celia A. Schiffer

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Structural basis of GLUT1 inhibition by cytoplasmic ATP, David M. Blodgett, Julie Kelley De Zutter, Kara B. Levine, Pusha Karim, and Anthony Carruthers

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Enterohaemorrhagic and enteropathogenic Escherichia coli Tir proteins trigger a common Nck-independent actin assembly pathway, Michael John Brady, Kenneth Geno Campellone, Megha Ghildiyal, and John M. Leong

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Crystallization and preliminary X-ray analysis of a domain in the Runx2 transcription factor that interacts with the 1alpha,25 dihydroxy vitamin D3 receptor, Carola Bruna, Gloria Arriagada, Jane B. Lian, Gary S. Stein, Marta Bunster, Jose Martinez-Oyanedel, and Martin A. Montecino

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The 1alpha,25-dihydroxy Vitamin D3 receptor preferentially recruits the coactivator SRC-1 during up-regulation of the osteocalcin gene, Loreto Carvallo, Berta Henriquez, Juan Olate, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Sergio Onate, Janet L. Stein, and Martin A. Montecino

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Cancer targeting using tumor suppressor genes, Sunil Chada, Kerstin B. Menander, Dora B. Bocangel, Jack A. Roth, and Rajagopal Ramesh

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Quantitative analysis of RNA-mediated protein-protein interactions in living cells by FRET, Ya-Lin Chiu, Hong Cao, and Tariq M. Rana

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Mutations in the stalk of the measles virus hemagglutinin protein decrease fusion but do not interfere with virus-specific interaction with the homologous fusion protein, Elizabeth Ann Corey and Ronald M. Iorio

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Altered selectivity of parathyroid hormone (PTH) and PTH-related protein (PTHrP) for distinct conformations of the PTH/PTHrP receptor, Thomas Dean, Jean-Pierre Vilardaga, John T. Potts, and Thomas James Gardella

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TALE-family homeodomain proteins regulate endodermal sonic hedgehog expression and pattern the anterior endoderm, Philip J. Diiorio, Kristen Alexa, Seong-Kyu Choe, Letitiah Etheridge, and Charles G. Sagerstrom

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Identification of tau stem loop RNA stabilizers, Christine Patricia Donahue, Jake Ni, Eriks Rozners, Marcie A. Glicksman, and Michael S. Wolfe

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YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA, Shuyun Dong, Chunfang Li, Daniel Zenklusen, Robert H. Singer, Allan Jacobson, and Feng He

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Tec kinases in T cell and mast cell signaling, Martin Felices, Markus Falk, Yoko Kosaka, and Leslie J. Berg

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Endoplasmic reticulum stress signaling in pancreatic beta-cells, Sonya G. Fonseca, Kathryn L. Lipson, and Fumihiko Urano

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The human Rad51 K133A mutant is functional for DNA double-strand break repair in human cells, Anthony L. Forget, Matthew S. Loftus, Dharia A. McGrew, Brian Thomas Bennett, and Kendall L. Knight

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Microscopic methods for measuring the elasticity of gel substrates for cell culture: microspheres, microindenters, and atomic force microscopy, Margo Tilley Frey, Adam Engler, Dennis E. Discher, Juliet Lee, and Yu-Li Wang

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ubiquilin antagonizes presenilin and promotes neurodegeneration in Drosophila, Atish Ganguly, R. M. Renny Feldman, and Ming Guo

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Cell cycle dependent phosphorylation and subnuclear organization of the histone gene regulator p220(NPAT) in human embryonic stem cells, Prachi N. Ghule, Klaus A. Becker, J. Wade Harper, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Danger-free autoimmune disease in Aire-deficient mice, Daniel H. D. Gray, Irina Catrinel Gavanescu, Christophe Benoist, and Diane Mathis

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Differential effects of EGF and TGF-beta1 on fibroblast activity in fibrin-based tissue equivalents, Jaime L. Grouf, Angela M. Throm, Jenna L. Balestrini, Katie A. Bush, and Kristen L. Billiar

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A chromatin landmark and transcription initiation at most promoters in human cells, Matthew G. Guenther, Stuart S. Levine, Laurie A. Boyer, Rudolf Jaenisch, and Richard A. Young

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Chromatin remodeling by SWI/SNF results in nucleosome mobilization to preferential positions in the rat osteocalcin gene promoter, Jose L. Gutierrez, Roberto Paredes, Fernando Cruzat, David A. Hill, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Janet L. Stein, Anthony N. Imbalzano, and Martin A. Montecino

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HOXA10 controls osteoblastogenesis by directly activating bone regulatory and phenotypic genes, Mohammad Q. Hassan, Rahul S. Tare, Suk Hee Lee, Matthew Mandeville, Brian Weiner, Martin A. Montecino, Andre J. Van Wijnen, Janet L. Stein, Gary S. Stein, and Jane B. Lian

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Evolutionarily conserved structural and functional roles of the FYVE domain, Akira Hayakawa, Susan J. Hayes, Deborah Marie Leonard, David G. Lambright, and Silvia Corvera

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In and out of the ER: protein folding, quality control, degradation, and related human diseases, Daniel N. Hebert and Maurizio Molinari

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Multispectral quantification of tissue types in a RIF-1 tumor model with histological validation. Part I, Erica C. Henning, Chieko Azuma, Christopher H. Sotak, and Karl G. Helmer

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Multispectral tissue characterization in a RIF-1 tumor model: monitoring the ADC and T2 responses to single-dose radiotherapy. Part II, Erica C. Henning, Chieko Azuma, Christopher H. Sotak, and Karl G. Helmer

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Verification of enhancement of the CSF space, not parenchyma, in acute stroke patients with early blood-brain barrier disruption, Erica C. Henning, Lawrence L. Latour, and Steven Warach

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CD40-CD40 ligand interaction between dendritic cells and CD8+ T cells is needed to stimulate maximal T cell responses in the absence of CD4+ T cell help, Maria Genevieve H. Hernandez, Lianjun Shen, and Kenneth L. Rock

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The transcription factor XBP-1 is essential for the development and survival of dendritic cells, Neal N. Iwakoshi, Marc Pypaert, and Laurie H. Glimcher

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A novel alloantigen-specific CD8+PD1+ regulatory T cell induced by ICOS-B7h blockade in vivo, Atsushi Izawa, Kazuhiro Yamaura, Monica J. Albin, Mollie Jurewicz, Katsunori Tanaka, Michael R. Clarkson, Takuya Ueno, Antje Habicht, Gordon J. Freeman, Hideo Yagita, Reza Abdi, Todd Pearson, Dale L. Greiner, Mohamed H. Sayegh, and Nader Najafian

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The nucleolar Net1/Cfi1-related protein Dnt1 antagonizes the septation initiation network in fission yeast, Quan-Wen Jin, Samriddha Ray, Sung Hugh Choi, and Dannel McCollum

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Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an ATR/Chk2 DNA damage response, Carla Andrea Klattenhoff, Diana P. Bratu, Nadine Schultz, Birgit S. Koppetsch, Heather A. Cook, and William E. Theurkauf

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SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster, Sharmistha Kundu, Peter J. Horn, and Craig L. Peterson

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Programmed death-1 (PD-1) defines a transient and dysfunctional oligoclonal T cell population in acute homeostatic proliferation, Sue-Jane Lin, Craig D. Peacock, Kapil Bahl, and Raymond M. Welsh

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The interactome of the histone gene regulatory factor HiNF-P suggests novel cell cycle related roles in transcriptional control and RNA processing, Angela Miele, Ricardo F. Medina, Andre J. Van Wijnen, Gary S. Stein, and Janet L. Stein

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Loss of centrosome integrity induces p38-p53-p21-dependent G1-S arrest, Keith Mikule, Benedicte Delaval, Philipp Kaldis, Agata Jurczyk, Polla J. Hergert, and Stephen J. Doxsey

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Nucleosome organization and targeting of SWI/SNF chromatin-remodeling complexes: contributions of the DNA sequence, Martin A. Montecino, Janet L. Stein, Gary S. Stein, Jane B. Lian, Andre J. Van Wijnen, Fernando Cruzat, Soraya E. Gutierrez, Juan Olate, Sylvain Marcellini, and Jose L. Gutierrez

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A derivatized scorpion toxin reveals the functional output of heteromeric KCNQ1-KCNE K+ channel complexes, Trevor J. Morin and William R. Kobertz

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Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5, John M. Pagano Jr., Brian M. Farley, Lisa M. McCoig, and Sean P. Ryder

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The alternative reading frame tumor suppressor antagonizes hypoxia-induced cancer cell migration via interaction with the COOH-terminal binding protein corepressor, Seema Paliwal, Ramesh C. Kovi, Bharath D. Nath, Ya-Wen Chen, Brian C. Lewis, and Steven R. Grossman

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Development of Ad-mda7/IL-24-resistant lung cancer cell lines, Abujiang Pataer, Sunil Chada, Jack A. Roth, Kelly K. Hunt, and Stephen G. Swisher

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Bioactive food components that enhance gammadelta T cell function may play a role in cancer prevention, Susan S. Percival, Jack F. Bukowski, and John A. Milner

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Progress, paradox, and potential: parathyroid hormone research over five decades, John T. Potts and Thomas James Gardella

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Effects of vpu start-codon mutations on human immunodeficiency virus type 1 replication in macrophages, Kathryn H. Richards and Paul R. Clapham

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Nitrite does not provide additional protection to thrombolysis in a rat model of stroke with delayed reperfusion, Bawarjan Schatlo, Erica C. Henning, Ryszard M. Pluta, Lawrence L. Latour, Nahal Golpayegani, Marsha J. Merrill, Naomi Lewin, Yong Chen, and Edward H. Oldfield

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Zebrafish ae2.2 encodes a second slc4a2 anion exchanger, Boris E. Shmukler, Jeffrey S. Clark, Ann Hsu, David H. Vandorpe, Andrew K. Stewart, Christine E. Kurschat, Seong-Kyu Choe, Yi Zhou, Julio D. Amigo, Barry H. Paw, and Seth L. Alper

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Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germ line by nuclear run-on, Alla A. Sigova, Vasily V. Vagin, and Phillip D. Zamore

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grp (chk1) replication-checkpoint mutations and DNA damage trigger a Chk2-dependent block at the Drosophila midblastula transition, Saeko Takada, Seongae Kwak, Birgit S. Koppetsch, and William E. Theurkauf

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Type 1 IFN mediates cross-talk between innate and adaptive immunity that abrogates transplantation tolerance, Thomas B. Thornley, Nancy E. Phillips, Britte C. Beaudette-Zlatanova, Thomas G. Markees, Kapil Bahl, Michael A. Brehm, Leonard D. Shultz, Evelyn A. Kurt-Jones, John P. Mordes, Raymond M. Welsh, Aldo A. Rossini, and Dale L. Greiner

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Serum sickness following treatment with rituximab, Derrick James Todd and Simon M. Helfgott

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Analysis of the role of bleomycin hydrolase in antigen presentation and the generation of CD8 T cell responses, Charles Fenton Towne, Ian A. York, Levi B. Watkin, John S. Lazo, and Kenneth L. Rock

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Translational unmasking of Emi2 directs cytostatic factor arrest in meiosis II, Jeffrey J. Tung, Kiran Padmanabhan, David V. Hansen, Joel D. Richter, and Peter K. Jackson

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Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells, Prasanna Venkatraman, Tina T. Nguyen, Matthieu Sainlos, Osman Bilsel, Sriram Chitta, Barbara Imperiali, and Lawrence J. Stern

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TRAIL is a novel antiviral protein against dengue virus, Rajas V. Warke, Katherine J. Martin, Krisanthi Giaya, Sunil K. Shaw, Alan L. Rothman, and Irene Bosch

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A tightly packed hydrophobic cluster directs the formation of an off-pathway sub-millisecond folding intermediate in the alpha subunit of tryptophan synthase, a TIM barrel protein, Ying Wu, Ramakrishna Vadrevu, Sagar V. Kathuria, Xiaoyan Yang, and C. Robert Matthews

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Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement, Xiaofang Yang, Roser Zaurin, Miguel Beato, and Craig L. Peterson

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Long-range side-chain-main-chain interactions play crucial roles in stabilizing the (betaalpha)8 barrel motif of the alpha subunit of tryptophan synthase, Xiaoyan Yang, Ramakrishna Vadrevu, Ying Wu, and C. Robert Matthews

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Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism, Yi Zhou, Deanna M. Navaroli, Metewo Selase Enuameh, and Craig T. Martin

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Finding Plk3, Wendy Cherie Zimmerman and Raymond L. Erikson

Publications from 2006

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The Tec family tyrosine kinases Itk and Rlk regulate the development of conventional CD8+ T cells, Luana O. Atherly, Julie Ann Lucas, Martin Felices, Catherine C. Yin, Steven L. Reiner, and Leslie J. Berg

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Reconstitution of Runx2/Cbfa1-null cells identifies a requirement for BMP2 signaling through a Runx2 functional domain during osteoblast differentiation, Jong-Sup Bae, Soraya E. Gutierrez, Radhika Narla, Jitesh Pratap, Rajitha Devados, Andre J. Van Wijnen, Janet L. Stein, Gary S. Stein, Jane B. Lian, and Amjad Javed

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IFN-induced attrition of CD8 T cells in the presence or absence of cognate antigen during the early stages of viral infections, Kapil Bahl, Sung-Kwon Kim, Claudia Calcagno, Dario Ghersi, Roberto Puzone, Franco Celada, Liisa K. Selin, and Raymond M. Welsh