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 2013

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Evaluating the Role of Macrocycles in the Susceptibility of Hepatitis C Virus NS3/4A Protease Inhibitors to Drug Resistance, Akbar Ali, Cihan Aydin, Reinhold Gildemeister, Keith P. Romano, Hong Cao, Aysegul Ozen, Djade Soumana, Alicia Newton, Christos J. Petropoulos, Wei Huang, and Celia A. Schiffer

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Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray micro-beam, Rita Graceffa, Robert P. Nobrega, Raul Barrea, Sagar V. Kathuria, Srinivas Chakravarthy, Osman Bilsel, and Thomas Irving

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Cognitive impairment and self-care in heart failure, Alexandra M. Hajduk, Stephenie C. Lemon, David D. McManus, Darleen M. Lessard, Jerry H. Gurwitz, Frederick A. Spencer, Robert J. Goldberg, and Jane S. Saczynski

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Latent effects of Hsp90 mutants revealed at reduced expression levels, Li Jiang, Parul Mishra, Ryan T. Hietpas, Konstantin B. Zeldovich, and Daniel N. A. Bolon

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Advances in turbulent mixing techniques to study microsecond protein folding reactions, Sagar V. Kathuria, Alexander Chan, Rita Graceffa, Robert P. Nobrega, C. Robert Matthews, Thomas C. Irving, Blair Perot, and Osman Bilsel

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UPF1 is Crucial for the Infectivity of Human Immunodeficiency Virus type 1 Progeny Virions, Anna Kristina Serquina, Suman R. Das, Elena Popova, Ogooluwa A. Ojelabi, Christian K. Roy, and Heinrich G. Gottlinger

Publications from 2012

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POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster, Brian M. Farley and Sean P. Ryder

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An optimized two-finger archive for ZFN-mediated gene targeting, Ankit Gupta, Amy L. Rayla, Abirami Lakshmanan, Scot A. Wolfe, Ryan G. Christensen, and Gary D. Stormo

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Fitness analyses of all possible point mutations for regions of genes in yeast, Ryan T. Hietpas, Benjamin P. Roscoe, Li Jiang, and Daniel N. A. Bolon

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Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease, Nancy M. King, Moses Prabu-Jeyabalan, Rajintha M. Bandaranayake, Madhavi N. L. Nalam, Ellen A. Nalivaika, Aysegul Ozen, Turkan Haliloglu, Nese Kurt Yilmaz, and Celia A. Schiffer

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Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease, Sook-Kyung Lee, Marc Potempa, Madhavi Kolli, Aysegul Ozen, Celia A. Schiffer, and Ronald I. Swanstrom

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Structural insights into neuronal K+ channel-calmodulin complexes, Karen Mruk, Shivender Shandilya, Robert O. Blaustein, Celia A. Schiffer, and William R. Kobertz

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Immune responses in cystic fibrosis: are they intrinsically defective?, Dmitry Ratner and Christian Mueller

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The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors, Keith P. Romano, Akbar Ali, Cihan Aydin, Djade Soumana, Aysegul Ozen, Laura M. Deveau, Casey Silver, Hong Cao, Alicia Newton, Christos J. Petropoulos, Wei Huang, and Celia A. Schiffer

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Sequence Determinants of GLUT1-mediated Accelerated-exchange Transport: Analysis by Homology-Scanning Mutagenesis, Sabrina S. Vollers and Anthony Carruthers

Publications from 2011

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Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease, Elif Sarinay Cenik, Ryuya Fukunaga, Gang Lu, Robert Dutcher, Yeming Wang, Traci M. Tanaka Hall, and Phillip D. Zamore

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Argonaute proteins, Elif Sarinay Cenik and Phillip D. Zamore

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A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity, Ryan G. Christensen, Ankit Gupta, Zheng Zuo, Lawrence A. Schriefer, Scot A. Wolfe, and Gary D. Stormo

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Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Ankit Gupta, Xiangdong Meng, Lihua Julie Zhu, Nathan D. Lawson, and Scot A. Wolfe

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Experimental illumination of a fitness landscape, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. A. Bolon

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FBF represses the Cip/Kip cell-cycle inhibitor CKI-2 to promote self-renewal of germline stem cells in C. elegans, Irene Kalchhauser, Brian M. Farley, Sandra Pauli, Sean P. Ryder, and Rafal Ciosk

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Structural insights into early folding events using continuous-flow time-resolved SAXS, Sagar V. Kathuria, Liang Guo, Rita Graceffa, Raul Barrea, R. Paul Nobrega, C. Robert Matthews, Tom Irving, and Osman Bilsel

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Xenopus laevis oocytes infected with multi-drug-resistant bacteria: implications for electrical recordings, Denice O'Connell, Karen Mruk, Jessica M. Rocheleau, and William R. Kobertz

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Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope, Aysegul Ozen, Turkan Haliloglu, and Celia A. Schiffer

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Conformational lability in the class II MHC 3-10 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange, Corrie A. Painter, Maria P. Negroni, Kathy A. Kellersberger, Zarixia Zavala-Ruiz, James E. Evans, and Lawrence J. Stern

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Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease, Keith P. Romano, Jennifer M. Laine, Laura M. Deveau, Hong Cao, Francesca Massi, and Celia A. Schiffer

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MicroRNA Expression Data Reveals a Signature of Kidney Damage following Ischemia Reperfusion Injury, Michael D. Shapiro, Jessamyn Bagley, Jeff Latz, Jonathan G. Godwin, Xupeng Ge, Stefan G. Tullius, and John Iacomini

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Translocation channel gating kinetics balances protein translocation efficiency with signal sequence recognition fidelity, Steven F. Trueman, Elisabet C. Mandon, and Reid Gilmore

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A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1, Jane E. Wright, Dimos Gaidatzis, Mathias Senften, Brian M. Farley, Eric Westhof, Sean P. Ryder, and Rafal Ciosk

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Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells, Nancy R. Zearfoss, Carina C. Clingman, Brian M. Farley, Lisa M. McCoig, and Sean P. Ryder

Publications from 2010

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Molecular Basis for Drug Resistance in HIV-1 Protease, Akbar Ali, Rajintha M. Bandaranayake, Yufeng Cai, Nancy M. King, Madhavi Kolli, Seema Mittal, Jennifer E. Foulkes-Murzycki, Madhavi N. L. Nalam, Ellen A. Nalivaika, Aysegul Ozen, Moses Prabu-Jeyabalan, Kelly Thayer, and Celia A. Schiffer

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The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways, Rajintha M. Bandaranayake, Madhavi Kolli, Nancy M. King, Ellen A. Nalivaika, Annie Heroux, Junko Kakizawa, Wataru Sugiura, and Celia A. Schiffer

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Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV, Yufeng Cai and Celia A. Schiffer

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Acute Modulation of Sugar Transport in Brain Capillary Endothelial Cell Cultures during Activation of the Metabolic Stress Pathway, Anthony J. Cura and Anthony Carruthers

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Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance, Madhavi N. L. Nalam, Akbar Ali, Michael D. Altman, G. S. Kiran Kumar Reddy, Sripriya Chellappan, Visvaldas Kairys, Aysegul Ozen, Hong Cao, Michael K. Gilson, Bruce Tidor, Tariq M. Rana, and Celia A. Schiffer

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Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding, Keith P. Romano, Akbar Ali, William E. Royer, and Celia A. Schiffer

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Discovery of a novel function for human Rad51: maintenance of the mitochondrial genome, Jay M. Sage, Otto S. Gildemeister, and Kendall L. Knight

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Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces., Shivender Shandilya, Madhavi N. L. Nalam, Ellen A. Nalivaika, Phillip J. Gross, Johnathan C. Valesano, Keisuke Shindo, Ming Li, Mary Munson, William E. Royer, Elena Harjes, Takahide Kono, Hiroshi Matsuo, Reuben S. Harris, Mohan Somasundaran, and Celia A. Schiffer

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Therapeutic targeting of C-terminal binding protein in human cancer, Michael W. Straza, Seema Paliwal, Ramesh C. Kovi, Barur R. Rajeshkumar, Peter Trenh, Daniel Parker, Giles F. Whalen, Stephen Lyle, Celia A. Schiffer, and Steven R. Grossman

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

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

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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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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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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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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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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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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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