This collection showcases the books, journal articles, book reviews, and other publications and presentations written by faculty and researchers of the Department of Biochemistry and Molecular Pharmacology.

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Publications from 2008

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DnaC inactivation in Escherichia coli K-12 induces the SOS response and expression of nucleotide biosynthesis genes, Anders Lobner-Olesen, Monika Slominska-Wojewodzka, Flemming G. Hansen, and Martin G. Marinus

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Unique Asn-linked oligosaccharides of the human pathogen Entamoeba histolytica, Paula Magnelli, John F. Cipollo, Daniel M. Ratner, Jike Cui, Daniel J. Kelleher, Reid Gilmore, Catherine E. Costello, Phillips W. Robbins, and John Samuelson

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Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells, Rajini R. Mudhasani, Zhiqing Zhu, Gyorgy Hutvagner, Christine M. Eischen, Stephen Lyle, Lisa L. Hall, Jeanne B. Lawrence, Anthony N. Imbalzano, and Stephen N. Jones

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Small-molecule inhibition of HIV-1 Vif, Robin S. Nathans, Hong Cao, Natalia Sharova, Akbar Ali, Mark E. Sharkey, Ruzena Stranska, Mario Stevenson, and Tariq M. Rana

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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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The Hsk1(Cdc7) replication kinase regulates origin efficiency, Prasanta K. Patel, Naveen Kommajosyula, Adam Rosebrock, Aaron Bensimon, Janet K. Leatherwood, John Bechhoefer, and Nicholas R. Rhind

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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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As functional nuclear actin comes into view, is it globular, filamentous, or both, Thoru Pederson

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Turning a PAGE: the overnight sensation of SDS-polyacrylamide gel electrophoresis, Thoru Pederson

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A construct with fluorescent indicators for conditional expression of miRNA, Linghua Qiu, Hongyan Wang, Xugang Xia, Hongxia Zhou, and Zuoshang Xu

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KCNE peptides differently affect voltage sensor equilibrium and equilibration rates in KCNQ1 K+ channels, Jessica M. Rocheleau and William R. Kobertz

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Combating Drug Resistance – Identifying Resilient Molecular Targets and Robust Drugs, Celia A. Schiffer

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Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA strands in flies, Herve Seitz, Megha Ghildiyal, and Phillip D. Zamore

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Sec6p anchors the assembled exocyst complex at sites of secretion, Jennifer A. Songer and Mary Munson

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Conversion of red fluorescent protein into a bright blue probe, Oksana M. Subach, Illia S. Gundorov, Masami Yoshimura, Fedor V. Subach, Jinghang Zhang, David Grunwald, Ekaterina A. Souslova, Dmitriy M. Chudakov, and Vladislav V. Verkhusha

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NMR analysis of partially folded states and persistent structure in the alpha subunit of tryptophan synthase: implications for the equilibrium folding mechanism of a 29-kDa TIM barrel protein, Ramakrishna Vadrevu, Ying Wu, and C. Robert Matthews

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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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Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease, Michael D. Altman, Ellen A. Nalivaika, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Bruce Tidor

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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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The evolution of N-glycan-dependent endoplasmic reticulum quality control factors for glycoprotein folding and degradation, Sulagna Banerjee, Prashanth Vishwanath, Jike Cui, Daniel J. Kelleher, Reid Gilmore, Phillips W. Robbins, and John Samuelson

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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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Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157:H7, Kenneth Geno Campellone, Andrew J. Roe, Anders Lobner-Olesen, Kenan C. Murphy, Loranne Magoun, Michael John Brady, Arthur Donohue-Rolfe, Saul Tzipori, David L. Gally, John M. Leong, and Martin G. Marinus

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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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Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease, Sripriya Chellappan, Visvaldas Kairys, Miguel X. Fernandes, Celia A. Schiffer, and Michael K. Gilson

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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis, Sripriya Chellappan, G. S. Kiran Kumar Reddy, Akbar Ali, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Visvaldas Kairys, Miguel X. Fernandes, Michael D. Altman, Bruce Tidor, Tariq M. Rana, Celia A. Schiffer, and Michael K. Gilson

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Competition between Ski and CREB-binding protein for binding to Smad proteins in transforming growth factor-beta signaling, Weijun Chen, Suvana S. Lam, Hema Srinath, Celia A. Schiffer, William E. Royer, and Kai Lin

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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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Therapeutic silencing of mutant huntingtin with siRNA attenuates striatal and cortical neuropathology and behavioral deficits, Marian DiFiglia, Miguel Sena-Esteves, Kathryn O. Chase, Ellen Sapp, Edith L. Pfister, Meghan B. Sass, Jennifer Yoder, P. Reeves, Rajendra K. Pandey, Kallanthottathil G. Rajeev, Muthiah Manoharan, Dinah W. Y. Sah, Phillip D. Zamore, and Neil Aronin

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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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Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1, Klaus Forstemann, Michael D. Horwich, LiangMeng Wee, Yukihide Tomari, and Phillip D. Zamore

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Topology and sequence in the folding of a TIM barrel protein: global analysis highlights partitioning between transient off-pathway and stable on-pathway folding intermediates in the complex folding mechanism of a (betaalpha)8 barrel of unknown function from B. subtilis, William R. Forsyth, Osman Bilsel, Zhenyu Gu, and C. Robert Matthews

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Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease, Jennifer E. Foulkes-Murzycki, Walter Robert Peter Scott, and Celia A. Schiffer

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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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Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Go model simulation, Zhenyu Gu, Maithreyi K. Rao, William R. Forsyth, John M. Finke, and C. Robert Matthews

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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 Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC, Michael D. Horwich, Chengjian Li, Christian B. Matranga, Vasily V. Vagin, Gwen Farley, Peng Wang, and Phillip D. Zamore

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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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ATP-Dependent Sugar Transport Complexity in Human Erythrocytes, Jeffry M. Leitch and Anthony Carruthers

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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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N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure, Yumi Mitsuya, Mark A. Winters, W. Jeffrey Fessel, Soo-Yon Rhee, Leo Hurley, Michael Horberg, Celia A. Schiffer, Andrew R. Zolopa, and Robert W. Shafer

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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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Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157:H7, Kenan C. Murphy, Jennifer M. Ritchie, Matthew K. Waldor, Anders Lobner-Olesen, and Martin G. Marinus

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Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease, Madhavi N. L. Nalam, Anik Peeters, Tim H. M. Jonckers, Inge Dierynck, and Celia A. Schiffer

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DNA mismatch repair-induced double-strand breaks, Anetta Nowosielska and Martin G. Marinus

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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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Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres, G. S. Kiran Kumar Reddy, Akbar Ali, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Robin S. Nathans, Celia A. Schiffer, and Tariq M. Rana

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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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Single-molecule tracking in eukaryotic cell nuclei, Jan Peter Siebrasse, David Grunwald, and Ulrich Kubitscheck

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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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Supply and Demand in Cerebral Energy Metabolism: the Role of Nutrient Transporters, Ian A. Simpson, Anthony Carruthers, and Susan J. Vannucci

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Distinct Roles for Two G{alpha} G Interfaces in Cell Polarity Control by a Yeast Heterotrimeric G Protein, Shelly Catherine Strickfaden and Peter M. Pryciak

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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

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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

Publications from 2006

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Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima G. Anjum, Madhavi N. L. Nalam, Celia A. Schiffer, and Tariq M. Rana

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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

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Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase, Klaus A. Becker, Prachi N. Ghule, Jaclyn A. Therrien, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Establishment of histone gene regulation and cell cycle checkpoint control in human embryonic stem cells, Klaus A. Becker, Janet L. Stein, Jane B. Lian, Andre J. Van Wijnen, and Gary S. Stein

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H2AX chromatin structures and their response to DNA damage revealed by 4Pi microscopy, Jorg Bewersdorf, Brian Thomas Bennett, and Kendall L. Knight