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 2010

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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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Maternal and zygotic aldh1a2 activity is required for pancreas development in zebrafish, Kristen Alexa, Seong-Kyu Choe, Nicolas Hirsch, Letitiah Etheridge, Elizabeth Laver, and Charles G. Sagerstrom

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Viral protease inhibitors, Jeffrey Anderson, Celia A. Schiffer, Sook-Kyung Lee, and Ronald I. Swanstrom

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MicroRNAs: regulating a change of heart, Kurt G. Barringhaus and Phillip D. Zamore

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Immunofluorescence imaging of DNA damage response proteins: optimizing protocols for super-resolution microscopy., Brian Thomas Bennett, Jorg Bewersdorf, and Kendall L. Knight

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Alpha- and Beta-Monosaccharide Transport in Human Erythrocytes, Anthony Carruthers and Jeffry M. Leitch

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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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The role of specific checkpoint-induced S-phase transcripts in resistance to replicative stress, Chaitali Dutta and Nicholas R. Rhind

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Long-term statin therapy and CSF cholesterol levels: implications for Alzheimer's disease, Barbara A. Evans, James E. Evans, Stephen P. Baker, Kevin J. Kane, Joan M. Swearer, Douglas A. Hinerfeld, Richard J. Caselli, Ekaterina Rogaeva, Peter St. George-Hyslop, Majaz Moonis, and Daniel A. Pollen

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Small silencing RNAs: an expanding universe, Megha Ghildiyal and Phillip D. Zamore

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Cancer stem cells: cell culture, markers, and targets for new therapies, Candace A. Gilbert and Alonzo H. Ross

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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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Mutations and Cell Defenses, Otto S. Gildemeister, Jay M. Sage, and Kendall L. Knight

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Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC, Jaafar N. Haidar, Brian G. Pierce, Yong Yu, Weiwei Tong, Michael Li, and Zhiping Weng

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Additivity in the analysis and design of HIV protease inhibitors, Robert N. Jorissen, G. S. Kiran Kumar Reddy, Akbar Ali, Michael D. Altman, Sripriya Chellappan, Saima G. Anjum, Bruce Tidor, Celia A. Schiffer, Tariq M. Rana, and Michael K. Gilson

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Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis, Visvaldas Kairys, Michael K. Gilson, Viney Lather, Celia A. Schiffer, and Miguel X. Fernandes

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Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance, Madhavi Kolli, Eric Stawiski, Colombe Chappey, and Celia A. Schiffer

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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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A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP, Sarah M. McWhirter, Roman Barbalat, Kathryn M. Monroe, Mary F. Fontana, Mamoru Hyodo, Nathalie T. Joncker, Ken J. Ishii, Shizuo Akira, Marco Colonna, Zhiliang Cheng, Katherine A. Fitzgerald, Yoshihiro Hayakawa, and Russell E. Vance

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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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New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors, Madhavi N. L. Nalam and Celia A. Schiffer

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Five siRNAs targeting three SNPs may provide therapy for three-quarters of Huntington's disease patients, Edith L. Pfister, Lori A. Kennington, Juerg R. Straubhaar, Sujata Wagh, Wanzhou Liu, Marian DiFiglia, Bernhard Landwehrmeyer, Jean-Paul Vonsattel, Phillip D. Zamore, and Neil Aronin

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Regulation of DNA replication by the S-phase DNA damage checkpoint., Nicholas Adrian Willis and Nicholas R. Rhind

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Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins, Xiaoyan Yang, Sagar V. Kathuria, Ramakrishna Vadrevu, and C. Robert Matthews

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Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling, Liqun Yu, Joana E. Coelho, Xiaoling Zhang, Yutao Fu, Abigail Tillman, Ulas Karaoz, Bertil B. Fredholm, Zhiping Weng, and Jiang-Fan Chen

Publications from 2008

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HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants, Michael D. Altman, Akbar Ali, G. S. Kiran Kumar Reddy, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Sripriya Chellappan, Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson, Celia A. Schiffer, Tariq M. Rana, and Bruce Tidor

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Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6., Rajintha M. Bandaranayake, Moses Prabu-Jeyabalan, Junko Kakizawa, Wataru Sugiura, and Celia A. Schiffer

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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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Analysis of Glucose Transporter Topology and Structural Dynamics., David M. Blodgett, Christopher A. Graybill, and Anthony Carruthers

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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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Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5, Weijun Chen, Suvana S. Lam, Hema Srinath, Zhaozhao Jiang, John J. Correia, Celia A. Schiffer, Katherine A. Fitzgerald, Kai Lin, and William E. Royer

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Contribution of Ser386 and Ser396 to activation of interferon regulatory factor 3, Weijun Chen, Hema Srinath, Suvana S. Lam, Celia A. Schiffer, William E. Royer, and Kai Lin

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Potent RNAi by short RNA triggers, Chia-ying Chu and Tariq M. Rana

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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 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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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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Sir2 mediates apoptosis through JNK-dependent pathways in Drosophila, Anthony J. Griswold, Karen T. Chang, Alexander Peter Runko, Melanie A. Knight, and Kyung-Tai Min

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Design and delivery of antisense oligonucleotides to block microRNA function in cultured Drosophila and human cells, Michael D. Horwich and Phillip D. Zamore

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Protein-protein docking benchmark version 3.0, Howook Hwang, Brian G. Pierce, Julian Mintseris, Joel Janin, and Zhiping Weng

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An interaction between the SRP receptor and the translocon is critical during cotranslational protein translocation, Ying Jiang, Zhiliang Cheng, Elisabet C. Mandon, and Reid Gilmore

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Kinetic traps in the folding of beta alpha-repeat proteins: CheY initially misfolds before accessing the native conformation., Sagar V. Kathuria, Iain J. Day, Louise A. Wallace, and C. Robert Matthews

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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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Evidence for Interindividual Heterogeneity in the Glucose Gradient across the Human Red Blood Cell Membrane and its Relationship to Hemoglobin Glycation, Paramjit K. Khera, Clinton H. Joiner, Anthony Carruthers, Christopher J. Lindsell, Eric P. Smith, Robert S. Franco, Yancey R. Holmes, and Robert M. Cohen

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Quantitative analysis of single nucleotide polymorphisms within copy number variation, Soohyun Lee, Simon Kasif, Zhiping Weng, and Charles R. Cantor

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Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir, Eric Lefebvre and Celia A. Schiffer

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Linking SNPs to CAG repeat length in Huntington's disease patients, Wanzhao Liu, Lori A. Kennington, H. Diana Rosas, Steven M. Hersch, Jang-Ho Cha, Phillip D. Zamore, and Neil Aronin

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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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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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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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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