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 2011

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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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Integrating atom-based and residue-based scoring functions for protein-protein docking, Thom Vreven, Howook Hwang, and Zhiping Weng

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A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression, Kevin C. Wang, Yul W. Yang, Bo Liu, Amartya Sanyal, Ryan Corces-Zimmerman, Yong Chen, Bryan R. Lajoie, Angeline Protacio, Ryan A. Flynn, Rajnish A. Gupta, Joanna Wysocka, Ming Lei, Job Dekker, Jill A. Helms, and Howard Y. Chang

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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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MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression, Jun Xie, Qing Xie, Hongwei Zhang, Stefan L. Ameres, Jui-Hung Hung, Qin Su, Ran He, Xin Mu, Seemin Seher Ahmed, Soyeon Park, Hiroki Kato, Chengjian Li, Christian Mueller, Craig C. Mello, Zhiping Weng, Terence R. Flotte, Phillip D. Zamore, and Guangping Gao

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Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Ozlem Yildirim, Ruowang Li, Jui-Hung Hung, Poshen B. Chen, Xianjun Dong, Ly-Sha Ee, Zhiping Weng, Oliver J. Rando, and Thomas G. Fazzio

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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

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Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains, Zhao Zhang, Jia Xu, Birgit S. Koppetsch, Jie Wang, Cindy Tipping, Shengmei Ma, Zhiping Weng, William E. Theurkauf, and Phillip D. Zamore

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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Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones, Akbar Ali, G. S. Kiran Kumar Reddy, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Celia A. Schiffer, and Tariq M. Rana

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Riding in silence: a little snowboarding, a lot of small RNAs, Stefan L. Ameres and Ryuya Fukunaga

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Target RNA-directed trimming and tailing of small silencing RNAs, Stefan L. Ameres, Michael D. Horwich, Jui-Hung Hung, Jia Xu, Megha Ghildiyal, Zhiping Weng, and Phillip D. Zamore

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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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Welcome to Silence, David C. Baulcombe and Phillip D. Zamore

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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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Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals, Benjamin R. Carone, Lucas Fauquier, Naomi Habib, Jeremy Shea, Caroline E. Hart, Ruowang Li, Christoph Bock, Chengjian Li, Hongcang Gu, Phillip D. Zamore, Alexander Meissner, Zhiping Weng, Hans A. Hofmann, Nir Friedman, and Oliver J. Rando

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A simple method for improving the specificity of anti-methyl histone antibodies, Caroline M. Connor, Iris Cheung, Andrew Simon, Mira Jakovcevski, Zhiping Weng, and Schahram Akbarian

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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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Specificity and membrane partitioning of Grsp1 signaling complexes with Grp1 family Arf exchange factors, Jonathan P. DiNitto, Meng-Tse Lee, Andrew W. Malaby, and David G. Lambright

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Gamma-secretase inhibitors enhance temozolomide treatment of human gliomas by inhibiting neurosphere repopulation and xenograft recurrence, Candace A. Gilbert, Marie-Claire Daou, Richard P. Moser, and Alonzo H. Ross

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In vivo imaging of labelled endogenous beta-actin mRNA during nucleocytoplasmic transport, David Grunwald and Robert H. Singer

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Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins, Soo-Jin Han, Jianhong Hu, Brian G. Pierce, Zhiping Weng, and Rolf Renne

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Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins., Ronald D. Hills, Sagar V. Kathuria, Louise A. Wallace, Iain J. Day, Charles L. Brooks, and C. Robert Matthews

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RNA processing and export, Sami Hocine, Robert H. Singer, and David Grunwald

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Identification of functional modules that correlate with phenotypic difference: the influence of network topology, Jui-Hung Hung, Troy W. Whitfield, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, and Charles Delisi

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Protein-protein docking benchmark version 4.0, Howook Hwang, Thom Vreven, Joel Janin, and Zhiping Weng

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Performance of ZDOCK and ZRANK in CAPRI rounds 13-19, Howook Hwang, Thom Vreven, Brian G. Pierce, Jui-Hung Hung, and Zhiping Weng

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Disulfide-Reduced ALS Variants of Cu, Zn Superoxide Dismutase Exhibit Increased Populations of Unfolded Species., Can Kayatekin, Jill A. Zitzewitz, and C. Robert Matthews

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Structure and function of nematode RNA-binding proteins, Ebru Kaymak, LiangMeng Wee, and Sean P. Ryder

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RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast, Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, and Oliver J. Rando

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Sequence features that drive human promoter function and tissue specificity, Jane M. Landolin, David S. Johnson, Nathan D. Trinklein, Shelley Force Aldred, Catherine Medina, Hennady P. Shulha, Zhiping Weng, and Richard M. Myers

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Myogenic microRNA expression requires ATP-dependent chromatin remodeling enzyme function, Chandrashekara Mallappa, Brian T. Nasipak, Letitiah Etheridge, Elliot J. Androphy, Stephen N. Jones, Charles G. Sagerstrom, Yasuyuki Ohkawa, and Anthony N. Imbalzano

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Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays, Ben McNally, Alon Singer, Zhiliang Yu, Yingjie Sun, Zhiping Weng, and Amit Meller

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Clinically relevant doses of chemotherapy agents reversibly block formation of glioblastoma neurospheres, Alicia M. Mihaliak, Candace A. Gilbert, Li Li, Marie-Claire Daou, Richard P. Moser, Andrew Reeves, Brent H. Cochran, and Alonzo H. Ross

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Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells, Zarmik Moqtaderi, Jie Wang, Debasish Raha, Robert J. White, Michael Snyder, Zhiping Weng, and Kevin Struhl

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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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Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease, Nevra Ozer, Celia A. Schiffer, and Turkan Haliloglu

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Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains, Brian G. Pierce, Jaafar N. Haidar, Yong Yu, and Zhiping Weng

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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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Bi-specific MHC heterodimers for characterization of cross-reactive T cells, Zu T. Shen, Michael A. Brehm, Keith A. Daniels, Alexander B. Sigalov, Liisa K. Selin, Raymond M. Welsh, and Lawrence J. Stern

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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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Cotranslational and posttranslational N-glycosylation of polypeptides by distinct mammalian OST isoforms, Catalina Ruiz-Canada, Daniel J. Kelleher, and Reid Gilmore

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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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Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study, Thomas Dange, David Grunwald, Antje Grunwald, Reiner Peters, and Ulrich Kubitscheck

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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

Probing intranuclear environments at the single-molecule level, David Grunwald, Robert M Martin, Volker Buschmann, David P Bazett-Jones, Heinrich Leonhardt, Ulrich Kubitscheck, and M Cristina Cardoso

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Calibrating excitation light fluxes for quantitative light microscopy in cell biology, David Grunwald, Shailesh M. Shenoy, Sean Burke, and Robert H. Singer

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Cell biology of mRNA decay, David Grunwald, Robert H. Singer, and Kevin Czaplinski

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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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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