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 2014

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Inhibiting AMPylation: a novel screen to identify the first small molecule inhibitors of protein AMPylation, Daniel M. Lewallen, Anju Sreelatha, Venkatasubramanian Dharmarajan, Franck Madoux, Peter Chase, Patrick R. Griffin, Kim Orth, Peter Hodder, and Paul R. Thompson

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The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL, Zhonghan Li, Ti-Chun Chao, Kung-Yen Chang, Nianwei Lin, Veena S. Patil, Chisato Shimizu, Steven R. Head, Jane C. Burns, and Tariq M. Rana

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HIV type 1 (HIV-1) proviral reservoirs decay continuously under sustained virologic control in HIV-1-infected children who received early treatment, Katherine Luzuriaga, Barbara Tabak, Manuel Garber, Ya Hui Chen, Carrie Ziemniak, Margaret M. McManus, Danielle Murray, Matthew Strain, Douglas Richman, Tae-Wook Chun, Coleen K. Cunningham, and Deborah Persaud

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An Integrated Structural Mechanism for Relief of Autoinhibition and Membrane Targeting in Cytohesin Family Guanine Nucleotide Exchange Factors: A Dissertation, Andrew W. Malaby

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The middle X residue influences cotranslational N-glycosylation consensus site skipping, Heidi Malaby and William R. Kobertz

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Identification of Molecular Determinants that Shift Co- and Post-Translational N-Glycosylation Kinetics in Type I Transmembrane Peptides: A Dissertation, Heidi L. H. Malaby

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Angiomotins link F-actin architecture to Hippo pathway signaling, Sebastian Mana-Capelli, Murugan Paramasivam, Shubham Dutta, and Dannel McCollum

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Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme, Benjamin J. Manning and Craig L. Peterson

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Clot injection technique affects thrombolytic efficacy in a rat embolic stroke model: implications for translaboratory collaborations, Marilena Marinescu, James P. Bouley, Juyu Chueh, Marc Fisher, and Nils Henninger

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Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe, Takeshi Mizuguchi, Geoffrey Fudenberg, Sameet Mehta, Jon-Matthew Belton, Nitika Taneja, Hernan Diego Folco, Peter FitzGerald, Job Dekker, Leonid Mirny, Jemima Barrowman, and Shiv I. S. Grewal

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Angiogenic biomarkers for prediction of early preeclampsia onset in high-risk women, Tiffany A. Moore Simas, Sybil L. Crawford, Susanne Bathgate, Jing Yan, Laura Robidoux, Melissa J. Moore, and Sharon E. Maynard

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Cnidarian microRNAs frequently regulate targets by cleavage, Yehu Moran, David Fredman, Daniela Praher, Xin Zhiguo Li, Liang Meng Wee, Fabian Rentzsch, Phillip D. Zamore, Ulrich Technau, and Herve Seitz

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Calmodulation meta-analysis: Predicting calmodulin binding via canonical motif clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, and William R. Kobertz

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To protect or reject, Mary Munson

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Early Folding Biases in the Folding Free-Energy Surface of βα-Repeat Proteins: A Dissertation, Robert P. Nobrega

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Modulation of frustration in folding by sequence permutation, Robert P. Nobrega, Karunesh Arora, Sagar V. Kathuria, Rita Graceffa, Raul A. Barrea, Liang Guo, Srinivas Chakravarthy, Osman Bilsel, Thomas C. Irving, Charles L. Brooks 3rd, and C. Robert Matthews

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Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease, Aysegul Ozen, Kuan-Hung Lin, Nese Kurt Yilmaz, and Celia A. Schiffer

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ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers, Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, and Zhiping Weng

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Regulation of cyclin-substrate docking by a G1 arrest signaling pathway and the Cdk inhibitor Far1, Patricia A. Pope, Samyabrata Bhaduri, and Peter M. Pryciak

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Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease, Debra A. Ragland, Ellen A. Nalivaika, Madhavi N. L. Nalam, Kristina L. Prachanronarong, Hong Cao, Rajintha M. Bandaranayake, Yufeng Cai, Nese Kurt Yilmaz, and Celia A. Schiffer

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Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro, Nicholas Renzette, Daniel R. Caffrey, Konstantin B. Zeldovich, Ping Liu, Glen R. Gallagher, Daniel Aiello, Alyssa J. Porter, Evelyn A. Kurt-Jones, Daniel N. Bolon, Yu-Ping Poh, Jeffrey D. Jensen, Celia A. Schiffer, Timothy F. Kowalik, Robert W. Finberg, and Jennifer P. Wang

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Staufen1 senses overall transcript secondary structure to regulate translation, Emiliano P. Ricci, Alper Kucukural, Can Cenik, Blandine C. Mercier, Guramrit Singh, Erin E. Heyer, Ami Ashar-Patel, Lingtao Peng, and Melissa J. Moore

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Analyses of All Possible Point Mutations within a Protein Reveals Relationships between Function and Experimental Fitness: A Dissertation, Benjamin P. Roscoe

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Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast, Benjamin P. Roscoe and Daniel N. A. Bolon

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Putting the Pieces Together: Exons and piRNAs: A Dissertation, Christian K. Roy

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Using unnatural amino acid mutagenesis to probe the regulation of PRMT1., Heather L. Rust, Venkataraman Subramanian, Graham M. West, Douglas D. Young, Peter G. Schultz, and Paul R. Thompson

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Kinome-wide functional analysis highlights the role of cytoskeletal remodeling in somatic cell reprogramming, Kumi Sakurai, Indrani Talukdar, Veena S. Patil, Jason Dang, Zhonghan Li, Kung-Yen Chang, Chih-Chung Lu, Violaine Delorme-Walker, Celine Dermardirossian, Karen Anderson, Dorit Hanein, Chao-Shun Yang, Dongmei Wu, Yang Liu, and Tariq M. Rana

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Functions of FUS/TLS from DNA repair to stress response: implications for ALS, Reddy Ranjith Kumar Sama, Catherine L. Ward, and Daryl A. Bosco

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A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif, Shivender Shandilya, Markus-Frederik Bohn, and Celia A. Schiffer

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Regulation of histone H3K4 methylation in brain development and disease, Erica Shen, Hennady P. Shulha, Zhiping Weng, and Schahram Akbarian

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A novel role for protein arginine deiminase 4 in pluripotency: the emerging role of citrullinated histone H1 in cellular programming., Daniel J. Slade, Sachi Horibata, Scott A. Coonrod, and Paul R. Thompson

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Chemical and biological methods to detect post-translational modifications of arginine., Daniel J. Slade, Venkataraman Subramanian, Jakob Fuhrmann, and Paul R. Thompson

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Pluripotency: citrullination unravels stem cells, Daniel J. Slade, Venkataraman Subramanian, and Paul R. Thompson

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Neutrophil extracellular trap-derived enzymes oxidize high-density lipoprotein: an additional proatherogenic mechanism in systemic lupus erythematosus., Carolyne K. Smith, Anuradha Vivekanandan-Giri, Chongren Tang, Jason S. Knight, Anna Mathew, Robin L. Padilla, Brenda W. Gillespie, Carmelo Carmona-Rivera, Xiaodan Liu, Venkataraman Subramanian, Sarfaraz Hasni, Paul R. Thompson, Jay W. Heinecke, Rajiv Saran, Subramaniam Pennathur, and Mariana J. Kaplan

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Structural analysis of asunaprevir resistance in HCV NS3/4A protease, Djade Soumana, Akbar Ali, and Celia A. Schiffer

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Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies, Beatriz Trastoy, Joseph V. Lomino, Brian G. Pierce, Lester G. Carter, Sebastian Gunther, John P. Giddens, Greg A. Snyder, Thomas M. Weiss, Zhiping Weng, Lai-Xi Wang, and Eric J. Sundberg

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Modulation of calcium-induced cell death in human neural stem cells by the novel peptidylarginine deiminase-AIF pathway., Kin Pong U, Venkataraman Subramanian, Antony P. Nicholas, Paul R. Thompson, and Patrizia Ferretti

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Evaluating template-based and template-free protein-protein complex structure prediction, Thom Vreven, Howook Hwang, Brian G. Pierce, and Zhiping Weng

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Resistance to vemurafenib resulting from a novel mutation in the BRAFV600E kinase domain, Timothy R. Wagenaar, Leyuan Ma, Benjamin P. Roscoe, Sung Mi Park, Daniel N. Bolon, and Michael R. Green

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Widespread spinal cord transduction by intrathecal injection of rAAV delivers efficacious RNAi therapy for amyotrophic lateral sclerosis, Hongyan Wang, Bin Yang, Linghua Qiu, Chunxing Yang, Joshua Kramer, Qin Su, Yansu Guo, Robert H. Brown Jr., Guangping Gao, and Zuoshang Xu

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Protein arginine methyltransferase 5 catalyzes substrate dimethylation in a distributive fashion., Min Wang, Jakob Fuhrmann, and Paul R. Thompson

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The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs, Wei Wang, Mayu Yoshikawa, Bo W. Han, Natsuko Izumi, Yukihide Tomari, Zhiping Weng, and Phillip D. Zamore

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The Cellular Consequences of FUS/TLS Depletion: A Loss of Function Model for Amyotrophic Lateral Sclerosis: A Dissertation, Catherine L. Ward

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Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish, Steven E. Weicksel, Ankit Gupta, Denise A. Zannino, Scot A. Wolfe, and Charles G. Sagerstrom

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Global CNS transduction of adult mice by intravenously delivered rAAVrh.8 and rAAVrh.10 and nonhuman primates by rAAVrh.10, Bin Yang, Shaoyong Li, Hongyan Wang, Yansu Guo, Dominic J. Gessler, Chunyan Cao, Qin Su, Joshua Kramer, Li Zhong, Seemin Seher Ahmed, Hongwei Zhang, Ran He, Ronald C. Desrosiers, Robert H. Brown Jr., Zuoshang Xu, and Guangping Gao

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Molecular Landscape of Induced Reprogramming: A Dissertation, Chao-Shun Yang

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Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming, Chao-Shun Yang, Kung-Yen Chang, and Tariq M. Rana

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A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters, Ozlem Yildirim, Jui-Hung Hung, Ryan J. Cedeno, Zhiping Weng, Christopher J. Lengner, and Oliver J. Rando

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A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC(50) determination, Liusong Yin and Lawrence J. Stern

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Measurement of Peptide Binding to MHC Class II Molecules by Fluorescence Polarization, Liusong Yin and Lawrence J. Stern

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A conserved three-nucleotide core motif defines Musashi RNA binding specificity, Nancy R. Zearfoss, Laura M. Deveau, Carina C. Clingman, Eric Schmidt, Emily S. Johnson, Francesca Massi, and Sean P. Ryder

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Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin, Zhao Zhang, Birgit S. Koppetsch, Jie Wang, Cindy Tipping, Zhiping Weng, William E. Theurkauf, and Phillip D. Zamore

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The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing, Zhao Zhang, Jie Wang, Nadine McGinnis-Schultz, Fan Zhang, Swapnil S. Parhad, Shikui Tu, Thom Vreven, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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Modulation of HIV protease flexibility by the T80N mutation, Hao Zhou, Shangyang Li, John Badger, Ellen A. Nalivaika, Yufeng Cai, Jennifer E. Foulkes-Murzycki, Celia A. Schiffer, and Lee Makowski

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TEMP: a computational method for analyzing transposable element polymorphism in populations, Jiali Zhuang, Jie Wang, William E. Theurkauf, and Zhiping Weng

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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The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities, Cihan Aydin, Sourav Mukherjee, Alicia M. Hanson, David N. Frick, and Celia A. Schiffer

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In Vivo Delivery of RNAi by Reducible Interfering Nanoparticles (iNOPs), Huricha Baigude, Jie Su, Joshua McCarroll, and Tariq M. Rana

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Amyotrophic lateral sclerosis-linked FUS/TLS alters stress granule assembly and dynamics, Desiree M. Baron, Laura J. Kaushansky, Catherine L. Ward, Reddy Ranjith Kumar Sama, Ru-ju Chian, Kristin J. Boggio, Alexandre J. C. Quaresma, Jeffrey A. Nickerson, and Daryl A. Bosco

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A structural role for the PHP domain in E. coli DNA polymerase III, Tiago Barros, Joel Guenther, Brian Kelch, Jordan Anaya, Arjun Prabhakar, Mike O'Donnell, John Kuriyan, and Meindert H. Lamers

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The protein arginine deiminases: Structure, function, inhibition, and disease., Kevin L. Bicker and Paul R. Thompson

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Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain, Markus-Frederik Bohn, Shivender M. D. Shandilya, John S. Albin, Takahide Kouno, Brett D. Anderson, Rebecca M. McDougle, Michael A. Carpenter, Anurag Rathore, Leah Evans, Ahkillah N. Davis, JingYing Zhang, Yongjian Lu, Mohan Somasundaran, Hiroshi Matsuo, Reuben S. Harris, and Celia A. Schiffer

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Identification of human monoclonal antibodies specific for human SOD1 recognizing distinct epitopes and forms of SOD1, Teresa J. Broering, Hongyan Wang, Naomi K. Boatright, Yang Wang, Katherine Baptista, Gilda Shayan, Kerry A. Garrity, Can Kayatekin, Daryl A. Bosco, C. Robert Matthews, Donna M. Ambrosino, Zuoshang Xu, and Gregory J. Babcock

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A long noncoding RNA mediates both activation and repression of immune response genes, Susan Carpenter, Daniel Aiello, Maninjay K. Atianand, Emiliano P. Ricci, Pallavi Gandhi, Lisa L. Hall, Meg Byron, Brian G. Monks, Meabh Henry-Bezy, Jeanne B. Lawrence, Luke A. J. O'Neill, Melissa J. Moore, Daniel R. Caffrey, and Katherine A. Fitzgerald

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Development of a Novel Screening Strategy Designed to Discover a New Class of HIV Drugs, Nancy Cheng, Sook-Kyung Lee, P. Scott Donover, Mel Reichman, Celia A. Schiffer, Emily A. Hull-Ryde, Ronald I. Swanstrom, and William P. Janzen

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Gudu, an Armadillo repeat-containing protein, is required for spermatogenesis in Drosophila, Wei Cheng, Y. Tony Ip, and Zuoshang Xu

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Painting by numbers: increasing the parts list for chromatin domains, Hsiuyi V. Chen and Oliver J. Rando

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Hdac6 regulates Tip60-p400 function in stem cells, Poshen B. Chen, Jui-Hung Hung, Taylor L. Hickman, Andrew H. Coles, James F. Carey, Zhiping Weng, Feixia Chu, and Thomas G. Fazzio

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Human monoclonal antibody MBL-HCV1 delays HCV viral rebound following liver transplantation: a randomized controlled study, R. T. Chung, F. D. Gordon, M. P. Curry, T. D. Schiano, S. Emre, K. Corey, J. F. Markmann, M. Hertl, J. J. Pomposelli, E. A. Pomfret, S. Florman, M. Schilsky, Teresa J. Broering, Robert W. Finberg, Gyongyi Szabo, Phillip D. Zamore, U. Khettry, Gregory J. Babcock, Donna M. Ambrosino, Brett A. Leav, Mark Leney, H. L. Smith, and Deborah C. Molrine

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Expanding the Known DNA-binding Specificity of Homeodomains for Utility in Customizable Sequence-specific Nucleases: A Dissertation, Stephanie W. Chu

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Metabolite sensing in eukaryotic mRNA biology, Carina C. Clingman and Sean P. Ryder

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Single-molecule colocalization FRET evidence that spliceosome activation precedes stable approach of 5' splice site and branch site, Daniel J. Crawford, Aaron A. Hoskins, Larry J. Friedman, Jeff Gelles, and Melissa J. Moore

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The induction of microRNA-16 in colon cancer cells by protein arginine deiminase inhibition causes a p53-dependent cell cycle arrest., Xiangli Cui, Erin E. Witalison, Alena P. Chumanevich, Alexander A. Chumanevich, Deepak Poudyal, Venkataraman Subramanian, Aaron J. Schetter, Curtis C. Harris, Paul R. Thompson, and Lorne J. Hofseth

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Folding principles of genomes, Job Dekker

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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Job Dekker, Marc A. Marti-Renom, and Leonid A. Mirny

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Biological techniques: Chromosomes captured one by one, Job Dekker and Leonid A. Mirny

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Nuclear biology: what's been most surprising, Job Dekker, Joanna Wysocka, Iain Mattaj, Erez Lieberman-Aiden, and Craig Pikaard

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GABAergic neuroactive steroids and resting-state functional connectivity in postpartum depression: a preliminary study, Kristina M. Deligiannidis, Elif M. Sikoglu, Scott A. Shaffer, Blaise Frederick, Abby E. Svenson, Andre Kopoyan, Chelsea A. Kosma, Anthony J. Rothschild, and Constance M. Moore

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Automethylation of protein arginine methyltransferase 8 (PRMT8) regulates activity by impeding S-adenosylmethionine sensitivity., Myles B.C. Dillon, Heather L. Rust, Paul R. Thompson, and Kerri A. Mowen

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The correlation between histone modifications and gene expression, Xianjun Dong and Zhiping Weng

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Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants, Metewo Selase Enuameh, Yuna Asriyan, Adam Richards, Ryan G. Christensen, Victoria L. Hall, Majid Kazemian, Cong Zhu, Hannah Pham, Qiong Cheng, Charles Blatti, Jessie A. Brasefield, Matthew D. Basciotta, Jianhong Ou, Joseph C. McNulty, Lihua Julie Zhu, Susan E. Celniker, Saurabh Sinha, Gary D. Stormo, Michael H. Brodsky, and Scot A. Wolfe

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Chemical screening identifies filastatin, a small molecule inhibitor of Candida albicans adhesion, morphogenesis, and pathogenesis, Ahmed Fazly, Charu Jain, Amie C. Dehner, Luca Issi, Elizabeth A. Lilly, Akbar Ali, Hong Cao, Paul L. Fidel Jr., Reeta P. Rao, and Paul D. Kaufman

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Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates, Carlos Fabian Flores-Jasso, William E. Salomon, and Phillip D. Zamore

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Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease, Jennifer E. Foulkes-Murzycki, Christina Rosi, Nese Kurt Yilmaz, Robert W. Shafer, and Celia A. Schiffer

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Design, synthesis, and kinetic characterization of protein N-terminal acetyltransferase inhibitors., Havard Foyn, Justin E. Jones, Dan Lewallen, Rashmi Narawane, Jan Erik Varhaug, Paul R. Thompson, and Thomas Arnesen

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Targeting the arginine phosphatase YwlE with a catalytic redox-based inhibitor., Jakob Fuhrmann, Venkataraman Subramanian, and Paul R. Thompson

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Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein, Basavanapura N. Gangadhara, Jennifer M. Laine, Sagar V. Kathuria, Francesca Massi, and C. Robert Matthews

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Small RNA-Directed Silencing: The Fly Finds Its Inner Fission Yeast, Daniel Tianfang Ge and Phillip D. Zamore

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The Hierarchy of the 3D Genome, Johan H. Gibcus and Job Dekker

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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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Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation, Flora S. Groothuizen, Alexander Fish, Maxim V. Petoukhov, Annet Reumer, Laura Manelyte, Herrie H.K. Winterwerp, Martin G. Marinus, Joyce H.G. Lebbink, Dmitri I. Svergun, Peter Friedhoff, and Titia K. Sixma

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HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism, Abigail I. Guce, Sarah E. Mortimer, Taejin Yoon, Corrie A. Painter, Wei Jiang, Elizabeth D. Mellins, and Lawrence J. Stern

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Targeted chromosomal deletions and inversions in zebrafish, Ankit Gupta, Victoria L. Hall, Fatma O. Kok, Masahiro Shin, Joseph C. McNulty, Nathan D. Lawson, and Scot A. Wolfe

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Theranostic Upconversion Nanoparticles (II), Gang Han and Guanying Chen

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Experimental Illumination of Comprehensive Fitness Landscapes: A Dissertation, Ryan T. Hietpas

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Shifting fitness landscapes in response to altered environments, Ryan T. Hietpas, Claudia Bank, Jeffrey D. Jensen, and Daniel N. A. Bolon

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Structure-based Targeting of Transcriptional Regulatory Complexes Implicated in Human Disease: A Dissertation, Brendan J. Hilbert

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Chemical derivatization and purification of peptide-toxins for probing ion channel complexes, Zhengmao Hua and William R. Kobertz

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The DNA damage and the DNA replication checkpoints converge at the MBF transcription factor, Tsvetomira Ivanova, Isabel Alves-Rodrigues, Blanca Gomez-Escoda, Chaitali Dutta, James A. DeCaprio, Nicholas R. Rhind, Elena Hidalgo, and Jose Ayte

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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