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 2013

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

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

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Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope, Vahbiz Jokhi, James A. Ashley, John J. Nunnari, Akiko Noma, Naoto ito, Noriko Wakabayashi-Ito, Melissa J. Moore, and Vivian Budnik

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High-throughput genome scaffolding from in vivo DNA interaction frequency, Noam Kaplan and Job Dekker

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

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Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development, Majid Kazemian, Hannah Pham, Scot A. Wolfe, Michael H. Brodsky, and Saurabh Sinha

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NETs are a source of citrullinated autoantigens and stimulate inflammatory responses in rheumatoid arthritis., Ritika Khandpur, Carmelo Carmona-Rivera, Anuradha Vivekanandan-Giri, Alison Gizinski, Srilakshmi Yalavarthi, Jason S. Knight, Sean Friday, Sam Li, Rajiv M. Patel, Venkataraman Subramanian, Paul R. Thompson, Pojen Chen, David A. Fox, Subramaniam Pennathur, and Mariana J. Kaplan

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Peptidylarginine deiminase inhibition is immunomodulatory and vasculoprotective in murine lupus., Jason S. Knight, Wenpu Zhao, Wei Luo, Venkataraman Subramanian, Alexander A. O'Dell, Srilakshmi Yalavarthi, Jeffrey B. Hodgin, Daniel T. Eitzman, Paul R. Thompson, and Mariana J. Kaplan

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ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq, Alper Kucukural, Hakan Ozadam, Guramrit Singh, Melissa J. Moore, and Can Cenik

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Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny, Satyendra Kumar, Robert Wuerffel, Ikbel Achour, Bryan R. Lajoie, Ranjan Sen, Job Dekker, Ann J. Feeney, and Amy L. Kenter

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Cycling of the signaling protein phospholipase D through cilia requires the BBSome only for the export phase, Karl-Ferdinand Lechtreck, Jason M. Brown, Julio L. Sampaio, Julie M. Craft, Andrej Shevchenko, James E. Evans, and George B. Witman

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A sensitive assay using a native protein substrate for screening HIV-1 maturation inhibitors targeting the protease cleavage site between the matrix and capsid, Sook-Kyung Lee, Nancy Cheng, Emily A. Hull-Ryde, Marc Potempa, Celia A. Schiffer, William P. Janzen, and Ronald I. Swanstrom

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An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes, Xin Zhiguo Li, Christian K. Roy, Xianjun Dong, Ewelina Bolcun-Filas, Jie Wang, Bo W. Han, Jia Xu, Melissa J. Moore, John C. Schimenti, Zhiping Weng, and Phillip D. Zamore

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The nucleolus stress response is coupled to an ATR-Chk1-mediated G2 arrest, Hanhui Ma and Thoru Pederson

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Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors, Andrew W. Malaby, Bert van den Berg, and David G. Lambright

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Molecular determinants of co- and post-translational N-glycosylation of type I transmembrane peptides, Heidi Malaby and William R. Kobertz

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Protein translocation across the rough endoplasmic reticulum, Elisabet C. Mandon, Steven F. Trueman, and Reid Gilmore

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High efficiency generalized transduction in Escherichia coli O157:H7, Martin G. Marinus and Anthony R. Poteete

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Gestational angiogenic biomarker patterns in high risk preeclampsia groups, Sharon E. Maynard, Sybil L. Crawford, Susanne Bathgate, Jing Yan, Laura Robidoux, Melissa J. Moore, and Tiffany A. Moore Simas

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Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome, Rachel Patton McCord, Ashley Nazario-Toole, Haoyue Zhang, Peter Chines, Ye Zhan, Michael Erdos, Francis Collins, Job Dekker, and Kan Cao

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Efficient targeted mutagenesis in the monarch butterfly using zinc finger nucleases, Christine Merlin, Lauren E. Beaver, Orley R. Taylor, Scot A. Wolfe, and Steven M. Reppert

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The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanism, Ashwini K. Mishra, Claudia M. Del Campo, Robert E. Collins, Craig R. Roy, and David G. Lambright

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The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanism, Ashwini K. Mishra, Claudia M. Del Campo, Robert E. Collins, Craig R. Roy, and David G. Lambright

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Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50, Seema Mittal, Rajintha M. Bandaranayake, Nancy M. King, Moses Prabu-Jeyabalan, Madhavi N. L. Nalam, Ellen A. Nalivaika, Nese Kurt Yilmaz, and Celia A. Schiffer

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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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Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Rocco Moretti, Sarel J. Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, Panagiotis L. Kastritis, Joao P.G.L.M Rodrigues, Mikael Trellet, Alexandre M.J.J. Bonvin, Meng Cui, Brian G. Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, and David Baker

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Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance, Madhavi N. L. Nalam, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima G. Anjum, Michael D. Altman, Nese Kurt Yilmaz, Bruce Tidor, Tariq M. Rana, and Celia A. Schiffer

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Organization of the mitotic chromosome, Natalia Naumova, Maxim Imakaev, Geoffrey Fudenberg, Ye Zhan, Bryan R. Lajoie, Leonid A. Mirny, and Job Dekker

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Measuring image resolution in optical nanoscopy, Robert P. J. Nieuwenhuizen, Keith A. Lidke, Mark Bates, Daniela Leyton Puig, David Grunwald, Sjoerd Stallinga, and Bernd Rieger

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Structure and Dynamics of Viral Substrate Recognition and Drug Resistance: A Dissertation, Aysegul Ozen

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Improving the Resistance Profile of Hepatitis C NS3/4A Inhibitors: Dynamic Substrate Envelope Guided Design, Aysegul Ozen, Woody Sherman, and Celia A. Schiffer

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A trifluoroacetic acid-labile sulfonate protecting group and its use in the synthesis of a near-IR fluorophore, Steven M. Pauff and Stephen C. Miller

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Life, redrawn: a memoir of Carl R. Woese (1928-2012), Thoru Pederson

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The persistent plausibility of protein synthesis in the nucleus: process, palimpsest or pitfall, Thoru Pederson

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Turning on a dime: the 75th anniversary of America's march against polio, Thoru Pederson

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Transposition-driven genomic heterogeneity in the Drosophila brain, Paola N. Perrat, Shamik DasGupta, Jie Wang, William E. Theurkauf, Zhiping Weng, Michael Rosbash, and Scott Waddell

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Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment, Jennifer E. Phillips-Cremins, Michael E. G. Sauria, Amartya Sanyal, Tatiana I. Gerasimova, Bryan R. Lajoie, Joshua S. K. Bell, Chin-Tong Ong, Tracy A. Hookway, Changying Guo, Yuhua Sun, Michael J. Bland, William Wagstaff, Stephen Dalton, Todd C. McDevitt, Ranjan Sen, Job Dekker, James Taylor, and Victor G. Corces

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A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes, Brian G. Pierce and Zhiping Weng

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Functional overlap among distinct G1/S inhibitory pathways allows robust G1 arrest by yeast mating pheromones, Patricia A. Pope and Peter M. Pryciak

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Widespread aggregation of mutant VAPB associated with ALS does not cause motor neuron degeneration or modulate mutant SOD1 aggregation and toxicity in mice, Linghua Qiu, Tao Qiao, Melissa Beers, Weijia Tan, Hongyan Wang, Bin Yang, and Zuoshang Xu

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Glioblastoma multiforme therapy and mechanisms of resistance, Yulian Ramirez, Jessica L. Weatherbee, Richard T. Wheelhouse, and Alonzo H. Ross

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DNA Replication Timing, Nicholas R. Rhind and David M. Gilbert

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Analyses of the effects of all ubiquitin point mutants on yeast growth rate, Benjamin P. Roscoe, Kelly M. Thayer, Konstantin B. Zeldovich, David Fushman, and Daniel N. A. Bolon

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Human Rad51 promotes mitochondrial DNA synthesis under conditions of increased replication stress, Jay M. Sage and Kendall L. Knight

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Interview with Celia Schiffer, Celia A. Schiffer

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Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments, Vlad Seitan, Andre Faure, Ye Zhan, Rachel Patton McCord, Bryan R. Lajoie, Elizabeth Ing-Simmons, Boris Lenhard, Luca Giorgetti, Edith Heard, Amanda Fisher, Paul Flicek, Job Dekker, and Matthias Merkenschlager

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

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Tunable Near Infrared to Ultraviolet Upconversion Luminescence Enhancement in (alpha-NaYF :Yb,Tm)/CaF Core/Shell Nanoparticles for In situ Real-time Recorded Biocompatible Photoactivation, Jie Shen, Guanying Chen, Tymish Y. Ohulchanskyy, Samuel J. Kesseli, Steven Buchholz, Zhipeng Li, Paras N. Prasad, and Gang Han

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Testing the substrate-envelope hypothesis with designed pairs of compounds, Yang Shen, Michael D. Altman, Akbar Ali, Madhavi N. L. Nalam, Hong Cao, Tariq M. Rana, Celia A. Schiffer, and Bruce Tidor

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Mutations in STT3A and STT3B cause two congenital disorders of glycosylation, Shiteshu Shrimal, Bobby G. Ng, Marie-Estelle Losfeld, James R. Gilmore, and Hudson H. Freeze

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Extreme C-terminal sites are posttranslocationally glycosylated by the STT3B isoform of the OST, Shiteshu Shrimal, Steven F. Trueman, and Reid Gilmore

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Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration, Nathaniel W. Silver, Bracken M. King, Madhavi N. L. Nalam, Hong Cao, Akbar Ali, G. S. Kiran Kumar Reddy, Tariq M. Rana, Celia A. Schiffer, and Bruce Tidor

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Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome, Egor Svidritskiy, Clarence Ling, Dmitri N. Ermolenko, and Andrei A. Korostelev

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A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels, Alex M. Tamburino, Sean P. Ryder, and Albertha J. M. Walhout

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Networking development by Boolean logic, Shikui Tu, Thoru Pederson, and Zhiping Weng

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Prototypical Recombinant Multi-Protease Inhibitor Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type-1, Vici Varghese, Yumi Mitsuya, W. Jeffrey Fessel, Tommy F. Liu, George L. Melikian, David A. Katzenstein, Celia A. Schiffer, Susan P. Holmes, and Robert W. Shafer

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Identification and Analysis of the Domain Required for Trans-Acceleration Kinetics in the Human Glucose Transporter GLUT1: A Dissertation, Sabrina S. Vollers

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Handbook of Systems Biology: Concepts and Insights, Albertha J. M. Walhout, Marc Vidal, and Job Dekker

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Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium, Jie Wang, Jiali Zhuang, Sowmya Iyer, Xinying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, and Zhiping Weng

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Substrate specificity, processivity, and kinetic mechanism of protein arginine methyltransferase 5., Min Wang, Rui-Ming Xu, and Paul R. Thompson

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A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme, Shinya Watanabe, Marta Radman-Livaja, Oliver J. Rando, and Craig L. Peterson