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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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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RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1, Ebru Kaymak and Sean P. Ryder

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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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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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Alternative spliceosome assembly pathways revealed by single-molecule fluorescence microscopy, Inna Shcherbakova, Aaron A. Hoskins, Larry J. Friedman, Victor Serebrov, Ivan R. Correa Jr., Ming-Qun Xu, Jeff Gelles, and Melissa J. Moore

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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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Disparate epitopes mediating protective heterologous immunity to unrelated viruses share peptide-MHC structural features recognized by cross-reactive T cells, Zu T. Shen, Tina T. Nguyen, Keith A. Daniels, Raymond M. Welsh, and Lawrence J. Stern

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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

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hox Gene Regulation and Function During Zebrafish Embryogenesis: A Dissertation, Steven E. Weicksel

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Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis, Steven Weicksel, Jia Xu, and Charles G. Sagerstrom

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hnRNP A1 and secondary structure coordinate alternative splicing of Mag, Nancy R. Zearfoss, Emily S. Johnson, and Sean P. Ryder

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Rapid reassortment of internal genes in avian influenza A(H7N9) virus, Liangsheng Zhang, Zhenguo Zhang, and Zhiping Weng

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Substitution rates of the internal genes in the novel avian H7N9 influenza virus, Liangsheng Zhang, Zhenguo Zhang, Zhiping Weng, and Weifeng Shi

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Downregulation of microRNA-9 in iPSC-derived neurons of FTD/ALS patients with TDP-43 mutations, Zhijun Zhang, Sandra Almeida, Yubing Lu, Agnes L. Nishimura, Lingtao Peng, Danqiong Sun, Bei Wu, Anna M. Karydas, Maria C. Tartaglia, Jamie C. Fong, Bruce L. Miller, Robert V. Farese Jr., Melissa J. Moore, Christopher E. Shaw, and Fen-Biao Gao

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Stem cell labeling using polyethylenimine conjugated (alpha-NaYbF4:Tm3+)/CaF2 upconversion nanoparticles, Liang Zhao, Artem Kutikov, Jie Shen, Chunying Duan, Jie Song, and Gang Han

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Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases, Cong Zhu, Ankit Gupta, Victoria L. Hall, Amy L. Rayla, Ryan G. Christensen, Benjamin Dake, Abirami Lakshmanan, Charlotte Kuperwasser, Gary D. Stormo, and Scot A. Wolfe

Publications from 2012

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Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease, Oscar Alvizo, Seema Mittal, Stephen L. Mayo, and Celia A. Schiffer

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Mass spectrometry tools for analysis of intermolecular interactions, Jared R. Auclair, Mohan Somasundaran, Karin M. Green, James E. Evans, Celia A. Schiffer, Dagmar Ringe, Gregory A. Petsko, and Jeffrey N. Agar

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Hepatitis C Virus Non-Structural Protein 3/4A: A Tale of Two Domains: A Dissertation, Cihan Aydin

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Hi-C: A comprehensive technique to capture the conformation of genomes, Jon-Matthew Belton, Rachel Patton McCord, Johan H. Gibcus, Natalia Naumova, Ye Zhan, and Job Dekker

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D-amino acid based protein arginine deiminase inhibitors: Synthesis, pharmacokinetics, and in cellulo efficacy., Kevin L. Bicker, Lynne Anguish, Alexander A. Chumanevich, Michael D. Cameron, Xiangli Cui, Erin E. Witalison, Venkataraman Subramanian, Xuesen Zhang, Alena P. Chumanevich, Lorne J. Hofseth, Scott A. Coonrod, and Paul R. Thompson

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Seeing citrulline: development of a phenylglyoxal-based probe to visualize protein citrullination., Kevin L. Bicker, Venkataraman Subramanian, Alexander A. Chumanevich, Lorne J. Hofseth, and Paul R. Thompson

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Decomposing the energetic impact of drug-resistant mutations: the example of HIV-1 protease-DRV binding, Yufeng Cai and Celia A. Schiffer

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Methyl- and Normal-Cytosine Deamination by the Foreign DNA Restriction Enzyme APOBEC3A, Michael A. Carpenter, Ming Li, Anurag Rathore, Lela Lackey, Emily R. Law, Allison M. Land, Brandon Leonard, Shivender M. D. Shandilya, Markus-Frederik Bohn, Celia A. Schiffer, William L. Brown, and Reuben S. Harris

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Understanding Small RNA Formation in Drosophila Melanogaster: A Dissertation, Elif Sarinay Cenik

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Understanding transcriptional regulation by integrative analysis of transcription factor binding data, Chao Cheng, Roger Alexander, Rengqiang Min, Jing Leng, Kevin Y. Yip, Joel Rozowsky, Koon-Kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, Carrie A. Davis, Piero Carninci, Timo Lassman, Thomas R. Gingeras, Roderic Guigo, Ewan Birney, Zhiping Weng, Michael Snyder, and Mark B. Gerstein

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(alpha-NaYbF4:Tm(3+))/CaF2 core/shell nanoparticles with efficient near-infrared to near-infrared upconversion for high-contrast deep tissue bioimaging, Guanying Chen, Jie Shen, Tymish Y. Ohulchansky, Nayan J. Patel, Artem Kutikov, Zhipeng Li, Jie Song, Ravindra K. Pandey, Hans Agren, Paras N. Prasad, and Gang Han

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Recognition models to predict DNA-binding specificities of homeodomain proteins, Ryan G. Christensen, Metewo Selase Enuameh, Marcus Blaine Noyes, Michael H. Brodsky, Scot A. Wolfe, and Gary D. Stormo

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Exploring the DNA-recognition potential of homeodomains, Stephanie W. Chu, Marcus Blaine Noyes, Ryan G. Christensen, Brian G. Pierce, Lihua Julie Zhu, Zhiping Weng, Gary D. Stormo, and Scot A. Wolfe

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CTCF and cohesin help neurons raise their self-awareness, Job Dekker

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3C-based technologies to study the shape of the genome, Wouter de Laat and Job Dekker

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Evidence for transcript networks composed of chimeric RNAs in human cells, Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge, Cedric Howald, Sylvain Foissac, Catherine Ucla, Jacqueline Chrast, Paolo Ribeca, David Marin, Ryan R. Murray, Xinping Yang, Lila Ghamasari, Chenwei Lin, Ian Bell, Erica Dumais, Jorg Drenkow, Michael L. Tress, Josep Lluis Gelpi, Modesto Orozco, Alfonso Valencia, Nynke L. van Berkum, Bryan R. Lajoie, Marc Vidal, John A. Stamatoyannopoulos, Philippe Batut, Alex Dobin, Jennifer Harrow, Tim Hubbard, Job Dekker, Adam Frankish, Kourosh Salehi-Ashtiani, Alexandre Reymond, Stylianos E. Antonarakis, Roderic Guigo, and Thomas R. Gingeras

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Modeling gene expression using chromatin features in various cellular contexts, Xianjun Dong, Melissa C. Greven, Anshul Kundaje, Sarah Djebali, James B. Brown, Chao Cheng, Thomas R. Gingeras, Mark B. Gerstein, Roderic Guigo, Ewan Birney, and Zhiping Weng

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Felty's syndrome autoantibodies bind to deiminated histones and neutrophil extracellular chromatin traps., Nishant Dwivedi, Jagriti Upadhyay, Indira Neeli, Salar Khan, Debendra Pattanaik, Linda Myers, Kyriakos A. Kirou, Bernhard Hellmich, Bryan Knuckley, Paul R. Thompson, Mary K. Crow, Ted R. Mikuls, Elena Csernok, and Marko Radic

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Human protein N-terminal acetyltransferase hNaa50p (hNAT5/hSAN) follows ordered sequential catalytic mechanism: combined kinetic and NMR study., Rune H. Evjenth, Annette K. Brenner, Paul R. Thompson, Thomas Arnesen, Nils Age Froystein, and Johan R. Lillehaug

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Sequence and Target Specificity of the C. elegans Cell Fate Specification Factor POS-1: A Dissertation, Brian M. Farley

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POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster, Brian M. Farley and Sean P. Ryder

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NURDs are required for diversity, Thomas G. Fazzio and Oliver J. Rando

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Genome architecture and expression, Gary Felsenfeld and Job Dekker

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From cells to chromatin: Capturing snapshots of genome organization with 5C technology, Maria A. Ferraiuolo, Amartya Sanyal, Natalia Naumova, Job Dekker, and Josee Dostie

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Dicer partner proteins tune the length of mature miRNAs in flies and mammals, Ryuya Fukunaga, Bo W. Han, Jui-Hung Hung, Jia Xu, Zhiping Weng, and Phillip D. Zamore

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The Acid-Sensitive, Anesthetic-Activated Potassium Leak Channel, KCNK3, Is Regulated By 14-3-3beta-Dependent, PKC-Mediated Endocytic Trafficking, Luke Gabriel, Anatoli Lvov, Demetra Orthodoxou, Ann R. Rittenhouse, William R. Kobertz, and Haley E. Melikian

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Multiscale dynamics in nucleocytoplasmic transport, David Grunwald and Robert H. Singer

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Getting a Tight Grip on DNA: Optimizing Zinc Fingers for Efficient ZFN-Mediated Gene Editing: A Dissertation, Ankit Gupta

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An optimized two-finger archive for ZFN-mediated gene targeting, Ankit Gupta, Amy L. Rayla, Abirami Lakshmanan, Scot A. Wolfe, Ryan G. Christensen, and Gary D. Stormo

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Cutting edge: Evidence for a dynamically driven T cell signaling mechanism, William F. Hawse, Matthew M. Champion, Michelle V. Joyce, Lance M. Hellman, Moushumi Hossain, Veronica Ryan, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Fitness analyses of all possible point mutations for regions of genes in yeast, Ryan T. Hietpas, Benjamin P. Roscoe, Li Jiang, and Daniel N. A. Bolon

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Unsupervised pattern discovery in human chromatin structure through genomic segmentation, Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, and William Stafford Noble