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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A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity, Ryan G. Christensen, Ankit Gupta, Zheng Zuo, Lawrence A. Schriefer, Scot A. Wolfe, and Gary D. Stormo

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Suppression of colitis in mice by Cl-amidine: a novel peptidylarginine deiminase inhibitor., Alexander A. Chumanevich, Corey P. Causey, Bryan Knuckley, Justin E. Jones, Deepak Poudyal, Tia Davis, Alena P. Chumanevich, Lydia E. Matesic, Paul R. Thompson, and Lorne J. Hofseth

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A perspective of the dynamic structure of the nucleus explored at the single-molecule level, Thomas Dange, Aviva Joseph, and David Grunwald

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TMC310911, a Novel Human Immunodeficiency Virus Type 1 Protease Inhibitor, Shows In Vitro an Improved Resistance Profile and Higher Genetic Barrier to Resistance Compared with Current Protease Inhibitors, Inge Dierynck, Herwig Van Marck, Marcia Van Ginderen, Tim H. M. Jonckers, Madhavi N. L. Nalam, Celia A. Schiffer, Araz Raoof, Guenter Kraus, and Gaston Picchio

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Community-wide assessment of protein-interface modeling suggests improvements to design methodology, Sarel J. Fleishman, Howook Hwang, Thom Vreven, Brian G. Pierce, and Zhiping Weng

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Nuclear export dynamics of RNA-protein complexes, David Grunwald, Robert H. Singer, and Michael Rout

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Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Ankit Gupta, Xiangdong Meng, Lihua Julie Zhu, Nathan D. Lawson, and Scot A. Wolfe

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The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1, Bo W. Han, Jui-Hung Hung, Zhiping Weng, Phillip D. Zamore, and Stefan L. Ameres

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Using Light to Observe and Control Cellular Function: Improving Bioluminescence Imaging and Photocontrol of Rho GTPase Activation States: A Dissertation, Katryn R. Harwood

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Experimental illumination of a fitness landscape, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. A. Bolon

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A machine learning approach for the prediction of protein surface loop flexibility, Howook Hwang, Thom Vreven, Troy W. Whitfield, Kevin Wiehe, and Zhiping Weng

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ACT: aggregation and correlation toolbox for analyses of genome tracks, Justin Jee, Joel Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert Bjornson, Guoneng Zhong, Zhengdong Zhang, Yutao Fu, Jie Wang, Zhiping Weng, and Mark B. Gerstein

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FBF represses the Cip/Kip cell-cycle inhibitor CKI-2 to promote self-renewal of germline stem cells in C. elegans, Irene Kalchhauser, Brian M. Farley, Sandra Pauli, Sean P. Ryder, and Rafal Ciosk

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A structure-based benchmark for protein-protein binding affinity, Panagiotis L. Kastritis, Iain H. Moal, Howook Hwang, Zhiping Weng, Paul A. Bates, Alexandre M. J. J. Bonvin, and Joel Janin

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Structural insights into early folding events using continuous-flow time-resolved SAXS, Sagar V. Kathuria, Liang Guo, Rita Graceffa, Raul Barrea, R. Paul Nobrega, C. Robert Matthews, Tom Irving, and Osman Bilsel

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Adaptation to P element transposon invasion in Drosophila melanogaster, Jaspreet S. Khurana, Jie Wang, Jia Xu, Birgit S. Koppetsch, Travis Thomson, Anetta Nowosielska, Chengjian Li, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1, Alexei V. Korennykh, Pascal F. Egea, Andrei A. Korostelev, Janet Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, and Peter Walter

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Structural and functional basis for RNA cleavage by Ire1, Alexei V. Korennykh, Andrei A. Korostelev, Pascal F. Egea, Janet Finer-Moore, Robert M. Stroud, Chao Zhang, Kevan M. Shokat, and Peter Walter

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Functional characterization of the Saccharomyces cerevisiae protein Chl1 reveals the role of sister chromatid cohesion in the maintenance of spindle length during S-phase arrest, Suparna Laha, Shankar Das, Sujata Hajra, Kaustuv Sanyal, and Pratima Sinha

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Protein deiminases: new players in the developmentally regulated loss of neural regenerative ability., Sigrun Lange, Stefanie Gogel, Kit-Yi Leung, Bertrand Vernay, Anthony P. Nicholas, Corey P. Causey, Paul R. Thompson, Nicholas D.E. Greene, and Patrizia Ferretti

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Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish, Nathan D. Lawson and Scot A. Wolfe

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Molecular Mechanisms of piRNA Biogenesis and Function in Drosophila: A Dissertation, Chengjian Li

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Nuclear physics: quantitative single-cell approaches to nuclear organization and gene expression, T. Lionnet, B. Wu, David Grunwald, Robert H. Singer, and D. R. Larson

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Overlapping regulation of CenH3 localization and histone H3 turnover by CAF-1 and HIR proteins in Saccharomyces cerevisiae, Jessica Lopes da Rosa Spiegler, John Holik, Erin M. Green, Oliver J. Rando, and Paul D. Kaufman

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Translocation mapping exposes the risky lifestyle of B cells, Rachel Patton McCord and Job Dekker

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Role of Protein Flexibility in Function, Resistance Pathways and Substrate Recognition Specificity in HIV-1 Protease: A Dissertation, Seema Mittal

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The human nucleolar protein FTSJ3 associates with NIP7 and functions in pre-rRNA processing, Luis G. Morello, Patricia P. Coltri, Alexandre J.C. Quaresma, Fernando M. Simabuco, Tereza C.L. Sila, Guramrit Singh, Jeffrey A. Nickerson, Carla C. Oliveira, Melissa J. Moore, and Nilson I. T. Zanchin

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Activity-based protein profiling of protein arginine methyltransferase 1, Obiamaka Obianyo, Corey P. Causey, Justin E. Jones, and Paul R. Thompson

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Xenopus laevis oocytes infected with multi-drug-resistant bacteria: implications for electrical recordings, Denice O'Connell, Karen Mruk, Jessica M. Rocheleau, and William R. Kobertz

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Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope, Aysegul Ozen, Turkan Haliloglu, and Celia A. Schiffer

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Conformational Lability in MHC II Proteins: A Dissertation, Corrie A. Painter

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Conformational lability in the class II MHC 3-10 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange, Corrie A. Painter, Maria P. Negroni, Kathy A. Kellersberger, Zarixia Zavala-Ruiz, James E. Evans, and Lawrence J. Stern

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Three residues in HIV-1 matrix contribute to protease inhibitor susceptibility and replication capacity, Chris M. Parry, Madhavi Kolli, Richard E. Myers, Patricia A. Cane, Celia A. Schiffer, and Deenan Pillay

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Hsp90-Mediated Maturation of Kinases and Nuclear Steroid Hormone Receptors: A Dissertation, Natalie W. Pursell

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A Non-Specific Effect Associated with Conditional Transgene Expression Based on Cre-loxP Strategy in Mice, Linghua Qiu, Jaime A. Rivera-Perez, and Zuoshang Xu

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Patterns and mechanisms of ancestral histone protein inheritance in budding yeast, Marta Radman-Livaja, Kitty F. Verzijlbergen, Assaf Weiner, Tibor van Welsem, Nir Friedman, Oliver J. Rando, and Fred van Leeuwen

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Yeast one-hybrid assays for gene-centered human gene regulatory network mapping, John S. Reece-Hoyes, A. Rasim Barutcu, Rachel Patton McCord, Jun Seop Jeong, Lizhi Jiang, Andrew Macwilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E. Hill, Seth Blackshaw, Heng Zhu, Job Dekker, and Albertha J. M. Walhout

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Yeast one-hybrid assays for gene-centered human gene regulatory network mapping, John S. Reece-Hoyes, A. Rasim Barutcu, Rachel Patton McCord, Jun Seop Jeong, Lizhi Jiang, Andrew Macwilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E. Hill, Seth Blackshaw, Heng Zhu, Job Dekker, and Albertha J. M. Walhout

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Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping, John S. Reece-Hoyes, Alos Diallo, Bryan R. Lajoie, Amanda Kent, Shaleen Shrestha, Sreenath Kadreppa, Colin Pesyna, Job Dekker, Chad L. Myers, and Albertha J. M. Walhout

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Mechanisms of Substrate Recognition by HCV NS3/4A Protease Provide Insights Into Drug Resistance: A Dissertation, Keith P. Romano

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Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease, Keith P. Romano, Jennifer M. Laine, Laura M. Deveau, Hong Cao, Francesca Massi, and Celia A. Schiffer

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Kinase consensus sequences: a breeding ground for crosstalk, Heather L. Rust and Paul R. Thompson

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Mechanistic studies on transcriptional coactivator protein arginine methyltransferase 1, Heather L. Rust, Cecilia I. Zurita-Lopez, Steven Clarke, and Paul R. Thompson

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Support of Mitochondrial DNA Replication by Human Rad51: A Dissertation, Jay M. Sage

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Chromatin globules: a common motif of higher order chromosome structure, Amartya Sanyal, Davide Bau, Marc A. Marti-Renom, and Job Dekker

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A 5'-uridine Amplifies miRNA/miRNA* Asymmetry in Drosophila by Promoting RNA-induced Silencing Complex Formation, Herve Seitz, Jogender S. Tushir, and Phillip D. Zamore

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Structural Studies of the Anti-HIV Human Protein APOBEC3G Catalytic Domain: A Dissertation, Shivender Shandilya

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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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Development and use of clickable activity based protein profiling agents for protein arginine deiminase 4., Jessica L. Slack, Corey P. Causey, Yuan Luo, and Paul R. Thompson

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Protein arginine deiminase 4: a target for an epigenetic cancer therapy, Jessica L. Slack, Corey P. Causey, and Paul R. Thompson

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Autodeimination of protein arginine deiminase 4 alters protein-protein interactions but not activity., Jessica L. Slack, Larry E. Jones Jr., Monica M. Bhatia, and Paul R. Thompson

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Insights Into ER Translocation Channel Gating. Structural Regulation of the Transition Between the Closed and Open Channel Conformations: A Dissertation, Steven F. Trueman

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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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The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation, Mark A. Umbarger, Esteban Toro, Matthew A. Wright, Gregory J. Porreca, Davide Bau, Sun-Hae Hong, Michael J. Fero, Lihua Julie Zhu, Marc A. Marti-Renom, Harley H. McAdams, Lucy Shapiro, Job Dekker, and George M. Church

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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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N-alpha-benzoyl-N5-(2-chloro-1-iminoethyl)-L-ornithine amide, a protein arginine deiminase inhibitor, reduces the severity of murine collagen-induced arthritis, Van C. Willis, Paul R. Thompson, and V. Michael Holers

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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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Several rAAV vectors efficiently cross the blood-brain barrier and transduce neurons and astrocytes in the neonatal mouse central nervous system, Hongwei Zhang, Bin Yang, Xin Mu, Seemin Seher Ahmed, Qin Su, Ran He, Hongyan Wang, Christian Mueller, Miguel Sena-Esteves, Robert H. Brown Jr., Zuoshang Xu, and Guangping Gao

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Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells., Xuesen Zhang, Matthew J. Gamble, Sonja Stadler, Brian D. Cherrington, Corey P. Causey, Paul R. Thompson, Mark S. Roberson, W Lee Kraus, and Scott A. Coonrod

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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

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Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish, Cong Zhu, Tom Smith, Joseph C. McNulty, Amy L. Rayla, Abirami Lakshmanan, Arndt F. Siekmann, Matthew Buffardi, Xiangdong Meng, Jimann Shin, Arun Padmanabhan, Daniel Cifuentes, Antonio J. Giraldez, A. Thomas Look, Jonathan A. Epstein, Nathan D. Lawson, and Scot A. Wolfe

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FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system, Lihua Julie Zhu, Ryan G. Christensen, Majid Kazemian, Christopher J. Hull, Metewo Selase Enuameh, Matthew D. Basciotta, Jessie A. Brasefield, Cong Zhu, Yuna Asriyan, David S. Lapointe, Saurabh Sinha, Scot A. Wolfe, and Michael H. Brodsky

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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Exploring Molecular Mechanisms of Drug Resistance in HIV-1 Protease through Biochemical and Biophysical Studies: A Dissertation, Rajintha M. Bandaranayake

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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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Glycosylation, Assembly and Trafficking of Cardiac Potassium Channel Complexes: A Dissertation, Kshama D. Chandrasekhar

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Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex, Iris Cheung, Hennady P. Shulha, Yan Jiang, Anouch Matevossian, Jie Wang, Zhiping Weng, and Schahram Akbarian

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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 Endothelial Cell Glucose Transport: A Dissertation, Anthony J. Cura

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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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The membrane-associated protein, supervillin, accelerates F-actin-dependent rapid integrin recycling and cell motility, Zhiyou Fang, Norio Takizawa, Korey A. Wilson, Tara C. Smith, Anna M. Delprato, Michael W. Davidson, David G. Lambright, and Elizabeth J. Luna

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Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene, Nele Gheldof, Emily M. Smith, Tomoko M. Tabuchi, Christoph M. Koch, Ian Dunham, John A. Stamatoyannopoulos, and Job Dekker

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Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway, Megha Ghildiyal, Jia Xu, Herve Seitz, Zhiping Weng, and Phillip D. Zamore

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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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Characterization and inactivation of an agmatine deiminase from Helicobacter pylori, Justin E. Jones, Corey P. Causey, Leslie Lovelace, Bryan Knuckley, Heather Flick, Lukasz Lebioda, and Paul R. Thompson

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Mechanistic studies of agmatine deiminase from multiple bacterial species, Justin E. Jones, Christina J. Dreyton, Heather Flick, Corey P. Causey, and Paul R. Thompson

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Mediator and cohesin connect gene expression and chromatin architecture, Michael H. Kagey, Jamie J. Newman, Steve Bilodeau, Ye Zhan, David A. Orlando, Nynke L. van Berkum, Christopher C. Ebmeier, Jesse Goossens, Peter B. Rahl, Stuart S. Levine, Dylan J. Taatjes, Job Dekker, and Richard A. Young

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Sequence Determinants of the Folding Free-Energy Landscape of beta alpha-Repeat Proteins: A Dissertation, Sagar V. Kathuria

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Chromatin as a potential carrier of heritable information, Paul D. Kaufman and Oliver J. Rando

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The Coupling Between Folding, Zinc Binding, and Disulfide Bond Status of Human Cu, Zn Superoxide Dismutase: A Dissertation, Can Kayatekin

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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