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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High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm, Benjamin R. Carone, Jui-Hung Hung, Sarah J. Hainer, Min-Te Chou, Dawn M. Carone, Zhiping Weng, Thomas G. Fazzio, and Oliver J. Rando

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription, Luca Giorgetti, Rafael Galupa, Elphege P. Nora, Tristan Piolot, France Lam, Job Dekker, Guido Tiana, and Edith Heard

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An improved predictive recognition model for Cys2-His2 zinc finger proteins, Ankit Gupta, Ryan G. Christensen, Heather A. Bell, Mathew Goodwin, Ronak Y. Patel, Manishi Pandey, Metewo Selase Enuameh, Amy L. Rayla, Cong Zhu, Stacey Thibodeau-Beganny, Michael H. Brodsky, J. Keith Joung, Scot A. Wolfe, and Gary D. Stormo

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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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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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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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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

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

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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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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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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 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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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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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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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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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

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Gene set enrichment analysis: performance evaluation and usage guidelines, Jui-Hung Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, and Charles Delisi