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 2015

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Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin, Elizabeth Ing-Simmons, Vlad C. Seitan, Andre J. Faure, Paul Flicek, Thomas Carroll, Job Dekker, Amanda G. Fisher, Boris Lenhard, and Matthias Merkenschlager

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A PH Domain with Dual Phospholipid Binding Sites Regulates the ARF GAP, ASAP1, Richard A. Kahn and David G. Lambright

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Combined inhibition of Bcl-2/Bcl-xL and Usp9X/Bag3 overcomes apoptotic resistance in glioblastoma in vitro and in vivo, Georg Karpel-Massler, Chang Shu, Lily Chau, Matei Banu, Marc-Eric Halatsch, Mike-Andrew Westhoff, Yulian P. Ramirez, Alonzo H. Ross, Jeffrey N. Bruce, Peter Canoll, and Markus D. Siegelin

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Investigating the Effects of Mutant FUS on Stress Response in Amyotrophic Lateral Sclerosis: A Thesis, Laura J. Kaushansky

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Functional annotation of native enhancers with a Cas9-histone demethylase fusion, Nicola A. Kearns, Hannah Pham, Barbara Tabak, Ryan M. J. Genga, Noah J. Silverstein, Manuel Garber, and Rene Maehr

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Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells, Jop Kind, Ludo Pagie, Sandra S. de Vries, Leila Nahidiazar, Siddharth S. Dey, Magda Bienko, Ye Zhan, Bryan Lajoie, Carolyn A. de Graaf, Mario Amendola, Geoffrey Fudenberg, Maxim Imakaev, Leonid A. Mirny, Kees Jalink, Job Dekker, Alexander van Oudenaarden, and Bas van Steensel

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Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G, Takahide Kouno, Elizabeth M. Luengas, Megumi Shigematsu, Shivender Shandilya, JingYing Zhang, Luan Chen, Mayuko Hara, Celia A. Schiffer, Reuben S. Harris, and Hiroshi Matsuo

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Chemical Proteomic Platform To Identify Citrullinated Proteins, Daniel M. Lewallen, Kevin L. Bicker, Venkataraman Subramanian, Kathleen W. Clancy, Daniel J. Slade, Julianne Martell, Christina J. Dreyton, Jeremy Sokolove, Eranthie Weerapana, and Paul R. Thompson

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Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation., Huw D. Lewis and Paul R. Thompson

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Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse, Jessica T. Lin, Nicholas J. Hathaway, David L. Saunders, Chanthap Lon, Sujata Balasubramanian, Oksana Kharabora, Panita Gosi, Sabaithip Sriwichai, Laurel Kartchner, Char Meng Chuor, Prom Satharath, Charlotte Lanteri, Jeffrey A. Bailey, and Jonathan J. Juliano

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Multicolor CRISPR labeling of chromosomal loci in human cells, Hanhui Ma, Ardalan Naseri, Pablo Reyes-Gutierrez, Scot A. Wolfe, Shaojie Zhang, and Thoru Pederson

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Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified, Georgi K. Marinov, Jie Wang, Dominik Handler, Barbara J. Wold, Zhiping Weng, Gregory J. Hannon, Alexei A. Aravin, Phillip D. Zamore, Julius Brennecke, and Katalin Fejes Toth

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Pushing The Boundaries of Bioluminescence Using Synthetic Luciferins: A Dissertation, David M. Mofford

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Luciferin Amides Enable in Vivo Bioluminescence Detection of Endogenous Fatty Acid Amide Hydrolase Activity, David M. Mofford, Spencer T. Adams Jr, G. S. Kiran Kumar Reddy, Gadarla Randheer Reddy, and Stephen C. Miller

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Opposing calcium-dependent signalling pathways control skeletal muscle differentiation by regulating a chromatin remodelling enzyme, Brian T. Nasipak, Teresita Padilla-Benavides, Karin M. Green, John D. Leszyk, Wenjie Mao, Silvana Konda, Said Sif, Scott A. Shaffer, Yasuyuki Ohkawa, and Anthony N. Imbalzano

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Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy, Jean Ndjomou, M Josie. Corby, Noreena L. Sweeney, Alicia M. Hanson, Cihan Aydin, Akbar Ali, Celia A. Schiffer, Kelin Li, Kevin J. Frankowski, Frank J. Schoenen, and David N. Frick

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Guanabenz (Wytensin) selectively enhances uptake and efficacy of hydrophobically modified siRNAs, Maire F. Osborn, Julia F. Alterman, Mehran Nikan, Hong Cao, Marie C. Didiot, Matthew R. Hassler, Andrew H. Coles, and Anastasia Khvorova

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Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution, Nevra Ozer, Aysegul Ozen, Celia A. Schiffer, and Turkan Haliloglu

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Advancements in the Synthesis and Application of Near-Infrared Imaging Reagents: A Dissertation, Steven M. Pauff

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Toward a sustainable biomedical research enterprise: Finding consensus and implementing recommendations, Christopher L. Pickett, Benjamin W. Corb, C. Robert Matthews, Wesley I. Sundquist, and Jeremy M. Berg

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A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro, Marc Potempa, Ellen A. Nalivaika, Debra A. Ragland, Sook-Kyung Lee, Celia A. Schiffer, and Ronald Swanstrom

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High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila, Fidel Ramirez, Thomas Lingg, Sarah Toscano, Kin Chung. Lam, Plamen Georgiev, Ho-Ryun Chung, Bryan R. Lajoie, Elzo de Wit, Ye Zhan, Wouter de Laat, Job Dekker, Thomas Manke, and Asifa Akhtar

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Evaluation of novel imidazotetrazine analogues designed to overcome temozolomide resistance and glioblastoma regrowth, Yulian P. Ramirez, Ann C. Mladek, Roger M. Phillips, Mikko Gynther, Jarkko Rautio, Alonzo H. Ross, Richard T. Wheelhouse, and Jann N. Sakaria

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Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis, Mayuri Rege, Vidya Subramanian, Chenchen Zhu, Tsung-Han S. Hsieh, Assaf Weiner, Nir Friedman, Sandra Clauder-Munster, Lars M. Steinmetz, Oliver J. Rando, Laurie A. Boyer, and Craig L. Peterson

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Caenorhabditis elegans microRNAs of the let-7 family act in innate immune response circuits and confer robust developmental timing against pathogen stress, Zhiji Ren and Victor R. Ambros

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Identifying, Targeting, and Exploiting a Common Misfolded, Toxic Conformation of SOD1 in ALS: A Dissertation, Melissa S. Rotunno

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Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation, Christian K. Roy, Sara Olson, Brenton R. Graveley, Phillip D. Zamore, and Melissa J. Moore

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The yeast genome undergoes significant topological reorganization in quiescence, Mark T. Rutledge, Mariano Russo, Jon-Matthew Belton, Job Dekker, and James R. Broach

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Caffeine inhibits glucose transport by binding at the GLUT1 nucleotide-binding site, Jay M. Sage, Anthony J. Cura, Kenneth P. Lloyd, and Anthony Carruthers

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Single-Molecule Imaging Reveals that Argonaute Re-Shapes the Properties of its Nucleic Acid Guides: A Dissertation, William E. Salomon

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Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides, William E. Salomon, Samson M. Jolly, Melissa J. Moore, Phillip D. Zamore, and Victor Serebrov

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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing, Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, and Emmanuel Barillot

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Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome, Jeremy Shea, Ryan W. Serra, Benjamin R. Carone, Hennady P. Shulha, Alper Kucukural, Michael Ziller, Markus Vallaster, Hongcang Gu, Andrew R. Tapper, Paul D. Gardner, Alexander Meissner, Manuel Garber, and Oliver J. Rando

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Simultaneous generation of many RNA-seq libraries in a single reaction, Alexander A. Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P. Bhattacharyya, Robert F. Rudy, Milesh M. Patel, Nathaniel Novod, Deborah T. Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman, and Jonathan Livny

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Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design, Daniel J. Slade, Pengfei Fang, Christina J. Dreyton, Ying Zhang, Jakob Fuhrmann, Don Rempel, Benjamin D. Bax, Scott A. Coonrod, Huw D. Lewis, Min Guo, Michael L. Gross, and Paul R. Thompson

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Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking, Carlas Smith, Sjoerd Stallinga, Keith A. Lidke, Bernd Rieger, and David Grunwald

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A 4D view on mRNA, Carlas Smith, Li-Chun Tu, and David Grünwald

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Circulating Levels of sFlt1 Splice Variants as Predictive Markers for the Development of Preeclampsia, Colby A. Souders, Sharon E. Maynard, Jing Yan, Yan Wang, Naomi Boatright, Jessica Sedan, David Balyozian, Peter S. Cheslock, Deborah C. Molrine, and Tiffany A. Moore Simas

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Hepatitis C Virus: Structural Insights into Protease Inhibitor Efficacy and Drug Resistance: A Dissertation, Djade I. Soumana

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Protection against Experimental Cryptococcosis following Vaccination with Glucan Particles Containing Cryptococcus Alkaline Extracts, Charles A. Specht, Chrono K. Lee, Haibin Huang, Donald J. Tipper, Zu T. Shen, Jennifer K. Lodge, John D. Leszyk, Gary R. Ostroff, and Stuart M. Levitz

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Design, synthesis, and biological evaluation of tetrazole analogs of Cl-amidine as protein arginine deiminase inhibitors., Venkataraman Subramanian, Jason S. Knight, Sangram Parelkar, Lynne Anguish, Scott A. Coonrod, Mariana J. Kaplan, and Paul R. Thompson

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The Shape of Silence: The Solution-State Conformation of Sir Heterochromatin: A Dissertation, Sarah G. Swygert

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Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS, Helene Tran, Sandra Almeida, Jill Moore, Tania F. Gendron, UmaDevi Chalasani, Yubing Lu, Xing Du, Jeffrey A. Nickerson, Leonard Petrucelli, Zhiping Weng, and Fen-Biao Gao

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Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data, Junko Tsuji and Zhiping Weng

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Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes, Shikui Tu, Monica Z. Wu, Jie Wang, Asher D. Cutter, Zhiping Weng, and Julie M. Claycomb

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Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex, Will Van Treuren, Loganathan Ponnusamy, R Jory Brinkerhoff, Antonio Gonzalez, Christian M. Parobek, Jonathan J. Juliano, Theodore G. Andreadis, Richard C. Falco, Lorenza Beati Ziegler, Nicholas J. Hathaway, Corinna Keeler, Michael Emch, Jeffrey A. Bailey, R. Michael Roe, Charles S. Apperson, Rob Knight, and Steven R. Meshnick

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Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation, Sergey V. Venev and Konstantin B. Zeldovich

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Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype, Natassia M. Vieira, Ingegerd Elvers, Matthew S. Alexander, Yuri B. Moreira, Alal Eran, Juliana P. Gomes, Jamie L. Marshall, Elinor K. Karlsson, Sergio Verjovski-Almeida, Kerstin Lindblad-Toh, Louis M. Kunkel, and Mayana Zatz

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Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2, Thom Vreven, Iain H. Moal, Anna Vangone, Brian G. Pierce, Panagiotis L. Kastritis, Mieczyslaw Torchala, Raphael Chaleil, Brian Jimenez-Garcia, Paul A. Bates, Juan Fernandez-Recio, Alexandre M. J. J. Bonvin, and Zhiping Weng

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Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses, Dan Wang, Haiwei Mou, Shaoyong Li, Yingxiang Li, Soren Hough, Karen Tran, Jia Li, Hao Yin, Daniel G. Anderson, Erik J. Sontheimer, Zhiping Weng, Guangping Gao, and Wen Xue

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Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms, Wei Wang, Bo W. Han, Cindy Tipping, Daniel Tianfang Ge, Zhao Zhang, Zhiping Weng, and Phillip D. Zamore

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Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis, Xindan Wang, Tung B. L. Le, Bryan R. Lajoie, Job Dekker, Michael T. Laub, and David Z. Rudner

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High-resolution chromatin dynamics during a yeast stress response, Assaf Weiner, Tsung-Han S. Hsieh, Alon Appleboim, Hsiuyi V. Chen, Ayelet Rahat, Ido Amit, Oliver J. Rando, and Nir Friedman

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Systemic AAV9 gene transfer in adult GM1 gangliosidosis mice reduces lysosomal storage in CNS and extends lifespan, Cara M. Weismann, Jennifer Ferreira, Allison M. Keeler, Qin Su, Linghua Qiu, Scott A. Shaffer, Zuoshang Xu, Guangping Gao, and Miguel Sena-Esteves

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Molecular targeting of protein arginine deiminases to suppress colitis and prevent colon cancer, Erin E. Witalison, Xiangli Cui, Corey P. Causey, Paul R. Thompson, and Lorne J. Hofseth

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Inhibiting protein arginine deiminases has antioxidant consequences., Erin E. Witalison, Xiangli Cui, Anne B. Hofseth, Venkataraman Subramanian, Corey P. Causey, Paul R. Thompson, and Lorne J. Hofseth

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Protein Arginine Deiminases and Associated Citrullination: Physiological Functions and Diseases Associated with Dysregulation., Erin E. Witalison, Paul R. Thompson, and Lorne J. Hofseth

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Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response, Seungchan Yang, Alexandre Jose Christino Quaresma, Jeffrey A. Nickerson, Karin M. Green, Scott A. Shaffer, Anthony N. Imbalzano, Lori A. Martin-Buley, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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An emerging role for prdm family genes in dorsoventral patterning of the vertebrate nervous system, Denise A. Zannino and Charles G. Sagerstrom

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Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment, Konstantin B. Zeldovich, Ping Liu, Nicholas Renzette, Matthieu Foll, Serena T. Pham, Sergey V. Venev, Glen R. Gallagher, Daniel N. Bolon, Evelyn A. Kurt-Jones, Jeffrey D. Jensen, Daniel R. Caffrey, Celia A. Schiffer, Timothy F. Kowalik, Jennifer P. Wang, and Robert W. Finberg

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Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing, Li Zhang, Ngoc-Tung Tran, Hairui Su, Rui Wang, Yuheng Lu, Haiping Tang, Sayura Aoyagi, Ailan Guo, Alireza Khodadadi-Jamayran, Dewang Zhou, Kun Qian, Todd Hricik, Jocelyn Cote, Xiaosi Han, Wenping Zhou, Suparna Laha, Omar Abdel-Wahab, Ross L. Levine, Glen Raffel, Yanyan Liu, Dongquan Chen, Haitao Li, Tim Townes, Hengbin Wang, Haiteng Deng, Yujun George Zheng, Christina Leslie, Minkui Luo, and Xinyang Zhao

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Increased CRF signalling in a ventral tegmental area-interpeduncular nucleus-medial habenula circuit induces anxiety during nicotine withdrawal, Rubing Zhao-Shea, Steven Degroot, Liwang Liu, Markus Vallaster, Xueyan Pang, Qin Su, Guangping Gao, Oliver J. Rando, Gilles E. Martin, Olivier George, Paul D. Gardner, and Andrew R. Tapper

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

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Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes, Jiali Zhuang and Zhiping Weng

Publications from 2014

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High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody, Gregory J. Babcock, Sowmya Iyer, Heidi L. Smith, Yan Wang, Kirk Rowley, Donna M. Ambrosino, Phillip D. Zamore, Brian G. Pierce, Deborah C. Molrine, and Zhiping Weng

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A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments, Claudia Bank, Ryan T. Hietpas, Alex Wong, Daniel N. Bolon, and Jeffrey D. Jensen

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Viewing protein fitness landscapes through a next-gen lens, Jeffrey I. Boucher, Pamela Cote, Julia Flynn, Li Jiang, Aneth Laban, Parul Mishra, Benjamin P. Roscoe, and Daniel N. Bolon

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Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease, Yufeng Cai, Wazo Myint, Janet L. Paulsen, Celia A. Schiffer, Rieko Ishima, and Nese Kurt Yilmaz

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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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Post-transcriptional regulation of gene expression in innate immunity, Susan Carpenter, Emiliano P. Ricci, Blandine C. Mercier, Melissa J. Moore, and Katherine A. Fitzgerald

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Principles of regulatory information conservation between mouse and human, Yong Cheng, Zhihai Ma, Bong-Hyun Kim, Weisheng Wu, Philip Cayting, Alan P. Boyle, Vasavi Sundaram, Xiaoyun Xing, Nergiz Dogan, Jingjing Li, Ghia Euskirchen, Shin Lin, Yiing Lin, Axel Visel, Trupti Kawli, Xinqiong Yang, Dorrelyn Patacsil, Cheryl A. Keller, Belinda Giardine, Anshul Kundaje, Ting Wang, Len A. Pennacchio, Zhiping Weng, Ross C. Hardison, and Michael P. Snyder

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Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein, Jianbo Chen, David Grünwald, Luca Sardo, Andrea Galli, Sergey Plisov, Olga A Nikolaitchik, De Chen, Stephen Lockett, Daniel R. Larson, Vinay K. Pathak, and Wei-Shau Hu

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Endogenous U2.U5.U6 snRNA complexes in S. pombe are intron lariat spliceosomes, Weijun Chen, Hennady P. Shulha, Ami Ashar-Patel, Jing Yang, Karin M. Green, Charles C. Query, Nicholas R. Rhind, Zhiping Weng, and Melissa J. Moore

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A Feedback Loop Couples Musashi-1 Activity to Omega-9 Fatty Acid Biosynthesis: A Dissertation, Carina C. Clingman

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Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite, Carina C. Clingman, Laura M. Deveau, Samantha A. Hay, Ryan M. J. Genga, Shivender Shandilya, Francesca Massi, and Sean P. Ryder

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Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture, Job Dekker

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Structural basis for PI(4)P-specific membrane recruitment of the Legionella pneumophila effector DrrA/SidM, Claudia M. Del Campo, Ashwini K. Mishra, Yu-Hsiu Wang, Craig R. Roy, Paul A. Janmey, and David G. Lambright

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Insights into the mechanism of streptonigrin-induced protein arginine deiminase inactivation., Christina J. Dreyton, Erin D. Anderson, Venkataraman Subramanian, Dale L. Boger, and Paul R. Thompson

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Mechanistic studies of protein arginine deiminase 2: evidence for a substrate-assisted mechanism, Christina J. Dreyton, Bryan Knuckley, Justin E. Jones, Daniel M. Lewallen, and Paul R. Thompson

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Deimination of linker histones links neutrophil extracellular trap release with autoantibodies in systemic autoimmunity, Nishant Dwivedi, Indira Neeli, Nicolas Schall, Haibao Wan, Dominic M. Desiderio, Elena Csernok, Paul R. Thompson, Hayet Dali, Jean-Paul Briand, Sylviane Muller, and Marko Radic

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Influenza virus drug resistance: a time-sampled population genetics perspective, Matthieu Foll, Yu Ping Poh, Nicholas Renzette, Anna Ferrer Admetlla, Claudia Bank, Hyunjin Shim, Anna Sapfo Malaspinas, Gregory Ewing, Ping Liu, Daniel Wegmann, Daniel R. Caffrey, Konstantin B. Zeldovich, Daniel N. A. Bolon, Jennifer Wang, Timothy F. Kowalik, Celia A. Schiffer, Robert W. Finberg, and Jeffrey D. Jensen

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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 Cys(2)-His(2) 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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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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Backbone flexibility of CDR3 and immune recognition of antigens, Jaafar N. Haidar, Wei Zhu, Jacqueline Lypowy, Brian G. Pierce, Amtul Bari, Kris Persaud, Xenia Luna, Marshall Snavely, Dale Ludwig, and Zhiping Weng

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Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design, Brendan J. Hilbert, Steven R. Grossman, Celia A. Schiffer, and William E. Royer

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Dissecting cis and trans Determinants of Nucleosome Positioning: A Dissertation, Amanda L. Hughes

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Mechanisms underlying nucleosome positioning in vivo, Amanda Hughes and Oliver J. Rando

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Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease, Manolis Kellis, Job Dekker, Zhiping Weng, and Ross C. Hardison

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A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans, Heesun Kim, Takao Ishidate, Krishna S. Ghanta, Meetu Seth, Darryl Conte Jr., Masaki Shirayama, and Craig C. Mello

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Peptidylarginine deiminase inhibition reduces vascular damage and modulates innate immune responses in murine models of atherosclerosis., Jason S. Knight, Wei Luo, Alexander A. O'Dell, Srilakshmi Yalavarthi, Wenpu Zhao, Venkataraman Subramanian, Chiao Guo, Robert C. Grenn, Paul R. Thompson, Daniel T. Eitzman, and Mariana J. Kaplan

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Peptidylarginine deiminase inhibition disrupts NET formation and protects against kidney, skin and vascular disease in lupus-prone MRL/lpr mice., Jason S. Knight, Venkataraman Subramanian, Alexander A. O'Dell, Srilakshmi Yalavarthi, Wenpu Zhao, Carolyne K. Smith, Jeffrey B. Hodgin, Paul R. Thompson, and Mariana J. Kaplan

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Construction and application of site-specific artificial nucleases for targeted gene editing, Fatma O. Kok, Ankit Gupta, Nathan D. Lawson, and Scot A. Wolfe

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HIV-1 protease-substrate coevolution in nelfinavir resistance, Madhavi Kolli, Aysegul Ozen, Nese Kurt Yilmaz, and Celia A. Schiffer

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Hox regulation of transcription: more complex(es), Franck Ladam and Charles G. Sagerstrom

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Insight into the allosteric mechanism of Scapharca dimeric hemoglobin, Jennifer M. Laine, Miguel Amat, Brittany R. Morgan, William E. Royer, and Francesca Massi

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The Hitchhiker's guide to Hi-C analysis: Practical guidelines, Bryan R. Lajoie, Job Dekker, and Noam Kaplan

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Peptidylarginine deiminases: novel drug targets for prevention of neuronal damage following hypoxic ischemic insult (HI) in neonates., Sigrun Lange, Eridan Rocha-Ferreira, Laura Thei, Priyanka Mawjee, Kate Bennett, Paul R. Thompson, Venkataraman Subramanian, Anthony P. Nicholas, Donald Peebles, Mariya Hristova, and Gennadij Raivich

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Blind prediction of interfacial water positions in CAPRI, Marc F. Lensink, Iain H. Moal, Paul A. Bates, Panagiotis L. Kastritis, Adrien S.J. Melquiond, Ezgi Karaca, Christophe Schmitz, Marc van Dijk, Alexandre M.J.J. Bonvin, Miriam Eisenstein, Brian G. Pierce, Howook Hwang, Thom Vreven, and Zhiping Weng

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A FluoPol-ABPP PAD2 high-throughput screen identifies the first calcium site inhibitor targeting the PADs., Daniel M. Lewallen, Kevin L. Bicker, Franck Madoux, Peter Chase, Lynne Anguish, Scott Coonrod, Peter Hodder, and Paul R. Thompson