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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Dissertations and Theses from 2016

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Single Molecule Visualization of the DEAH-Box ARPase Prp22 Interacting with the Spliceosome: A Dissertation, Eric G. Anderson

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Tumor necrosis factor alpha, citrullination, and peptidylarginine deiminase 4 in lung and joint inflammation, Mandar Bawadekar, Annette Gendron-Fitzpatrick, Ryan Rebernick, Daeun Shim, Thomas F. Warner, Anthony P. Nicholas, Lennart K. Lundblad A, Paul R. Thompson, and Miriam A. Shelef

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Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming, Jonathan A. Beagan, Thomas G. Gilgenast, Jesi Kim, Zachary Plona, Heidi K. Norton, Gui Hu, Sarah C. Hsu, Emily J. Shields, Xiaowen Lyu, Effie Apostolou, Konrad Hochedlinger, Victor G. Corces, Job Dekker, and Jennifer E. Phillips-Cremins

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How structural adaptability exists alongside HLA-A2 bias in the human alphabeta TCR repertoire, Sydney J. Blevins, Brian G. Pierce, Nishant K. Singh, Timothy P. Riley, Yuan Wang, Timothy T. Spear, Michael I. Nishimura, Zhiping Weng, and Brian M. Baker

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Synthesis and Testing of Modular Dual-Modality Nanoparticles for Magnetic Resonance and Multispectral Photoacoustic Imaging, Alexei A. Bogdanov Jr., Adam J. Dixon, Suresh Gupta, Lejie Zhang, Shaokuan Zheng, Mohammed S. Shazeeb, Surong Zhang, and Alexander L. Klibanov

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A benchmark testing ground for integrating homology modeling and protein docking, Tanggis Bohnuud, Lingqi Luo, Shoshana J. Wodak, Alexandre M. J. J. Bonvin, Zhiping Weng, Sandor Vajda, Ora Schueler-Furman, and Dima Kozakov

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Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs, Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman, Jacob H. Hanna, Aviv Regev, and Manuel Garber

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Detection and identification of protein citrullination in complex biological systems, Kathleen W. Clancy, Eranthie Weerapana, and Paul R. Thompson

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The 3D Genome as Moderator of Chromosomal Communication, Job Dekker and Leonid A. Mirny

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Activity-Based Profiling Reveals a Regulatory Link between Oxidative Stress and Protein Arginine Phosphorylation, Jakob Fuhrmann, Venkataraman Subramanian, Douglas J. Kojetin, and Paul R. Thompson

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Protein Arginine Methylation and Citrullination in Epigenetic Regulation, Jakob Fuhrmann and Paul R. Thompson

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Structural organization of the inactive X chromosome in the mouse, Luca Giorgetti, Bryan R. Lajoie, Ava C. Carter, Mikael Attia, Ye Zhan, Jin Xu, Chong Jian Chen, Noam Kaplan, Howard Y. Chang, Edith Heard, and Job Dekker

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Redefining the Translational Status of 80S Monosomes, Erin E. Heyer and Melissa J. Moore

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Activation of proto-oncogenes by disruption of chromosome neighborhoods, Denes Hnisz, Abraham S. Weintraub, Daniel S. Day, Anne-Laure Valton, Rasmus O. Bak, Charles H. Li, Johanna Goldmann, Bryan R. Lajoie, Zi Peng Fan, Alla A. Sigova, Jessica Reddy, Diego Borges-Rivera, Tong Ihn Lee, Rudolf Jaenisch, Matthew H. Porteus, Job Dekker, and Richard A. Young

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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance, Li Jiang, Ping Liu, Claudia Bank, Nicholas Renzette, Kristina L. Prachanronarong, L. Safak Yilmaz, Daniel R. Caffrey, Konstantin B. Zeldovich, Celia A. Schiffer, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, and Daniel N. Bolon

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Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Marc F. Lensink, Zhiping Weng, Thom Vreven, Brian G. Pierce, and Tyler M. Borrman

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Peptidylarginine Deiminase 3 (PAD3) Is Upregulated by Prolactin Stimulation of CID-9 Cells and Expressed in the Lactating Mouse Mammary Gland, Guangyuan Li, Isaac N. Hayward, Brittany R. Jenkins, Heather M. Rothfuss, Coleman H. Young, Marja T. Nevalainen, Aaron Muth, Paul R. Thompson, Amy M. Navratil, and Brian D. Cherrington

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Ribosome*RelA structures reveal the mechanism of stringent response activation, Anna B. Loveland, Eugene Bah, Rohini Madireddy, Ying Zhang, Axel F. Brilot, Nikolaus Grigorieff, and Andrei A. Korostelev

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The Identification and Targeting of Partially-Folded Conformations on the Folding Free-Energy Landscapes of ALS-Linked Proteins for Therapeutic Intervention: A Dissertation, Brian C. Mackness

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Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow, Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grünwald, and Thoru Pederson

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Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis, Matthew J. Markert, Ying Zhang, Metewo Selase Enuameh, Steven M. Reppert, Scot A. Wolfe, and Christine Merlin

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Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma, Michael J. McGeachie, Gaurav Jain, Amartya Sanyal, Ye Zhan, Bryan R. Lajoie, Job Dekker, Scott T. Weiss, and CAMP Research Group

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A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections, Nicole Mideo, Jeffrey A. Bailey, Nicholas J. Hathaway, Billy Ngasala, David L. Saunders, Chanthap Lon, Oksana Kharabora, Andrew Jamnik, Sujata Balasubramanian, Anders Bjorkman, Andreas Martensson, Steven R. Meshnick, Andrew F. Read, and Jonathan J. Juliano

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Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire, Lindsey Montefiori, Robert Wuerffel, Damian Roqueiro, Bryan R. Lajoie, Changying Guo, Tatiana Gerasimova, Supriyo De, William Wood, Kevin G. Becker, Job Dekker, Jie Liang, Ranjan Sen, and Amy L. Kenter

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Inhibition of APOBEC3G activity impedes double-stranded DNA repair, Ponnandy Prabhu, Shivender Shandilya, Elena Britan-Rosich, Adi Nagler, Celia A. Schiffer, and Moshe Kotler

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Computational Modeling of T Cell Receptor Complexes, Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals, Upasna Sharma, Colin C. Conine, Jeremy Shea, Ana Boskovic, Alan G. Derr, Xin Y. Bing, Clemence Belleannee, Alper Kucukural, Ryan W. Serra, Fengyun Sun, Lina Song, Benjamin R. Carone, Emiliano P. Ricci, Xin Z. Li, Lucas Fauquier, Melissa J. Moore, Robert Sullivan, Craig C. Mello, Manuel Garber, and Oliver J. Rando

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Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus, Emily M. Smith, Bryan R. Lajoie, Gaurav Jain, and Job Dekker

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Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172, Djade I. Soumana, Nese Kurt Yilmaz, Kristina L. Prachanronarong, Cihan Aydin, Akbar Ali, and Celia A. Schiffer

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The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans, Wen Tang, Shikui Tu, Heng-Chi Lee, Zhiping Weng, and Craig C. Mello

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MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory, Alex Tek, Andrei A. Korostelev, and Samuel Coulbourn Flores

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TAD disruption as oncogenic driver, Anne-Laure Valton and Job Dekker

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Improving Viral Protease Inhibitors to Counter Drug Resistance, Nese Kurt Yilmaz, Ronald I. Swanstrom, and Celia A. Schiffer

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Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo, Hao Yin, Chun-Qing Song, Joseph R. Dorkin, Lihua Julie Zhu, Yingxiang Li, Qiongqiong Wu, Angela I. Park, Junghoon Yang, Sneha Suresh, Aizhan Bizhanova, Ankit Gupta, Mehmet Fatih Bolukbasi, Stephen Walsh, Roman L. Bogorad, Guangping Gao, Zhiping Weng, Yizhou Dong, Victor Koteliansky, Scot A. Wolfe, Robert Langer, Wen Xue, and Daniel G. Anderson

Publications from 2015

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The PsychENCODE project, Schahram Akbarian, Zhiping Weng, Eugenio Mattei, Michael Purcaro, Junko Tsuji, Geetha Senthil, Thomas Lehner, Pamela Sklar, Nenad Sestan, and PsychENCODE Consortium

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Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains, Guang Bai, Iris Cheung, Hennady P. Shulha, Joana E. Coelho, Ping Li, Xianjun Dong, Mira Jakovcevski, Yumei Wang, Anastasia Grigorenko, Yan Jiang, Andrew Hoss, Krupal Patel, Ming Zheng, Evgeny Rogaev, Richard H. Myers, Zhiping Weng, Schahram Akbarian, and Jiang-Fan Chen

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A systematic survey of an intragenic epistatic landscape, Claudia Bank, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. Bolon

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Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells, Ahmet Rasim Barutcu, Bryan R. Lajoie, Rachel Patton McCord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, Andre J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano, and Gary S. Stein

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A Simple Proteomics-Based Approach to Identification of Immunodominant Antigens from a Complex Pathogen: Application to the CD4 T Cell Response against Human Herpesvirus 6B, Aniuska Becerra-Artiles, Omar Dominguez-Amorocho, Lawrence J. Stern, and J. Mauricio Calvo-Calle

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Chromosome Conformation Capture (3C) in Budding Yeast, Jon-Matthew Belton and Job Dekker

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Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast, Jon-Matthew Belton and Job Dekker

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Hi-C in Budding Yeast, Jon-Matthew Belton and Job Dekker

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Measuring Chromatin Structure in Budding Yeast, Jon-Matthew Belton and Job Dekker

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Randomized ligation control for chromosome conformation capture, Jon-Matthew Belton and Job Dekker

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The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer, Jon-Matthew Belton, Bryan R. Lajoie, Sylvain Audibert, Sylvain Cantaloube, Imen Lassadi, Isabelle Goiffon, Davide Bau, Marc A. Marti-Renom, Kerstin Bystricky, and Job Dekker

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Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets, David M. Blodgett, Anetta Nowosielska, Shaked Afik, Susanne Pechhold, Anthony J. Cura, Norman J. Kennedy, Soyoung Kim, Alper Kucukural, Roger J. Davis, Sally C. Kent, Dale L. Greiner, Manuel Garber, David M. Harlan, and Philip J. diLorio Jr.

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Gold nanoparticles stabilized with MPEG-grafted poly(l-lysine): in vitro and in vivo evaluation of a potential theranostic agent, Alexei A. Bogdanov Jr., Suresh Gupta, Nadezhda Koshkina, Stuart J. Corr, Surong Zhang, Steven A. Curley, and Gang Han

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REdiii: a pipeline for automated structure solution, Markus-Frederik Bohn and Celia A. Schiffer

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The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization, Markus-Frederik Bohn, Shivender Shandilya, Tania V. Silvas, Ellen A. Nalivaika, Takahide Kouno, Brian Kelch, Sean P. Ryder, Nese Kurt Yilmaz, Mohan Somasundaran, and Celia A. Schiffer

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DNA-binding-domain fusions enhance the targeting range and precision of Cas9, Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua Julie Zhu, and Scot A. Wolfe

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Structural basis for mutation-induced destabilization of profilin 1 in ALS, Sivakumar Boopathy, Tania V. Silvas, Maeve Tischbein, Silvia Jansen, Shivender Shandilya, Jill A. Zitzewitz, John E. Landers, Bruce L. Goode, Celia A. Schiffer, and Daryl A. Bosco

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R loops regulate promoter-proximal chromatin architecture and cellular differentiation, Poshen B. Chen, Hsiuyi V. Chen, Diwash Acharya, Oliver J. Rando, and Thomas G. Fazzio

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Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs, Min-Te Chou, Bo W. Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, and Jui-Hung Hung

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Condensin-driven remodelling of X chromosome topology during dosage compensation, Emily Crane, Qian Bian, Rachel Patton McCord, Bryan R. Lajoie, Bayly S. Wheeler, Edward J. Ralston, Satoru Uzawa, Job Dekker, and Barbara J. Meyer

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard

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Long-Range Chromatin Interactions, Job Dekker and Tom Misteli

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The Lipid Droplet Protein Hypoxia-inducible Gene 2 Promotes Hepatic Triglyceride Deposition by Inhibiting Lipolysis, Marina T. DiStefano, Laura V. Danai, Rachel J. Roth Flach, Anil K. Chawla, David J. Pedersen, Adilson L. Guilherme, and Michael P. Czech

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POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA, Ahmed M. Elewa, Masaki Shirayama, Ebru Kaymak, Paul F. Harrison, David R. Powell, Zhuo Du, Christopher D. Chute, Hannah Woolf, Dongni Yi, Takao Ishidate, Jagan Srinivasan, Zhirong Bao, Traude H. Beilharz, Sean P. Ryder, and Craig C. Mello

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Epigenomics and the structure of the living genome, Nir Friedman and Oliver J. Rando

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Chemical Biology of Protein Arginine Modifications in Epigenetic Regulation, Jakob Fuhrmann, Kathleen W. Clancy, and Paul R. Thompson

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Synthesis and Use of a Phosphonate Amidine to Generate an Anti-Phosphoarginine-Specific Antibody, Jakob Fuhrmann, Venkataraman Subramanian, and Paul R. Thompson

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Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements, Ming Gao, Travis Thomson, T Michael Creed, Shikui Tu, Sudan N. Loganathan, Christina A. Jackson, Patrick McCluskey, Yanyan Lin, Scott E. Collier, Zhiping Weng, Paul Lasko, Melanie D. Ohi, and Alexey L. Arkov

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Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF, Sarah J. Hainer, Weifeng Gu, Benjamin R. Carone, Benjamin D. Landry, Oliver J. Rando, Craig C. Mello, and Thomas G. Fazzio

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Using Experimental and Computational Strategies to Understand the Biogenesis of microRNAs and piRNAs: A Dissertation, Bo W. Han

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Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production, Bo W. Han, Wei Wang, Chengjian Li, Zhiping Weng, and Phillip D. Zamore

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piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing, Bo W. Han, Wei Wang, Phillip D. Zamore, and Zhiping Weng

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Near-infrared photoactivatable control of Ca signaling and optogenetic immunomodulation, Lian He, Yuanwei Zhang, Guolin Ma, Peng Tan, Zhan Jun Li, Shengbing Zhang, Xiang Wu, Ji Jing, Shaohai Fang, Lijuan Zhou, Youjun Wang, Yun Huang, Patrick Hogan, Gang Han, and Yubin Zhou

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Optimizing RNA Library Preparation to Redefine the Translational Status of 80S Monosomes: A Dissertation, Erin E. Heyer

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An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments, Erin E. Heyer, Hakan Ozadam, Emiliano P. Ricci, Can Cenik, and Melissa J. Moore

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Structure-Guided Design of a High Affinity Inhibitor to Human CtBP, Brendan J. Hilbert, Benjamin L. Morris, Keith C. Ellis, Janet L. Paulsen, Celia A. Schiffer, Steven R. Grossman, and William E. Royer

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Utilization of the Soft Agar Colony Formation Assay to Identify Inhibitors of Tumorigenicity in Breast Cancer Cells, Sachi Horibata, Tommy V. Vo, Venkataraman Subramanian, Paul R. Thompson, and Scott A. Coonrod

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miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. MacDonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, and Richard H. Myers

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Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C, Tsung-Han S. Hsieh, Assaf Weiner, Bryan R. Lajoie, Job Dekker, Nir Friedman, and Oliver J. Rando

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Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo, Amanda Hughes and Oliver J. Rando

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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