Areas of research within the Department of Biology include microbiology, cell biology, developmental biology, physiology, neuroscience, animal behavior, plant biology, genomics, computational biology, evolution, ecology and biodiversity.

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Submissions from 2017

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The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell, Mark M. Slabodnick, J. G. Ruby, Sarah B. Reiff, Estienne C. Swart, Sager J. Gosai, Sudhakaran Prabakaran, Ewa Witkowska, Graham E. Larue, Brian D. Gregory, Mariusz Nowacki, Joseph Derisi, Scott W. Roy, Wallace F. Marshall, and Pranidhi Sood

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Genome-Wide TOP2A DNA Cleavage is Biased Toward Translocated and Highly Transcribed Loci, Xiang Yu, James W. Davenport, Karen A. Urtishak, Marie L. Carillo, Sager J. Gosai, Christos P. Kolaris, Jo Ann W. Byl, Eric F. Rappaport, Neil Osheroff, Brian D. Gregory, and Carolyn A. Felix

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Chromatin Dynamics during the Differentiation of Long-Term Hematopoietic Stem Cells to Multipotent Progenitors, Xiang Yu, Chao Wu, Dheeraj Bhavanasi, Hong Wang, Brian D. Gregory, and Jian Huang

Submissions from 2016

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A Comprehensive Database of High-Throughput Sequencing-Based RNA Secondary Structure Probing Data (Structure Surfer), Nathan D. Berkowitz, Ian M. Silverman, Daniel M. Childress, Hilal Kazan, Li-San Wang, and Brian D. Gregory

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Changes in the Transcriptome of Human Astrocytes Accompanying Oxidative Stress-Induced Senescence, Elizabeth P. Crowe, Ferit Tuzer, Brian D. Gregory, Greg Donahue, Sager J. Gosai, Justin Cohen, Yuk Y. Leung, Emre Yetkin, Raffaella Nativio, Shelley L. Berger, F. B. Johnson, and Claudio Torres

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Stable and Sporadic Symbiotic Communities of Coral and Algal Holobionts, Eric R. Hester, Katie Barott, Jim Nulton, Mark J.A Vermeij, and Forest Rohwer

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Cytoplasmic Poly(A) Binding Protein-1 Binds to Genomically Encoded Sequences Within Mammalian mRNAs, Hemant K. Kini, Ian M. Silverman, Xinjun Ji, Brian D. Gregory, and Stephen A. Liebhaber

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Microbial Community Structure Affects Marine Dissolved Organic Matter Composition, Elizabeth B. Kujawinski, Krista Longnecker, Katie Barott, Ralf J.M Weber, and Melissa C. Kido Soule

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DASHR: Database of Small Human Noncoding RNAs, Yuk Y. Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, and Li-San Wang

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Local Admixture of Amplified and Diversified Secreted Pathogenesis Determinants Shapes Mosaic Toxoplasma gondii Genomes, Hernan Lorenzi, Asis Kahn, Michael S. Behnke, Sivaranjani Namasivayam, Lakshmipuram S. Swapna, Michalis Hadjithomas, Svetlana Karamycheva, Deborah Pinney, Brian P. Brunk, James W. Ajioka, Daniel Ajzenberg, John C. Boothroyd, Jon P. Boyle, Marie Dardé, Marie A. Diaz-Miranda, Jitender P. Dubey, Heather M. Fritz, Solange M. Gennari, Brian D. Gregory, Kami Kim, Jeroen PJ Saeij, Chunlei Su, Michael W. White, Xing-Quan Zhu, Daniel K. Howe, Benjamin M. Rosenthal, Michael E. Grigg, John Parkinson, Liang Liu, Jessica C. Kissinger, David S. Roos, and L. D. Sibley

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Terpene Metabolic Engineering via Nuclear or Chloroplast Genomes Profoundly and Globally Impacts Off-Target Pathways Through Metabolite Signalling, Elise K. Pasoreck, Jin Su, Ian M. Silverman, Sager J. Gosai, Brian D. Gregory, Joshua S. Yuan, and Henry Daniell

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Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis, Xiang Yu, Matthew R. Willmann, Stephen J. Anderson, and Brian D. Gregory

Submissions from 2015

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Evolutionary Models of Mutualism, Erol Akçay

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Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Revel Dysregulation of Histone Transcripts and Nuclear Chromatin, Alexandre Amlie-Wolf, Paul Ryvkin, Rui Tong, Isabelle Dragomir, EunRan Suh, Yan Xu, Vivianna M. Van Deerlin, Brian D. Gregory, Linda K. Kwong, John Q. Trojanowski, Virginia Man-Yee Lee, Li-San Wang, and Edward B. Lee

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Immunolocalization of Proteins in Corals: The V-Type H+-ATPase Proton Pump, Katie Barott and Martin Tresguerres

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Coral Host Cells Acidify Symbiotic Algal Microenvironment to Promote Photosynthesis, Katie Barott, Alexander A. Venn, Sidney O. Perez, Sylvie Tambutté, and Martin Tresguerres

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Social Inheritance Can Explain the Structure of Animal Social Networks, Amiyaal Ilany and Erol Akçay

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The Msi Family of RNA-Binding Proteins Function Redundantly as Intestinal Oncoproteins, Ning Li, Maryam Yousefi, Angela Nakauka-Ddamba, Fan Li, Lee Vandivier, Kimberly Parada, Dong-Hun Woo, Shan Wang, Ammar S. Naqvi, Shilpa Rao, John Tobias, Ryan J. Cedeno, Gerard Minuesa, Katz Y, Trevor S. Barlowe, Alexander James Valvezan, Sheila Shankar, Raquel R. Deering, Peter S. Klein, Shane T. Jensen, Michael G. Kharas, Brian D. Gregory, Zhengquan Yu, and Christopher J. Lengner

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Detection of Pol IV/RDR2-Dependent Transcripts at the Genomic Scale in Arabidopsis Reveals Features and Regulation of siRNA Biogenesis, Shaofang Li, Lee E. Vandivier, Bin Tu, Lei Gao, So Youn Won, Shengben Li, Binglian Zheng, Brian D. Gregory, and Xuemei Chen

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Sexual Selection Studies: A NESCent Catalyst Meeting, Joan Roughgarden, Elizabeth Adkins-Regan, Erol Akçay, Jeremy Chase Crawford, Raghavendra Gadagkar, Simon C. Griffith, Camilla A. Hinde, Thierry Hoquet, Cailin O'Connor, Zofia M. Prokop, Richard O. Prum, Sharoni Shafir, Samuel S. Snow, Daniel Taylor, Jeremy Van Cleve, and Michael Weisberg

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H3K36 Methylation Promotes Longevity by Enhancing Transcriptional Fidelity, Payel Sen, Weiwei Dang, Greg Donahue, Junbiao Dai, Wei Liu, Kajia Cao, Rocco Perry, Jun Y. Lee, Brian M. Wasko, Daniel T. Carr, Chong He, Brett Robison, John Wagner, Brian D. Gregory, Matt Kaeberlein, Brian K. Kennedy, Jef D. Boeke, and Shelley L. Berger

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Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes, Paula Stein, Nikolay V. Rozhkov, Fan Li, Fabián L. Cárdenas, Olga Davydenko, Lee Vandivier, Brian D. Gregory, Gregory J. Hannon, and Richard M. Schultz

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Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidposis, Lee E. Vandivier, Rafael Campos, Pavel P. Kuksa, Ian M. Silverman, Li-San Wang, and Brian D. Gregory

Submissions from 2014

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Paternal Poly (ADP-ribose) Metabolism Modulates Retention of Inheritable Sperm Histones and Early Embryonic Gene Expression, Motomasa Ihara, Mirella L. Meyer-Ficca, N. A. Leu, Shilpa Rao, Fan Li, Brian D. Gregory, Irina A. Zalenskaya, Richard M. Schultz, and Ralph G. Meyer

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Local Genomic Adaptation of Coral Reef-Associated Microbiomes to Gradients of Natural Variability and Anthropogenic Stressors, Linda W. Kelly, Gareth J. Williams, Katie Barott, Craig A. Carlson, Elizabeth A. Dinsdale, Robert A. Edwards, Andreas F. Haas, Matthew Haynes, Yan W. Lim, Tracey McDole, Craig E. Nelson, Enric Sala, Stuart A. Sandin, Jennifer E. Smith, Mark J.A Vermeij, Merry Youle, and Forest Rohwer

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Evolution of TNF-Induced Apoptosis Reveals 550 My of Functional Conservation, Steven D. Quistad, Aleksandr Stotland, Katie Barott, Cameron A. Smurthwaite, Brett J. Hilton, Juris A. Grasis, Roland Wolkowicz, and Forest Rohwer

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Group Size and Social Conflict in Complex Societies, Sheng-Feng Shen, Erol Akçay, and Dustin R. Rubenstein

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RNase-Mediated Protein Footprint Sequencing Reveals Protein-Binding Sites Throughout the Human Transcriptome, Ian M. Silverman, Fan Li, Anissa Alexander, Loyal Goff, Cole Trapnell, John L. Rinn, and Brian D. Gregory

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Established and Potential Physiological Roles of Bicarbonate-Sensing Soluble Adenylyl Cyclase (sAC) in Aquatic Animals, Martin Tresguerres, Katie Barott, Megan E. Barron, and Jinae N. Roa

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Pathways to Social Evolution: Reciprocity, Relatedness, and Synergy, Jeremy Van Cleve and Erol Akçay

Submissions from 2013

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Biological Institutions: The Political Science of Animal Cooperation, Erol Akçay, Joan Roughgarden, James Fearon, John Ferejohn, and Barry R. Weingast

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High Adenylyl Cyclase Activity and In Vivo cAMP Fluctuations in Corals Suggest Central Physiological Role, Katie Barott, Y. Helman, L. Haramaty, Megan E. Barron, K. C. Hess, J. Buck, L. R. Levin, and Martin Tresguerres

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Analysis of the Host Transcriptome from Demyelinating Spinal Cord of Murine Coronavirus-Infected Mice, Ruth Elliott, Fan Li, Isabelle Dragomir, Ming Ming W. Chua, Brian D. Gregory, and Susan R. Weiss

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Biological Oxygen Demand Optode Analysis of Coral Reef-Associated Microbial Communities Exposed to Algal Exudates, Allison K. Gregg, Mark Hatay, Andreas F. Haas, Nathan L. Robinett, Katie Barott, Mark J.A Vermeij, Kristen L. Marhaver, Pedro M. Meirelles, Fabiano Thompson, and Forest Rohwer

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High-Throughput Identification of Long-Range Regulatory Elements and Their Target Promoters in the Human Genome, Yih-Chii Hwang, Qi Zheng, Brian D. Gregory, and Li-San Wang

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CoRAL: Predicting Non-Coding RNAs from Small RNA-Sequencing Data, Yuk Y. Leung, Paul Ryvkin, Lyle H. Ungar, Brian D. Gregory, and Li-San Wang

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Evaluating the Impacts of Sequencing Depth on Transcriptome Profiling in Human Adipose, Yichuan Liu, Jane F. Ferguson, Chenyi Xue, Ian M. Silverman, Brian D. Gregory, Muredach P. Reilly, and Mingyao Li

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Water Stress Strengthens Mutualism Among Ants, Trees, and Scale Insects, Elizabeth G. Pringle, Erol Akçay, Ted K. Raab, Rodolfo Dirzo, and Deborah M. Gordon

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Viral Information, Forest Rohwer and Katie Barott

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HAMR: High-Throughput Annotation of Modified Ribonucleotides, Paul Ryvkin, Yuk Y. Leung, Ian M. Silverman, Micah Childress, Otto Valladares, Isabelle Dragomir, Brian D. Gregory, and Li-San Wang

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Dicer-2 Processes Diverse Viral RNA Species, Leah R Sabin, Qi Zheng, Pramod Thekkat, Jamie Yang, Gregory J. Hannon, Brian D. Gregory, Matthew Tudor, and Sara Cherry

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Lamin B1 Depletion in Senescent Cells Triggers Large-Scale Changes in Gene Expression and the Chromatin Landscape, Parisha P. Shah, Greg Donahue, Gabriel Otte, Brian C. Capell, David M. Nelson, Kajia Cao, Varun Aggarwala, Hazel A. Cruickshanks, Taranjit Singh Rai, Tony McBryan, Brian D. Gregory, Peter D. Adams, and Shelley L. Berger

Submissions from 2012

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Behavioral Responses in Structured Populations Pave the Way to Group Optimality, Erol Akçay and Jeremy Van Cleve

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Natural History of Coral-Algae Competition across a Gradient of Human Activity in the Line Islands, Katie Barott, Gareth J. Williams, Mark J.A Vermeij, Jill Harris, Jennifer E. Smith, Forest Rohwer, and Stuart A. Sandin

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SAVoR: A Server for Sequencing Annotation and Visualization of RNA Structures, Fan Li, Paul Ryvkin, Daniel M. Childress, Otto Valladares, Brian D. Gregory, and Li-San Wang

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Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome, Fan Li, Lee E. Vandivier, Matthew R. Willmann, Ying Chen, and Brian D. Gregory

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Global Analysis of RNA Secondary Structure in Two Metazoans, Fan Li, Qi Zheng, Paul Ryvkin, Isabelle Dragomir, Yaanik Desai, Subhadra Aiyer, Otto Valladares, Jamie Yang, Shelley Bambina, Leah R Sabin, John I. Murray, Todd Lamitina, Arjun Rai, Sara Cherry, Li-San Wang, and Brian D. Gregory

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Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score, Tracey McDole, Jim Nulton, Katie Barott, Ben Feits, Carol Hand, Mark Hatay, Hochul Lee, Mark O. Nadon, Bahador Nosrat, Peter Salamon, Barbara Bailey, Stuart A. Sandin, Bernardo Vargas-Angel, Merry Youle, Brian J. Zgliczynski, Russell E. Brainard, and Forest Rohwer

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Spatial and Functional Relationships Among Pol V-Associated Loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome, Andrzej T. Wierzbicki, Ross Cocklin, Anoop Mayampurath, Ryan Lister, M. J. Rowley, Brian D. Gregory, Joseph R. Ecker, Haixu Tang, and Craig S. Pikaard

Submissions from 2011

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The Evolution of Payoff Matrices: Providing Incentives to Cooperate, Erol Akçay and Joan Roughgarden

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Negotiation, Sanctions, and Context Dependency in the Legume-Rhizobium Mutualism, Erol Akçay and Ellen L. Simms

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The Functions of RNA-Dependent RNA Polymerases in Arabidopsis, Matthew R. Willmann, Matthew W. Endres, Rebecca T. Cook, and Brian D. Gregory

Submissions from 2010

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The Lagoon at Caroline/Millennium Atoll, Republic of Kiribati: Natural History of a Nearly Pristine Ecosystem, Katie Barott, Jennifer E. Caselle, Elizabeth A. Dinsdale, Alan M. Friedlander, James E. Maragos, David Obura, Forest Rohwer, Stuart A. Sandin, Jennnifer E. Smith, and Brian Zgliczynski

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An Endogenous F-Box Protein Regulates ARGONAUTE1 in Arabidopsis thaliana, K. Earley, M. R. Smith, R. Weber, Brian D. Gregory, and R. S. Poethig

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Two Plant Viral Suppressors of Silencing Require the Ethylene-Inducible Host Transcription Factor RAV2 to Block RNA Silencing, Matthew W. Endres, Brian D. Gregory, Zhihuan Gao, Amy W. Foreman, Sizolwenkosi Mlotshwa, Xin Ge, Gail J. Pruss, Joseph R. Ecker, Lewis H. Bowman, and Vicki Vance

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Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis, Qi Zheng, Paul Ryvkin, Fan Li, Isabelle Dragomir, Otto Valladares, Jamie Yang, Kajia Cao, Li-San Wang, and Brian D. Gregory

Submissions from 2009

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New Approaches to the Evolution of Social Behavior, Erol Akçay

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The Perfect Family: Decision Making in Biparental Care, Erol Akçay and Joan Roughgarden

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The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes, Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmeider, Rebecca L.V Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. M. Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, and Forest Rohwer

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Hyperspectral and Physiological Analyses of Coral-Algal Interactions, Katie Barott, Jennifer Smith, Elizabeth A. Dinsdale, Mark Hatay, Stuart A. Sandin, and Forest Rohwer

Submissions from 2008

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Metagenomic Analysis Indicates that Stressors Induce Production of Herpes-Like Viruses in Coral Porites compressa, Rebecca L.V Thurber, Katie Barott, Dana Hall, Hong Liu, Beltran Rodriguez-Mueller, Christelle Desnues, Robert A. Edwards, Matthew Haynes, Florent E. Angly, Linda Wegley, and Forest Rohwer

Submissions from 2007

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Extra-Pair Parentage: A New Theory Based on Transactions in a Cooperative Game, Erol Akçay and Joan Roughgarden

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Extra-Pair Paternity in Birds: Review of the Genetic Benefits, Erol Akçay and Joan Roughgarden

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Negotiation of Mutualism: Rhizobia and Legumes, Erol Akçay and Joan Roughgarden

Submissions from 2006

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ETHYLENE-INSENSITIVE5 Encodes a 5'→3' Exoribonuclease Required for Regulation of the EIN3-Targeting F-Box Proteins EDF1⁄2, Gabriela Olmedo, Hongwei Guo, Brian D. Gregory, Saeid D. Nourizadeh, Laura Aguilar-Henonin, Hongjiang Li, Fengying An, Plinio Guzman, and Joseph R. Ecker

Submissions from 2004

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A Regulator That Inhibits Transcription by Targeting an Intersubunit Interaction of the RNA Polymerase Holoenzyme, Brian D. Gregory, B. E. Nickels, S. J. Garrity, E. Severinova, L. Minakhin, R.J. B. Urbauer, J. L. Urbauer, and T. Heyduk

Submissions from 1999

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The Arabidopsis dwarf1 Mutant is Defective in the Conversion of 24-Methylenecholesterol to Campesterol in Brassinosteroid Biosynthesis, Sunghwa Choe, Brian P. Dilkes, Brian D. Gregory, Amanda S. Ross, Heng Yuan, Takahiro Noguchi, Shozo Fujioka, Suguru Takatsuto, Atsushi Tanaka, Shigeo Yoshida, Frans E. Tax, and Kenneth A. Feldmann

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The Arabidopsis dwf/ste1 Mutant is Defective in the Δ7 Sterol C-5 Desaturation Step Leading to Brassinosteroid Biosynthesis, Sunghwa Choe, Takahiro Noguchi, Shozo Fujioka, Suguru Takatsuto, Christophe P. Tissier, Brian D. Gregory, Amanda S. Ross, Atsushi Tanaka, Shigeo Yoshida, Frans E. Tax, and Kenneth A. Feldmann