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2012

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Influence of aphid honeydew on the foraging behavior of Hippodamia convergens larvae, Swapna R. Purandare and Brigitte Tenhumberg

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Bacterial community structure of contrasting soils underlying Bornean rain forests: Inferences from microarray and next-generation sequencing methods, Sabrina E. Russo, Ryan Legge, Karrie A. Weber, Eoin L. Brodie, Katherine C. Goldfarb, Andrew K. Benson, and Sylvester Tan

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Covariation between understorey light environments and soil resources in Bornean mixed dipterocarp rain forest, Sabrina E. Russo, Lin Zhang, and Sylvester Tan

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Family Dynamics Through Time: Brood Reduction Followed by Parental Compensation with Aggression and Favoritism, Daizaburo Shizuka and Bruce E. Lyon

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A Social Network Perspective on Measurements of Dominance Hierarchies, Daizaburo Shizuka and David B. McDonald

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Tradeoffs limit the evolution of male traits that are attractive to females, William E. Wagner, Oliver M. Beckers, Amanda E. Tolle, and Alexandra Basolo

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Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics, David W. Weisrock, Stacey DeWitt Smith, Lauren M. Chan, Karla Biebouw, Peter M. Kappeler, and Anne D. Yoder

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SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity, Bo Yao, Lin Zhang, Shide Liang, and Chi Zhang

2011

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SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation, Catherine L. Anderson, Cory L. Strope, and Etsuko N. Moriyama

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Use of Nape Tags for Marking Offspring of Precocial Waterbirds, Todd W. Arnold, Daizaburo Shizuka, Bruce E. Lyon, Jeffrey T. Pelayo, Katherine R. Mehl, Joshua J. Traylor, Wendy L. Reed, and Courtney L. Amundson

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Crystallization of Chlorella deoxyuridine triphosphatase, Laura Badalucco, Ishwari Poudel, Mamoru Yamanishi, Chandrasekhar Natarajan, and Hideaki Moriyama

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Survival Rates of Planidial Larvae of the Parasitoid Fly Ormia ochracea (Diptera: Tachinidae), Oliver M. Beckers, Cassandra M. Martin, and William E. Wagner Jr.

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Male Field Crickets Infested by Parasitoid Flies Express Phenotypes that May Benefit the Parasitoids, Oliver M. Beckers and William E. Wagner

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Composite Effects of Polymorphisms near Multiple Regulatory Elements Create a Major-Effect QTL, Ryan D. Bickel, Artyom Kopp, and Sergey V. Nuzhdin

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EFFECTS OF POSTMORTEM INTERVAL AND PRESERVATION METHOD ON RNA ISOLATED FROM FIELD-PRESERVED AVIAN TISSUES Efectos del Intervalo Post-Mortem y del Método de Preservación en el ARN Aislado de Tejidos de Aves Preservados en el Campo, Zachary A. Cheviron, Matthew D. Carling, and Robb T. Brumfield

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Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila, Cássia C. de Oliveira, Maura H. Manfrin, Fábio de M Sene, Larry L. Jackson, and William J. Etges

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The Effects of Belowground Resources on Aboveground Allometric Growth in Bornean Tree Species, Katherine D. Heineman, Ethan Jensen, Autumn Shapland, Brett Bogenrief, Sylvester Tan, Richard Rebarber, and Sabrina E. Russo

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Increased transsulfuration mediates longevity and dietary restriction in Drosophila, Hadise Kabil, Omer Kabil, Ruma Banerjee, Lawrence G. Harshman, and Scott D. Pletcher

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Population Dynamics of the Western Prickly Pear, Opuntia macrorhiza (Cactaceae), Kathleen H. Keeler and Brigitte Tenhumberg

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Characterization of a Dipartite Iron Uptake System from Uropathogenic Escherichia coli Strain, Doreen Koch, Anson C. K. Chan, Michael E.P. Murphy, Hauke Lilie, Gregor Grass, and Dietrich H. Nies

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Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: Enrichment cultures with different short-chain fatty acids as electron donors, Huijuan Li, Jingjing Peng, Karrie A. Weber, and Yongguan Zhu

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Morphologic Clues to the Origins of Iron Oxide–Cemented Spheroids, Boxworks, and Pipelike Concretions, Navajo Sandstone of South-Central Utah, U.S.A., David B. Loope, Richard M. Kettler, and Karrie A. Weber

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Priority resource access mediates competitive intensity between an invasive weevil and native floral herbivores, Svata M. Louda, Tatyana A. Rand, A. A. R. Kula, A. E. Arnett, N. M. West, and Brigitte Tenhumberg

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VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus, Yukari Maezato, Amanda Daugherty, Karl Dana, Edith Soo, Charlotte Cooper, Sabrina Tachdjian, Robert M. Kelly, and Paul Blum

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A cytoplasm-specific activity encoded by the Trithorax-like ATX1 gene, Ivan Ndamukong, Hanna Lapko, Ronald L. Cerny, and Zoya Avramova

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Integral projection model of insect herbivore effects on Cirsium altissimum populations along productivity gradients, Karen E. Rose, F. Leland Russell, and Svata M. Louda

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Genomic and Resistance Gene Homolog Diversity of the Dominant Tallgrass Prairie Species across the U.S. Great Plains Precipitation Gradient, Matthew N. Rouse, Amgad A. Saleh, Amadou Seck, Kathleen H. Keeler, Steven E. Travers, Scot H. Hulbert, and Karen A. Garrett

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Evidence for Air Movement Signals in the Agonistic Behaviour of a Nocturnal Arachnid (Order Amblypygi), Roger D. Santer and Eileen A. Hebets

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Comparative genomics of proteins involved in RNA nucleocytoplasmic export, Mariana Serpeloni, Newton M. Vidal, Samuel Goldenberg, Andréa R. Ávila, and Federico G. Hoffmann

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Analyses of Fruit Flies That Do Not Express Selenoproteins or Express the Mouse Selenoprotein, Methionine Sulfoxide Reductase B1, Reveal a Role of Selenoproteins in Stress Resistance, Valentina A. Shchedrina, Hadise Kabil, Gerd Vorbruggen, Byung Cheon Lee, Anton A. Turanov, Mitsuko Hirosawa- Takamori, Hwa- Young Kim, Lawrence G. Harshman, Dolph L. Hatfield, and Vadim N. Gladyshev

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Hosts Improve the Reliability of Chick Recognition by Delaying the Hatching of Brood Parasitic Eggs, Daizaburo Shizuka and Bruce E. Lyon

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Molecular evolution of urea amidolyase and urea carboxylase in fungi, Pooja K. Strope, Kenneth W. Nickerson, Steven D. Harris, and Etsuko N. Moriyama

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Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils, J. Ian Van Trump, Kelly C. Wrighton, J. Cameron Thrash, Karrie A. Weber, Gary L. Andersen, and John D. Coates

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dtorsin, the Drosophila Ortholog of the Early-Onset Dystonia TOR1A (DYT1), Plays a Novel Role in Dopamine Metabolism, Noriko Wakabayashi-Ito, Olugbenga M. Doherty, Hideaki Moriyama, Xandra O. Breakefield, James F. Gusella, Janis M. O’Donnell, and Naoto Ito

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Environmental and Taxonomic Bacterial Diversity of Anaerobic Uranium(IV) Bio-Oxidation, Karrie A. Weber, J. Cameron Thrash, J. Ian Van Trump, Laurie A. Achenbach, and John D. Coates

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Interferon Regulatory Factor 4 (IRF-4) Targets IRF-5 to Regulate Epstein-Barr Virus Transformation, Dongsheng Xu, Florencia Meyer, Erica Ehlers, Laura Blasnitz, and Luwen Zhang

2010

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Association of rs780094 in GCKR with Metabolic Traits and Incident Diabetes and Cardiovascular Disease: The ARIC Study, Mark Bi, Wen Hong Linda Kao, Eric Boerwinkle, Ron C. Hoogeveen, Laura J. Rasmussen-Torvik, Brad C. Astor, Kari E. North, Joseph Coresh, and Anna Kottgen

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The spatial influence of aboveground diversity on belowground communities, T. Bliss, Tom Powers, and Chad Brassil

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Cognitive Representation in Transitive Inference: A Comparison of Four Corvid Species, Alan B. Bond, Cynthia A. Wei, and Alan C. Kamil

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Structured Population Dynamics: An Introduction to Integral Modeling, Joseph Briggs, Kathryn Dabbs, Michael Holm, Joan Lubben, Richard Rebarber, Brigitte Tenhumberg, and Daniel Riser-Espinoza

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Genome Sequence of the Pea Aphid Acyrthosiphon pisum, Jennifer A. Brisson, Stephen Richards, and International Aphid Genomics Consortium

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Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY, Kathryne G. Byrne-Bailey, Karrie A. Weber, Antinea H. Chair, Saumyaditya Bose, Traci Knox, Trisha L. Spanbauer, Olga Chertkov, and John D. Coates

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The Capsid Protein of Turnip Crinkle Virus Overcomes Two Separate Defense Barriers to Facilitate Systemic Movement of the Virus in Arabidopsis, Mingxia Cao, Xiaohong Yi, Kristen Willie, Junyan Lin, Xiuchun Zhang, Margaret G. Redinbaugh, Anne E. Simon, Thomas Jack Morris, and Feng Qu

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Glycopeptidome of a Heavily N-Glycosylated Cell Surface Glycoprotein of Dictyostelium Implicated in Cell Adhesion, Christa L. Feasley, Jennifer M. Johnson, Christopher M. West, and Catherine P. Chia

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The polypeptide Syn67 interacts physically with human holocarboxylase synthetase, but is not a target for biotinylation, Yousef I. Hassan, Hideaki Moriyama, and Janos Zempleni

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Effects of Plant Sex on Range Distributions and Allocation to Reproduction, Marc T.J. Johnson, Stacey DeWitt Smith, and Mark D. Rausher

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Activity and Toxicity of Farnesol towards Candida albicans Are Dependent on Growth Conditions, Melanie L. Langford, Sahar Hasim, Kenneth W. Nickerson, and Audrey L. Atkin

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EPSVR and EPMeta: Prediction of Antigenic Epitopes Using Support Vector Regression and Multiple Server Results, Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, and Chi Zhang

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Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine, Debabrata Mandal, Caroline Köhrer, Dan Su, Susan P. Russell, Kady Krivos, Colette M. Castleberry, Paul H. Blum, Patrick A. Limbach, Dieter Söll, and Uttam L. RajBhandary

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Female Field Crickets Incur Increased Parasitism Risk When Near Preferred Song, Cassandra M. Martin and William E. Wagner Jr.

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Contributions of demography and dispersal parameters to the spatial spread of a stage-structured insect invasion, Tom E. X. Miller and Brigitte Tenhumberg

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Phosphatidylinositol 5-Phosphate Links Dehydration Stress to the Activity of Arabidopsis Trithorax-Like Factor ATX1, Ivan Ndamukong, David R. Jones, Hanna Lapko, Nullin Divecha, and Zoya V. Avramova

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Evolution of the Kdo2-lipid A Biosynthesis in Bacteria, Stephen O. Opiyo, Rosevelt L. Pardy, Hideaki Moriyama, and Etsuko Moriyama

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Viral trans-Factor Independent Replication of Human Papillomavirus Genomes, Daraporn Pittayakhajonwut and Peter C. Angeletti

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Seed availability and insect herbivory limit recruitment and adult density of native tall thistle, F. Leland Russell, Karen E. Rose, and Svata M. Louda

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Variation in Leaf Stomatal Traits of 28 Tree Species in Relation to Gas Exchange along an Edaphic Gradient in a Bornean Rain Forest, Sabrina E. Russo, Whitney Logan Cannon, Christian Gary Elowsky, Sylvester Tan, and Stuart J. Davies

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Interspecific Relationships among Growth, Mortality and Xylem Traits of Woody Species from New Zealand, Sabrina E. Russo, Kerry L. Jenkins, Susan K. Wiser, Maria Uriarte, Richard P. Duncan, and David A. Coomes

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Isolation and Characterization of Bacteria Resistant to Metallic Copper Surfaces, Christophe Espírito Santo, Paula Vasconcelos Morais, and Gregor Grass

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The Effects of Flower Color Transitions on Diversification Rates in Morning Glories (Ipomoea subg. Quamoclit, Convolvulaceae), Stacey DeWitt Smith, Richard E. Miller, Sarah P. Otto, Richard G. FitzJohn, and Mark D. Rausher

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Ignoring Population Structure Can Lead to Erroneous Predictions of Future Population Size, Brigitte Tenhumberg

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Dynamic Changes in Genome-Wide Histone H3 Changes Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana, Karen van Dijk, Yong Ding, Sridar Achary Malkaram, Jean-Jack M. Riethoven, Rong Liu, Jingyi Yang, Peter Laczko, Han Chen, Yuannan Xia, Istvan Ladunga, Zoya V. Avramova, and Michael E. Fromm

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Differences in HIV Burden and Immune Activation within the Gut of HIV-Positive Patients Receiving Suppressive Antiretroviral Therapy, Steven A. Yukl, Sara Gianella, Elizabeth Sinclair, Lorrie Epling, Qingsheng Li, Lijie Duan, Alex L.M. Choi, Valerie Girling, Terence Ho, Peilin Li, Katsuya Fujimoto, Harry Lampiris, C. Bradley Hare, Mark Pandori, Ashley T. Haase, Huldrych F. Günthard, Marek Fischer, Amandeep K. Shergill, Kenneth McQuaid, Diane V. Havlir, and Joseph K. Wong

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Microevolution of intermediary metabolism: evolutionary genetics meets metabolic biochemistry, Anthony J. Zera

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Purification and characterization of cytoplasmic NADP+- isocitrate dehydrogenase, and amplification of the Nadp+-Idh gene from the wing-dimorphic sand field cricket, Gryllus firmus, Anthony J. Zera, Susan Newman, David Berkheim, Christine Black, Lindsay Klug, and Erica Crone

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Molecular Determinants of HIV-1 Subtype C Coreceptor Transition from R5 to R5X4, Hong Zhang, Damien C. Tully, Tiejun Zhang, Hideaki Moriyama, Jesse Thompson, and Charles Wood

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Dual Functions of Interferon Regulatory Factors 7C in Epstein-Barr Virus–Mediated Transformation of Human B Lymphocytes, Yong Zhao, Dongsheng Xu, Yanjun Jiang, and Luwen Zhang

2009

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Similar Patterns of Linkage Disequilibrium and Nucleotide Diversity in Native and Introduced Populations of the Pea Aphid, Acyrthosiphon pisum, Jennifer A. Brisson, Sergey V. Nuzhdin, and David L. Stern

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BLOOD SAMPLING REDUCES ANNUAL SURVIVAL IN CLIFF SWALLOWS (PETROCHELIDON PYRRHONOTA) -- La Toma de Muestras de Sangre Reduce la Supervivencia Anual en Petrochelidon pyrrhonota, Charles R. Brown and Mary Bomberger Brown

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Arginine-Induced Germ Tube Formation in Candida albicans Is Essential for Escape from Murine Macrophage Line RAW 264.7, Suman Ghosh, Dhammika H. M. L. P. Navarathna, David D. Roberts, Jake T. Cooper, Audrey L. Atkin, Thomas M. Petro, and Kenneth Nickerson

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Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase, Kohei Homma and Hideaki Moriyama

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Plant Sex and the Evolution of Plant Defenses against Herbivores, Marc T.J. Johnson, Stacey DeWitt Smith, Marc D. Rausher, and Douglas J. Futuyma

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Species-driven changes in nitrogen cycling can provide a mechanism for plant invasions, Johannes M. H. Knops and Ramesh Laungani

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Natural History Note No Trade-Off between Seed Size and Number in the Valley Oak Quercus lobata, Walter D. Koenig, Johannes M. N. Knops, William J. Carmen, and Richard D. Sage

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Parameterizing the growth-decline boundary for uncertain population projection models, Joan Lubben, Derek Boeckner, Richard Rebarber, Stuart Townley, and Brigitte Tenhumberg

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Something Old, Something New, Something Borrowed; How the Thermoacidophilic Archaeon Sulfolobus solfataricus Responds to Oxidative Stress, Walid S. Maaty, Blake Wiedenheft, Pavel Tarlykov, Nathan Schaff, Joshua Heinemann, Jim Robinson-Cox, Jacob Valenzuela, Amanda Dougherty, Paul Blum, C. Martin Lawrence, Trevor Douglas, Mark J. Young, and Brian Bothner

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Impacts of insect herbivory on cactus population dynamics: experimental demography across an environmental gradient, Tom E. X. Miller, Svata M. Louda, Karen A. Rose, and James O. Eckberg

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Natural Genetic Variation in Transcriptome Reflects Network Structure Inferred with Major Effect Mutations: Insulin/TOR and Associated Phenotypes in Drosophila melanogaster, Sergey Nuzhdin, Jennifer A. Brisson, Andrew Pickering, Marta Wayne, Lawrence G. Harshman, and Lauren McIntyre

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Natural Genetic Variation in Transcriptome Reflects Network Structure Inferred with Major Effect Mutations: Insulin/TOR and Associated Phenotypes in Drosophila melanogaster, Sergey V. Nuzhdin, Jennifer A. Brisson, Andrew Pickering, Marta L. Wayne, Lawrence G. Harshman, and Lauren M. McIntyre

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Transcriptional Profiling of the Sperm Storage Organs of Drosophila melanogaster, Adrianne M. Prokupek, Stephen D. Kachman, Istvan Ladunga, and Lawrence G. Harshman

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Macroevolutionary Tests of Pollination Syndromes: A Reply to Fenster et al., Stacey DeWitt Smith, Cécile Ané, and David A. Baum

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Computational Prediction of Novel Non-Coding RNAs in Arabidopsis thaliana, Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, and Tao Jiang

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Gene Duplication and the Resolution of Adaptive Conflict, Jay F. Storz

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Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin, Jay F. Storz, Amy M. Runck, Stephen J. Sabatino, John K. Kelly, Nuno Ferrand, Hideaki Moriyama, Roy E. Weber, and Angela Fago

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Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors, Yvonne Sun, Ruth L. Gustavson, Nadia Ali, Karrie A. Weber, Lacey L. Westphal, and John D. Coates

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Occurrence of Trichosirocalus horridus (Coleoptera: Curculionidae) on Native Cirsium altissimum Versus Exotic C. vulgare in North American Tallgrass Prairie, Masaru Takahashi, Svata M. Louda, Tom E. X. Miller, and Charles W. O'Brien

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Model complexity affects transient population dynamics following a dispersal event: A case study with pea aphids, Brigitte Tenhumberg, Andrew J. Tyre, and Richard Rebarber

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Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002, Karrie A. Weber, David B. Hedrick, Aaron D. Peacock, J. Cameron Thrash, David C. White, Laurie A. Achenbach, and John D. Coates

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Sex effects on life span and senescence in the wild when dates of birth and death are unknown, Felix Zajitschek, Chad Brassil, Russell Bonduriansky, and Robert C. Brooks

2008

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Tissue and stage-specific juvenile hormone esterase (JHE) and epoxide hydrolase (JHEH) enzyme activities and Jhe transcript abundance in lines of the cricket Gryllus assimilis artificially selected for plasma JHE activity: Implications for JHE microevolution, Anurag Anand, Erica Crone, and Anthony J. Zera

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Vulnerability of Rehabilitated Agricultural Production Systems to Invasion by Nontarget Plant Species, Sara G. Baer, David M. Engle, Johannes M. N. Knops, Kenneth A. Langeland, Bruce D. Maxwell, Fabian D. Menalled, and Amy J. Symstad

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Review of Archaea: Molecular and Cellular Biology, Paul Blum

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Pea Aphid, Jennifer A. Brisson and Gregory K. Davis

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Rarity of Males in Pea Aphids Results in Mutational Decay, Jennifer A. Brisson and Sergey V. Nuzhdin

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Evidence for contrasting modes of selection at interacting globin genes in the European rabbit (Oryctolagus cuniculus), R. Campos, Jay F. Storz, and N. Ferrand

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NUCLEIC ACID SEQUENCES FOUND IN DROSOPHILA MELANOGASTER THAT ENCODE PROTEINS ESSENTIAL FOR VIABILITY AND METHOD OF USE: U.S. Patent No. US 7,384,745 B2, Alan C. Christensen and Douglas R. Dorer

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Parasite-Mediated Disruptive Selection in a Natural Daphnia Population, Meghan Duffey, Chad Brassil, Spencer Hall, Alan Tessier, Carla Cáceres, and Jeffrey Conner

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Molecular evolution of cytochrome b in high- and low-altitude deer mice (genus Peromyscus), E.J. Gering, J. C. Opazo, and Jay F. Storz

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Regulation of Aromatic Alcohol Production in Candida albicans, Suman Ghosh, Bessie W. Kebaara, Audrey L. Atkin, and Kenneth W. Nickerson

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Substrate-dependent signaling success in the wolf spider, Schizocosa retrorsa, Eileen Hebets, Damian O. Elias, Andrew C. Mason, Gary L. Miller, and Gail E. Stratton

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Diet influences mate choice selectivity in adult female wolf spiders, Eileen Hebets, Jennifer Wesson, and Paul S. Shamble