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Submissions from 2009

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AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2, Hana Kim, Keunsoo Kang, and Joomyeong Kim

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YY1's role in DNA methylation of Peg3 and Xist, Jeong Do Kim, Keunsoo Kang, and Joomyeong Kim

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YY1's longer DNA-binding motifs, Jeong do Kim and Joomyeong Kim

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YY1 is autoregulated through its own DNA-binding sites, Jeong D. Kim, Sungryul Yu, and Joomyeong Kim

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Integrating ELF4 into the circadian system through combined structural and functional studies, Elsebeth Kolmos, Monika Nowak, Maria Werner, Katrin Fischer, Guenter Schwarz, Sarah Mathews, Heiko Schoof, Ferenc Nagy, Janusz M. Bujnicki, and Seth J. Davis

Fifteen polymorphic microsatellite loci from Jamaican streamertail hummingbirds (Trochilus), Stacey L. Lance, Cris Hagen, Travis C. Glenn, Robb T. Brumfield, Katherine Faust Stryjewski, and Gary R. Graves

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Morphological Evolution: By Any Means Necessary?, John C. Larkin

Intra- and intersexual functions of singing by male blue Grosbeaks: The role of within-Song Variation, C. Lattin and G. Ritchison

Yeast Elc1 plays an important role in global genomic repair but not in transcription coupled repair, Danielle Lejeune, Xuefeng Chen, Christine Ruggiero, Shannon Berryhill, Baojin Ding, and Shisheng Li

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The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and bayesian inference, Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall, and Emily Moriarty Lemmon

Cocktail: A Play About the Life and HIV Drug Development Work of Dr. Krisana Kraisintu, Vincent J. LiCata

Research progress on Merremia boisiana, Daijiang Li

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Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements, Jing Li, Kyudong Han, Jinchuan Xing, Heui Soo Kim, Jeffrey Rogers, Oliver A. Ryder, Todd Disotell, Bisong Yue, and Mark A. Batzer

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Functional complementation of the Arabidopsis thaliana psbo1 mutant phenotype with an N-terminally His6-tagged PsbO-1 protein in photosystem II, Haijun Liu, Laurie K. Frankel, and Terry M. Bricker

Characterization and complementation of a psbR mutant in Arabidopsis thaliana, Haijun Liu, Laurie K. Frankel, and Terry M. Bricker

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Rationally designed integrin β3 mutants stabilized in the high affinity conformation, Bing Hao Luo, John Karanicolas, Laura D. Harmacek, David Baker, and Timothy A. Springer

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An RIG-I-like RNA helicase mediates antiviral RNAi downstream of viral siRNA biogenesis in Caenorhabditis elegans, Rui Lu, Erbay Yigit, Wan Xiang Li, and Shou Wei Ding

The Evolution of Modularity in the Mammalian Skull II: Evolutionary Consequences, Gabriel Marroig, Leila T. Shirai, Arthur Porto, Felipe B. de Oliveira, and Valderes De Conto

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Encoding properties of auditory neurons in the brain of a soniferous damselfish: Response to simple tones and complex conspecific signals, Karen P. Maruska and Timothy C. Tricas

Innate immune responses to Encephalitozoon species infections, Amber Mathews, Anne Hotard, and Hollie Hale-Donze

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Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data, Sarah Mathews

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A tale of two functions: Enzymatic activity and translational repression by carboxyltransferase, Glen Meades, Brian K. Benson, Anne Grove, and Grover L. Waldrop

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Occurrence of mitochondria-targeted late embryogenesis abundant (LEA) gene in animals increases organelle resistance to water stress, Michael A. Menze, Leaf Boswell, Mehmet Toner, and Steven C. Hand

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How do animal mitochondria tolerate water stress?, Michael A. Menze and Steven C. Hand

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Polyubiquitination of the demethylase Jhd2 controls histone methylation and gene expression, Douglas P. Mersman, Hai Ning Du, Ian M. Fingerman, Paul F. South, and Scott D. Briggs

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Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008, Mayako Michino, Enrique Abola, Charles L. Brooks, J. Scott Dixon, John Moult, Raymond C. Stevens, Arthur Olson, Wiktor Jurkowski, Arne Elofsson, Slawomir Filipek, et al.

Liquid chromatography-electrospray ionization-mass spectrometric quantitation of juvenile hormone III in whole body extracts of the Formosan subterranean termite., Miyazaki M, Mao L, Henderson G, and Laine RA

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Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides), Robert G. Moyle, R. Terry Chesser, Robb T. Brumfield, Jose G. Tello, Daniel J. Marchese, and Joel Cracraft

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Mycobacterium smegmatis histone-like protein Hlp is nucleoid associated: Research Letter, Anirban Mukherjee, Patrick J. DiMario, and Anne Grove

Local immigration, competition from dominant guilds, and the ecological assembly of high-diversity pine savannas, Jonathan A. Myers and Kyle E. Harms

Seed arrival, ecological filters, and plant species richness: a meta-analysis, Jonathan A. Myers and Kyle E. Harms

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The 1.85 Å structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity, David B. Neau, Nathaniel C. Gilbert, Sue G. Bartlett, William Boeglin, Alan R. Brash, and Marcia E. Newcomer

Umbrella sampling simulations of biotin carboxylase: is a structure with an open ATP grasp domain stable in solution?, Brian R. Novak, Dorel Moldovan, Grover L. Waldrop, and Marcio S. de Queiroz

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Loss of Halophytism by interference with SOS1 expression, Dong Ha Oh, Eduardo Leidi, Quan Zhang, Sung Min Hwang, Youzhi Li, Francisco J. Quintero, Xingyu Jiang, Matilde Paino D'urzo, Sang Yeol Lee, Yanxiu Zhao, et al.

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SOS1 and halophytism., Dong Ha Oh, Ali Zahir, Dae Jin Yun, Ray A. Bressan, and Hans J. Bohnert

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Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution, John K. Pace, Shurjo K. Sen, Mark A. Batzer, and Cédric Feschotte

Quantifying the effects of seed arrival and environmental conditions on tropical seedling community structure, C E. Paine and Kyle E. Harms

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Supplemental irrigation increases seedling performance and diversity in a tropical forest, C. E.Timothy Paine, Kyle E. Harms, and Jess Ramos

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The structure and peroxidase activity of a 33-kDa catalase-related protein from Mycobacterium avium ssp. paratuberculosis, Svetlana Pakhomova, Benlian Gao, William E. Boeglin, Alan R. Brash, and Marcia E. Newcomer

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Adipose tissue collagen VI in obesity, Magdalena Pasarica, Barbara Gowronska-Kozak, David Burk, Isabel Remedios, David Hymel, Jeff Gimble, Eric Ravussin, George A. Bray, and Steven R. Smith

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Reduced adipose tissue oxygenation in human obesity evidence for rarefaction, macrophage chemotaxis, and inflammation without an angiogenic response, Magdalena Pasarica, Olga R. Sereda, Leanne M. Redman, Diana C. Albarado, David T. Hymel, Laura E. Roan, Jennifer C. Rood, David H. Burk, and Steven R. Smith

The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes, Arthur Porto, Felipe B. de Oliveira, Leila T. Shirai, Valderes De Conto, and Gabriel Marroig

Evolução da modularidade no crânio de mamíferos, Arthur Guimarães Carvalho Porto

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Decomposition in tropical forests: A pan-tropical study of the effects of litter type, litter placement and mesofaunal exclusion across a precipitation gradient, Jennifer S. Powers, Rebecca A. Montgomery, E. Carol Adair, Francis Q. Brearley, Saara J. Dewalt, Camila T. Castanho, Jerome Chave, Erika Deinert, Jörg U. Ganzhorn, Matthew E. Gilbert, et al.

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Reading between the LINEs to see into the past, David A. Ray, Roy N. Platt, and Mark A. Batzer

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The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends, Sreerupa Ray and Anne Grove

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Redox control of the DNA damage-inducible protein DinG helicase activity via its iron-sulfur cluster, Binbin Ren, Xuewu Duan, and Huangen Ding

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Decoupling development and energy flow during embryonic diapause in the cricket, Allonemobius socius, Julie A. Reynolds and Steven C. Hand

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Embryonic diapause highlighted by differential expression of mRNAs for ecdysteroidogenesis, transcription and lipid sparing in the cricket Allonemobius socius, Julie A. Reynolds and Steven C. Hand

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High-throughput single cell arrays as a novel tool in biopreservation, Kenneth L. Roach, Kevin R. King, Korkut Uygun, Steven C. Hand, Isaac S. Kohane, Martin L. Yarmush, and Mehmet Toner

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Knockdown of the Drosophila GTPase nucleostemin 1 impairs large ribosomal subunit biogenesis, cell growth, and midgut precursor cell maintenance, Raphyel Rosby, Cui Zhengfang, Emily Rogers, Megan A. DeLivron, Victoria L. Robinson, and Patrick J. DiMario

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High frequency of the D allele of the angiotensin-converting enzyme gene in Arabic populations, Abdel Halim Salem and Mark A. Batzer

Distribution of four HIV type 1-resistance polymorphisms (CCR5-Δ32, CCR5-m303, CCR2-64I, and SDF1-3′A) in the Bahraini population, Abdel Halim Salem, Eman Farid, Raouf Fadel, Marwan Abu-Hijleh, Wassim Almawi, Kyudong Han, and Mark A. Batzer

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Allele frequencies of the human platelet antigen-1 in the Egyptian population, Abdel Halim Salem, Kyudong Han, and Mark A. Batzer

Tetranucleotide microsatellite loci from the black bear (Ursus americanus), JAMIE SKVARLA SANDERLIN, BRANT C. FAIRCLOTH, BRIAN SHAMBLIN, and MICHAEL J. CONROY

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An efficient and economic asymmetric synthesis of (+)-nootkatone, tetrahydronootkatone, and derivatives, Anne M. Sauer, William E. Crowe, Gregg Henderson, and Roger A. Laine

Tetranucleotide markers from the loggerhead sea turtle (Caretta caretta) and their cross-amplification in other marine turtle species, Brian M. Shamblin, Brant C. Faircloth, Mark G. Dodd, Dean A. Bagley, Llewellyn M. Ehrhart, Peter H. Dutton, Amy Frey, and Campbell J. Nairn

Effects of phenanthrene- and metal-contaminated sediment on the feeding activity of the Harpacticoid Copepod, Schizopera knabeni, Soraya J. Silva, Kevin R. Carman, John W. Fleeger, Tonya Marshall, and Sidney J. Marlborough

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The continuity of protein structure space is an intrinsic property of proteins, Jeffrey Skolnick, Adrian K. Arakaki, Yup Lee Seung, and Michal Brylinski

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FINDSITE: A combined evolution/structure-based approach to protein function prediction, Jeffrey Skolnick and Michal Brylinski

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Reply to Zimmerman et al.: The space of single domain protein structures is continuous and highly connected, Jeffrey Skolnick, Michal Brylinski, and Seung Yup Lee

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Internal priming: An opportunistic pathway for L1 and Alu retrotransposition in hominins, Deepa Srikanta, Shurjo K. Sen, Erin M. Conlin, and Mark A. Batzer

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An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair, Deepa Srikanta, Shurjo K. Sen, Charles T. Huang, Erin M. Conlin, Ryan M. Rhodes, and Mark A. Batzer

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Flow cytometric and immunohistochemical detection of in vivo BrdU-labeled cells in mouse fat depots, Jaroslaw Staszkiewicz, Jeffrey Gimble, Courtney Cain, Marilyn Dietrich, David Burk, Heather Kirk-Ballard, and Barbara Gawronska-Kozak

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IscA/SufA paralogues are required for the [4Fe-4S] cluster assembly in enzymes of multiple physiological pathways in Escherichia coli under aerobic growth conditions, Guoqiang Tan, Jianxin Lu, Jacob P. Bitoun, Hao Huang, and Huangen Ding

Kinetic mechanism and structural requirements of the amine-catalyzed decarboxylation of oxaloacetic acid, Nabil K. Thalji, William E. Crowe, and Grover L. Waldrop

Acute nicotine exposure and modulation of a spinal motor circuit in embryonic zebrafish, Latoya T. Thomas, Lillian Welsh, Fernando Galvez, and Kurt R. Svoboda

A qualitative approach to enzyme inhibition, Grover L. Waldrop

Smaller is better for antibiotic discovery, Grover L. Waldrop

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Growth-regulated expression of a bacteriocin, produced by the sweet potato pathogen streptomyces ipomoeae, that exhibits interstrain inhibition, Jing Wang, Kevin L. Schultyp, and Gregg S. Pettis

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Modulation of lung inflammation by vessel dilator in a mouse model of allergic asthma, Xiaoqin Wang, Weidong Xu, Xiaoyuan Kong, Dongqing Chen, Gary Hellermann, Terry A. Ahlert, Joseph D. Giaimo, Stephania A. Cormier, Xu Li, Richard F. Lockey, et al.

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Water stress impacts on bacterial carbon monoxide oxidation on recent volcanic deposits, Carolyn F. Weber and Gary M. King

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Alu repeats increase local recombination rates, David J. Witherspoon, W. Scott Watkins, Yuhua Zhang, Jinchuan Xing, Whitney L. Tolpinrud, Dale J. Hedges, Mark A. Batzer, and Lynn B. Jorde

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Coordination of ribosomal protein and ribosomal RNA gene expression in response to TOR signaling, Li Juan Xiao and Anne Grove

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Mobile elements create structural variation: Analysis of a complete human genome, Jinchuan Xing, Yuhua Zhang, Kyudong Han, Abdel Halim Salem, Shurjo K. Sen, Chad D. Huff, Qiong Zhou, Ewen F. Kirkness, Samuel Levy, Mark A. Batzer, et al.

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The PsbP protein, but not the PsbQ protein, is required for normal thylakoid architecture in Arabidopsis thaliana, Xiaoping Yi, Stefan R. Hargett, Laurie K. Frankel, and Terry M. Bricker

The effect of marker choice on estimated levels of introgression across an avian (Pipridae: Manacus) hybrid zone, Tamaki Yuri, Robert W. Jernigan, Robb T. Brumfield, Nirmal K. Bhagabati, and Michael J. Braun

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Alternative mRNA splicing produces a novel biologically active short isoform of PGC-1α, Yubin Zhang, Peter Huypens, Aaron W. Adamson, Ji Suk Chang, Tara M. Henagan, Anik Boudreau, Natalie R. Lenard, David Burk, Johannes Klein, Nina Perwitz, et al.

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The Structure of a Receptor with Two Associating Transmembrane Domains on the Cell Surface: Integrin αIIbβ3, Jieqing Zhu, Bing Hao Luo, Patrick Barth, Jack Schonbrun, David Baker, and Timothy A. Springer

Submissions from 2008

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Springer correspondences for dihedral groups, P. N. Achar and A. M. Aubert

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Représentations de Springer pour les groupes de réflexions complexes imprimitifs, Pramod N. Achar and Anne Marie Aubert

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Orbit closures in the enhanced nilpotent cone, Pramod N. Achar and Anthony Henderson

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On special pieces, the Springer correspondence, and unipotent characters, Pramod N. Achar and Daniel S. Sage

Checklist and comments on the terrestrial amphibian and reptile fauna from Utai, northwestern Papua New Guinea, Christopher C. Austin, Christopher J. Hayden, Ilaiah Bigilale, Chris Dahl, and Jim Anaminiato

ANYL 338-Combustion generated nanoparticles: Pro-inflammatory effects and role of oxidative stress in neonatal rat exposure models, S. Balakrishna, B. Fahmy, S. Lomnicki, B. Dellinger, T. Ahlert, D. You, and S. A. Cormier

Diversification in the neotropics: Phylogenetic patterns and historical processes, John M. Bates, Carlos Daniel Cadena, Jose G. Tello, and Robb T. Brumfield

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Identification of a functionally essential amino acid for Arabidopsis cyclic nucleotide gated ion channels using the chimeric AtCNGC11/12 gene, Joyce Baxter, Wolfgang Moeder, William Urquhart, Dea Shahinas, Kimberley Chin, Dinesh Christendat, Hong Gu Kang, Magdalena Angelova, Naohiro Kato, and Keiko Yoshioka

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The Sinorhizobium meliloti MsbA2 protein is essential for the legume symbiosis, Sebastian Beck, Victoria L. Marlow, Katy Woodall, William T. Doerrler, Euan K. James, and Gail P. Ferguson

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Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: Tribes and trichomes revisited, Mark A. Beilstein, Ihsan A. Al-Shehbaz, Sarah Mathews, and Elizabeth A. Kellogg

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DNA inhibits catalysis by the carboxyltransferase subunit of acetyl-CoA carboxylase: Implications for active site communication, Brian K. Benson, Glen Meades, Anne Grove, and Grover L. Waldrop

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Escherichia coli FtnA acts as an iron buffer for re-assembly of iron-sulfur clusters in response to hydrogen peroxide stress, Jacob P. Bitoun, Genfu Wu, and Huangen Ding

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Collpas: Activity hotspots for frugivorous bats (Phyllostomidae) in the Peruvian Amazon, Adriana Bravo, Kyle E. Harms, Richard D. Stevens, and Louise H. Emmons

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The psbo1 mutant of Arabidopsis cannot efficiently use calcium in support of oxygen evolution by photosystem II, Terry M. Bricker and Laurie K. Frankel

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Constitutive Expressor of Pathogenesis-Related Genes5 affects cell wall biogenesis and trichome development, Ginger Brininstool, Remmy Kasili, L. Alice Simmons, Viktor Kirik, Martin Hülskamp, and John C. Larkin

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Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data, Robb T. Brumfield, Liang Liu, David E. Lum, and Scott V. Edwards

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A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation, Michal Brylinski and Jeffrey Skolnick

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Q-dock: Low-resolution flexible ligand docking with pocket-specific threading restraints, Michal Brylinski and Jeffrey Skolnick

Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments, Ryan P. Callegan, M Fernanda Nobre, Patrick M. McTernan, John R. Battista, Rafael Navarro-González, Christopher P. McKay, Milton S. da Costa, and Fred A. Rainey

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Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings, Matt D. Carling and Robb T. Brumfield

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Haldane's rule in an avian system: Using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone, Matthew D. Carling and Robb T. Brumfield