Genome Biology and Evolution

Editorial

Takashi Gojobori and William Martin

Welcome to Genome Biology and Evolution
Genome Biol Evol (2009) Vol. 2009, 1; doi:10.1093/gbe/evp004 published on May 5, 2009 [Extract] [FREE Full Text] [PDF]  

Research Articles

Get checked abstract Marc P. Hoeppner, Simon White, Daniel C. Jeffares, and Anthony M. Poole

Evolutionarily Stable Association of Intronic snoRNAs and microRNAs with Their Host Genes
Genome Biology and Evolution Advance Access published on November 5, 2009
Genome Biol Evol (2009) Vol. 2009, 420-428; doi:10.1093/gbe/evp045 published on November 23, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Kousuke Hanada, Takashi Kuromori, Fumiyoshi Myouga, Tetsuro Toyoda, Wen-Hsiung Li, and Kazuo Shinozaki

Evolutionary Persistence of Functional Compensation by Duplicate Genes in Arabidopsis
Genome Biology and Evolution Advance Access published on October 29, 2009
Genome Biol Evol (2009) Vol. 2009, 409-414; doi:10.1093/gbe/evp043 published on November 18, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Jan A. C. Vriezen, Michael Valliere, and Margaret A. Riley

The Evolution of Reduced Microbial Killing
Genome Biology and Evolution Advance Access published on October 20, 2009
Genome Biol Evol (2009) Vol. 2009, 400-408; doi:10.1093/gbe/evp042 published on November 17, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Michael S. Barker, Heiko Vogel, and M. Eric Schranz

Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales
Genome Biology and Evolution Advance Access published on October 5, 2009
Genome Biol Evol (2009) Vol. 2009, 391-399; doi:10.1093/gbe/evp040 published on November 3, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Liran Carmel and Eugene V. Koonin

A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes
Genome Biology and Evolution Advance Access published on September 22, 2009
Genome Biol Evol (2009) Vol. 2009, 382-390; doi:10.1093/gbe/evp038 published on October 20, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Elie Desmond and Simonetta Gribaldo

Phylogenomics of Sterol Synthesis: Insights into the Origin, Evolution, and Diversity of a Key Eukaryotic Feature
Genome Biology and Evolution Advance Access published on September 10, 2009
Genome Biol Evol (2009) Vol. 2009, 364-381; doi:10.1093/gbe/evp036 published on October 20, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Sara C. Di Rienzi, David Collingwood, M. K. Raghuraman, and Bonita J. Brewer

Fragile Genomic Sites Are Associated with Origins of Replication
Genome Biology and Evolution Advance Access published on September 9, 2009
Genome Biol Evol (2009) Vol. 2009, 350-363; doi:10.1093/gbe/evp034 published on October 5, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Claudia C. Weber and Laurence D. Hurst

Protein Rates of Evolution Are Predicted by Double-Strand Break Events, Independent of Crossing-over Rates
Genome Biology and Evolution Advance Access published on September 2, 2009
Genome Biol Evol (2009) Vol. 2009, 340-349; doi:10.1093/gbe/evp033 published on September 23, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Olga Zhaxybayeva, W. Ford Doolittle, R. Thane Papke, and J. Peter Gogarten

Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus
Genome Biology and Evolution Advance Access published on September 2, 2009
Genome Biol Evol (2009) Vol. 2009, 325-339; doi:10.1093/gbe/evp032 published on September 23, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Jochen B. W. Wolf, Axel Künstner, Kiwoong Nam, Mattias Jakobsson, and Hans Ellegren

Nonlinear Dynamics of Nonsynonymous (d_N) and Synonymous (d_S) Substitution Rates Affects Inference of Selection
Genome Biology and Evolution Advance Access published on August 13, 2009
Genome Biol Evol (2009) Vol. 2009, 308-319; doi:10.1093/gbe/evp030 published on September 4, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Benjamin Dickins and Anton Nekrutenko

High-Resolution Mapping of Evolutionary Trajectories in a Phage
Genome Biology and Evolution Advance Access published on August 11, 2009
Genome Biol Evol (2009) Vol. 2009, 294-307; doi:10.1093/gbe/evp029 published on September 2, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Mihai Albu, Xiang Jia Min, G. Brian Golding, and Donal Hickey

Nucleotide Substitution Bias within the Genus Drosophila Affects the Pattern of Proteome Evolution
Genome Biology and Evolution Advance Access published on August 4, 2009
Genome Biol Evol (2009) Vol. 2009, 288-293; doi:10.1093/gbe/evp028 published on August 21, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Andrew T. Beckenbach and Jeffrey B. Joy

Evolution of the Mitochondrial Genomes of Gall Midges (Diptera: Cecidomyiidae): Rearrangement and Severe Truncation of tRNA Genes
Genome Biology and Evolution Advance Access published on August 3, 2009
Genome Biol Evol (2009) Vol. 2009, 278-287; doi:10.1093/gbe/evp027 published on August 21, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract M. Ziemann, M. Bhave, and S. Zachgo

Origin and Diversification of Land Plant CC-Type Glutaredoxins
Genome Biology and Evolution Advance Access published on July 31, 2009
Genome Biol Evol (2009) Vol. 2009, 265-277; doi:10.1093/gbe/evp025 published on August 21, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Dong Dong, Guimei He, Shuyi Zhang, and Zhaolei Zhang

Evolution of Olfactory Receptor Genes in Primates Dominated by Birth-and-Death Process
Genome Biology and Evolution Advance Access published on August 4, 2009
Genome Biol Evol (2009) Vol. 2009, 258-264; doi:10.1093/gbe/evp026 published on August 20, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Hui Cai, Rebecca Thompson, Mateo F. Budinich, Jeff R. Broadbent, and James L. Steele

Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution
Genome Biology and Evolution Advance Access published on July 14, 2009
Genome Biol Evol (2009) Vol. 2009, 239-257; doi:10.1093/gbe/evp019 published on August 17, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Pascal-Antoine Christin, Emanuela Samaritani, Blaise Petitpierre, Nicolas Salamin, and Guillaume Besnard

Evolutionary Insights on C₄ Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics
Genome Biology and Evolution Advance Access published on July 20, 2009
Genome Biol Evol (2009) Vol. 2009, 221-230; doi:10.1093/gbe/evp020 published on August 13, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Cédric Feschotte, Umeshkumar Keswani, Nirmal Ranganathan, Marcel L. Guibotsy, and David Levine

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes
Genome Biology and Evolution Advance Access published on July 23, 2009
Genome Biol Evol (2009) Vol. 2009, 205-220; doi:10.1093/gbe/evp023 published on August 12, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Paz Polak and Peter F. Arndt

Long-Range Bidirectional Strand Asymmetries Originate at CpG Islands in the Human Genome
Genome Biology and Evolution Advance Access published on August 3, 2009
Genome Biol Evol (2009) Vol. 2009, 189-197; doi:10.1093/gbe/evp024 published on August 6, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Richard P. Meisel, Mira V. Han, and Matthew W. Hahn

A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes
Genome Biology and Evolution Advance Access published on July 7, 2009
Genome Biol Evol (2009) Vol. 2009, 176-188; doi:10.1093/gbe/evp018 published on July 31, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Xiaowei (Sylvia) Chen, Lesley J. Collins, Patrick J. Biggs, and David Penny

High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis
Genome Biology and Evolution Advance Access published on July 6, 2009
Genome Biol Evol (2009) Vol. 2009, 165-175; doi:10.1093/gbe/evp017 published on July 24, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract István Miklós and Aaron E. Darling

Efficient Sampling of Parsimonious Inversion Histories with Application to Genome Rearrangement in Yersinia
Genome Biology and Evolution Advance Access published on June 22, 2009
Genome Biol Evol (2009) Vol. 2009, 153-164; doi:10.1093/gbe/evp015 published on Jul 14 2009 [Abstract] [FREE Full Text] [PDF]  

Get checked abstract Chih-Horng Kuo and Howard Ochman

Deletional Bias across the Three Domains of Life
Genome Biology and Evolution Advance Access published on June 27, 2009
Genome Biol Evol (2009) Vol. 2009, 145-152; doi:10.1093/gbe/evp016 published on Jul 14 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract James J. Cai, Elhanan Borenstein, Rong Chen, and Dmitri A. Petrov

Similarly Strong Purifying Selection Acts on Human Disease Genes of All Evolutionary Ages
Genome Biology and Evolution Advance Access published on May 27, 2009
Genome Biol Evol (2009) Vol. 2009, 131-144; doi:10.1093/gbe/evp013 published on June 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract George E. Liu, Lu Jiang, Fei Tian, Bin Zhu, and Jiuzhou Song

Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats
Genome Biology and Evolution Advance Access published on May 27, 2009
Genome Biol Evol (2009) Vol. 2009, 119-130; doi:10.1093/gbe/evp014 published on June 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Adrian Schneider, Alexander Souvorov, Niv Sabath, Giddy Landan, Gaston H. Gonnet, and Dan Graur

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment
Genome Biology and Evolution Advance Access published on June 5, 2009
Genome Biol Evol (2009) Vol. 2009, 114-118; doi:10.1093/gbe/evp012 published on June 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Igor B. Rogozin, Malay Kumar Basu, Miklós Csürös, and Eugene V. Koonin

Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes
Genome Biology and Evolution Advance Access published on May 25, 2009
Genome Biol Evol (2009) Vol. 2009, 99-113; doi:10.1093/gbe/evp011 published on June 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Wolfgang Otto, Peter F. Stadler, Francesc López-Giraldéz, Jeffrey P. Townsend, Vincent J. Lynch, and Günter P. Wagner

Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Genome Biology and Evolution Advance Access published on May 25, 2009
Genome Biol Evol (2009) Vol. 2009, 85-98; doi:10.1093/gbe/evp010 published on June 22, 2009 [Abstract] [FREE Full Text] [PDF]  

Get checked abstract Andrej Benjak, Stéphanie Boué, Astrid Forneck, and Josep M. Casacuberta

Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.)
Genome Biology and Evolution Advance Access published on May 20, 2009
Genome Biol Evol (2009) Vol. 2009, 75-84; doi:10.1093/gbe/evp009 published on June 22, 2009 [Abstract] [FREE Full Text] [PDF]  

Get checked abstract Vanessa L. Bauer DuMont, Nadia D. Singh, Mark H. Wright, and Charles F. Aquadro

Locus-Specific Decoupling of Base Composition Evolution at Synonymous Sites and Introns along the Drosophila melanogaster and Drosophila sechellia Lineages
Genome Biology and Evolution Advance Access published on May 25, 2009
Genome Biol Evol (2009) Vol. 2009, 67-74; doi:10.1093/gbe/evp008 published on June 17, 2009 [Abstract] [FREE Full Text] [PDF]  

Get checked abstract Claire Lemaitre, Marilia D. V. Braga, Christian Gautier, Marie-France Sagot, Eric Tannier, and Gabriel A. B. Marais

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes
Genome Biology and Evolution Advance Access published on April 30, 2009
Genome Biol Evol (2009) Vol. 2009, 56-66; doi:10.1093/gbe/evp006 published on May 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract W. A. Findlay and R. J. Redfield

Coevolution of DNA Uptake Sequences and Bacterial Proteomes
Genome Biology and Evolution Advance Access published on May 5, 2009
Genome Biol Evol (2009) Vol. 2009, 45-55; doi:10.1093/gbe/evp005 published on May 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Yoshihito Niimura

On the Origin and Evolution of Vertebrate Olfactory Receptor Genes: Comparative Genome Analysis Among 23 Chordate Species
Genome Biology and Evolution Advance Access published on April 30, 2009
Genome Biol Evol (2009) Vol. 2009, 34-44; doi:10.1093/gbe/evp003 published on May 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Zhi Wang and Jianzhi Zhang

Abundant Indispensable Redundancies in Cellular Metabolic Networks
Genome Biology and Evolution Advance Access published on April 30, 2009
Genome Biol Evol (2009) Vol. 2009, 23-33; doi:10.1093/gbe/evp002 published on May 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Catherine J. Pink, Siva K. Swaminathan, Ian Dunham, Jane Rogers, Andrew Ward, and Laurence D. Hurst

Evidence That Replication-Associated Mutation Alone Does Not Explain Between-Chromosome Differences In Substitution Rates
Genome Biology and Evolution Advance Access published on April 30, 2009
Genome Biol Evol (2009) Vol. 2009, 13-22; doi:10.1093/gbe/evp001 published on May 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Mina Rho, Mo Zhou, Xiang Gao, Sun Kim, Haixu Tang, and Michael Lynch

Independent Mammalian Genome Contractions Following the KT Boundary
Genome Biology and Evolution Advance Access published on May 5, 2009
Genome Biol Evol (2009) Vol. 2009, 2-12; doi:10.1093/gbe/evp007 published on May 22, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Letters

Get checked abstract Chun-Hsi Chen, Trees-Juen Chuang, Ben-Yang Liao, and Feng-Chi Chen

Scanning for the Signatures of Positive Selection for Human-Specific Insertions and Deletions
Genome Biology and Evolution Advance Access published on October 20, 2009
Genome Biol Evol (2009) Vol. 2009, 415-419; doi:10.1093/gbe/evp041 published on November 23, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Fabien Burki, Yuji Inagaki, Jon Bråte, John M. Archibald, Patrick J. Keeling, Thomas Cavalier-Smith, Miako Sakaguchi, Tetsuo Hashimoto, Ales Horak, Surendra Kumar, Dag Klaveness, Kjetill S. Jakobsen, Jan Pawlowski, and Kamran Shalchian-Tabrizi

Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates
Genome Biology and Evolution Advance Access published on July 27, 2009
Genome Biol Evol (2009) Vol. 2009, 231-238; doi:10.1093/gbe/evp022 published on August 13, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Wenfeng Qian and Jianzhi Zhang

Protein Subcellular Relocalization in the Evolution of Yeast Singleton and Duplicate Genes
Genome Biology and Evolution Advance Access published on July 22, 2009
Genome Biol Evol (2009) Vol. 2009, 198-204; doi:10.1093/gbe/evp021 published on August 6, 2009 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]  

Get checked abstract Jeffrey D. Jensen

On Reconciling Single and Recurrent Hitchhiking Models
Genome Biology and Evolution Advance Access published on September 2, 2009
Genome Biol Evol (2009) Vol. 2009, 320-324; doi:10.1093/gbe/evp031 published on September 18, 2009 [Abstract] [FREE Full Text] [PDF]  

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