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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 3 of 8

  1. Content type: Research article

    Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. ...

    Authors: Dorothée Huchon, Amir Szitenberg, Sigal Shefer, Micha Ilan and Tamar Feldstein

    Citation: BMC Evolutionary Biology 2015 15:278

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  2. Content type: Research article

    A deeper understanding of differences and similarities in transcriptional regulation between species can uncover important information about gene functions and the role of genes in disease. Deciphering such pa...

    Authors: Gianni Monaco, Sipko van Dam, João Luis Casal Novo Ribeiro, Anis Larbi and João Pedro de Magalhães

    Citation: BMC Evolutionary Biology 2015 15:259

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  3. Content type: Research article

    Bacillus cereus sensu lato comprises eight closely related species including the human pathogens Bacillus anthracis and Bacillus cereus. Within B. cereus sensu lato, chromosomally and ...

    Authors: Maria-Elisabeth Böhm, Christopher Huptas, Viktoria Magdalena Krey and Siegfried Scherer

    Citation: BMC Evolutionary Biology 2015 15:246

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  4. Content type: Research article

    Sex chromosomes of extant eutherian species are too ancient to reveal the process that initiated sex-chromosome differentiation. By contrast, the neo-sex chromosomes generated by sex-autosome fusions of recent...

    Authors: Chie Murata, Yoko Kuroki, Issei Imoto, Masaru Tsukahara, Naoto Ikejiri and Asato Kuroiwa

    Citation: BMC Evolutionary Biology 2015 15:234

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  5. Content type: Research article

    Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative v...

    Authors: Russell A. Hermansen, Brian K. Mannakee, Wolfgang Knecht, David A. Liberles and Ryan N. Gutenkunst

    Citation: BMC Evolutionary Biology 2015 15:232

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  6. Content type: Research article

    USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partiall...

    Authors: Caitlyn Vlasschaert, Xuhua Xia, Josée Coulombe and Douglas A. Gray

    Citation: BMC Evolutionary Biology 2015 15:230

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  7. Content type: Research article

    Defining factors that contributed to the fixation of a high number of underdominant chromosomal rearrangements is a complex task because not only molecular mechanisms must be considered, but also the uniquenes...

    Authors: Cibele G. Sotero-Caio, Marianne Volleth, Federico G. Hoffmann, LuAnn Scott, Holly A. Wichman, Fengtang Yang and Robert J. Baker

    Citation: BMC Evolutionary Biology 2015 15:220

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  8. Content type: Research article

    Poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that have important functions in the regulation of translation and the control of mRNA stability in eukaryotes. Most PABPs encode a C-term...

    Authors: Domingo Jiménez-López, Jaime Bravo and Plinio Guzmán

    Citation: BMC Evolutionary Biology 2015 15:195

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  9. Content type: Research article

    The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of vir...

    Authors: Izza Nasrullah, Azeem M Butt, Shifa Tahir, Muhammad Idrees and Yigang Tong

    Citation: BMC Evolutionary Biology 2015 15:174

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  10. Content type: Research article

    Analyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in pr...

    Authors: Thorsten Thiergart, Giddy Landan and William F Martin

    Citation: BMC Evolutionary Biology 2014 14:266

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  11. Content type: Research article

    Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nons...

    Authors: Karen B Barnard-Kubow, Daniel B Sloan and Laura F Galloway

    Citation: BMC Evolutionary Biology 2014 14:268

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  12. Content type: Research article

    X chromosome inactivation is the transcriptional silencing of one X chromosome in the somatic cells of female mammals. In eutherian mammals (e.g. humans) one of the two X chromosomes is randomly chosen for sil...

    Authors: Claudia L Rodríguez-Delgado, Shafagh A Waters and Paul D Waters

    Citation: BMC Evolutionary Biology 2014 14:267

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  13. Content type: Research article

    G protein-coupled receptors (GPCRs) play a central role in eukaryotic signal transduction. However, the GPCR component of this signalling system, at the early origins of metazoans is not fully understood. Here...

    Authors: Arunkumar Krishnan, Rohit Dnyansagar, Markus Sällman Almén, Michael J Williams, Robert Fredriksson, Narayanan Manoj and Helgi B Schiöth

    Citation: BMC Evolutionary Biology 2014 14:270

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  14. Content type: Research article

    The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundan...

    Authors: Kalina TJ Davies, Georgia Tsagkogeorga and Stephen J Rossiter

    Citation: BMC Evolutionary Biology 2014 14:261

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  15. Content type: Research article

    Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the ...

    Authors: Lei Wei, Jian He, Xian Jia, Qi Qi, Zhisheng Liang, Hao Zheng, Yao Ping, Shuyu Liu and Jingchen Sun

    Citation: BMC Evolutionary Biology 2014 14:262

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  16. Content type: Research article

    Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We h...

    Authors: Matthew J Greenwold, Weier Bao, Erich D Jarvis, Haofu Hu, Cai Li, M Thomas P Gilbert, Guojie Zhang and Roger H Sawyer

    Citation: BMC Evolutionary Biology 2014 14:249

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  17. Content type: Research article

    Sex chromosomes exhibit many unusual patterns in sequence and gene expression relative to autosomes. Birds have evolved a female heterogametic sex system (male ZZ, female ZW), through stepwise suppression of r...

    Authors: Zongji Wang, Jilin Zhang, Wei Yang, Na An, Pei Zhang, Guojie Zhang and Qi Zhou

    Citation: BMC Evolutionary Biology 2014 14:250

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  18. Content type: Research article

    The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs i...

    Authors: Niles Lehman, Tess Bernhard, Brian C Larson, Andrew JN Robinson and Christopher CB Southgate

    Citation: BMC Evolutionary Biology 2014 14:248

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  19. Content type: Research article

    Young genes and genes under positive selection commonly contribute to adaptive phenotypic evolution. Early developmental stages are very important for establishing phenotypes, which might be helpful for studyi...

    Authors: He-Qun Liu, Yan Li, David M Irwin, Ya-Ping Zhang and Dong-Dong Wu

    Citation: BMC Evolutionary Biology 2014 14:241

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  20. Content type: Research article

    Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability a...

    Authors: Amanda M Larracuente

    Citation: BMC Evolutionary Biology 2014 14:233

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  21. Content type: Research article

    Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of th...

    Authors: Sivakumar Kannan, Igor B Rogozin and Eugene V Koonin

    Citation: BMC Evolutionary Biology 2014 14:237

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  22. Content type: Research article

    Elucidating the mechanisms underlying coevolution of ligands and receptors is an important challenge in molecular evolutionary biology. Peptide hormones and their receptors are excellent models for such effort...

    Authors: Barry L Williams, Yasuhisa Akazome, Yoshitaka Oka and Heather L Eisthen

    Citation: BMC Evolutionary Biology 2014 14:215

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  23. Content type: Research article

    Phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathway...

    Authors: Juanjuan Chai, Guruprasad Kora, Tae-Hyuk Ahn, Doug Hyatt and Chongle Pan

    Citation: BMC Evolutionary Biology 2014 14:207

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  24. Content type: Research article

    The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous st...

    Authors: Evan K Maxwell, Christine E Schnitzler, Paul Havlak, Nicholas H Putnam, Anh-Dao Nguyen, R Travis Moreland and Andreas D Baxevanis

    Citation: BMC Evolutionary Biology 2014 14:212

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  25. Content type: Research article

    Myxozoa are a diverse group of metazoan parasites with a very simple organization, which has for decades eluded their evolutionary origin. Their most prominent and characteristic feature is the polar capsule: ...

    Authors: Erez Shpirer, E Sally Chang, Arik Diamant, Nimrod Rubinstein, Paulyn Cartwright and Dorothée Huchon

    Citation: BMC Evolutionary Biology 2014 14:205

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  26. Content type: Research article

    MicroRNAs (miRNAs) are small non-coding RNA molecules with an important role upon post-transcriptional regulation. These molecules have been shown essential for several cellular processes in vertebrates, inclu...

    Authors: Pedro Gabriel Nachtigall, Marcos Correa Dias and Danillo Pinhal

    Citation: BMC Evolutionary Biology 2014 14:196

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  27. Content type: Research article

    Human bitter taste receptors are encoded by a gene family consisting of 25 functional TAS2R loci. In addition, humans carry 11 TAS2R pseudogenes, some of which display evidence for substantial diversification amo...

    Authors: Davide Risso, Sergio Tofanelli, Gabriella Morini, Donata Luiselli and Dennis Drayna

    Citation: BMC Evolutionary Biology 2014 14:198

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  28. Content type: Research article

    Lysozyme g is an antibacterial enzyme that was first found in the eggs of some birds, but recently has been found in additional species, including non-vertebrates. Some previously characterized lysozyme g sequenc...

    Authors: David M Irwin

    Citation: BMC Evolutionary Biology 2014 14:188

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  29. Content type: Research article

    Hypoxia-inducible factor (HIF) is a master regulator that mediates major changes in gene expression under hypoxic conditions. Though HIF family has been identified in many organisms, little is known about this...

    Authors: Lihong Guan, Wei Chi, Wuhan Xiao, Liangbiao Chen and Shunping He

    Citation: BMC Evolutionary Biology 2014 14:192

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  30. Content type: Research article

    Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (“T-P spacers”) have been ob...

    Authors: Tor Erik Jørgensen, Ingrid Bakke, Anita Ursvik, Morten Andreassen, Truls Moum and Steinar D Johansen

    Citation: BMC Evolutionary Biology 2014 14:182

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  31. Content type: Research article

    Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical interco...

    Authors: Hong-Hu Meng, Frédéric MB Jacques, Tao Su, Yong-Jiang Huang, Shi-Tao Zhang, Hong-Jie Ma and Zhe-Kun Zhou

    Citation: BMC Evolutionary Biology 2014 14:181

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  32. Content type: Research article

    Dacts are multi-domain adaptor proteins. They have been implicated in Wnt and Tgfβ signaling and serve as a nodal point in regulating many cellular activities. Dact genes have so far only been identified in bony ...

    Authors: Frank Richard Schubert, Débora Rodrigues Sobreira, Ricardo Guerreiro Janousek, Lúcia Elvira Alvares and Susanne Dietrich

    Citation: BMC Evolutionary Biology 2014 14:157

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  33. Content type: Research article

    The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mR...

    Authors: Xiu-Qing Li and Donglei Du

    Citation: BMC Evolutionary Biology 2014 14:162

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  34. Content type: Research article

    The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected...

    Authors: Dianne I Lou, Ross M McBee, Uyen Q Le, Anne C Stone, Gregory K Wilkerson, Ann M Demogines and Sara L Sawyer

    Citation: BMC Evolutionary Biology 2014 14:155

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  35. Content type: Research article

    Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most ch...

    Authors: Hui Huang, Chao Shi, Yuan Liu, Shu-Yan Mao and Li-Zhi Gao

    Citation: BMC Evolutionary Biology 2014 14:151

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  36. Content type: Research article

    Heat stress transcription factors (Hsfs) regulate gene expression in response to heat and many other environmental stresses in plants. Understanding the adaptive evolution of Hsf genes in the grass family will pr...

    Authors: Zefeng Yang, Yifan Wang, Yun Gao, Yong Zhou, Enying Zhang, Yunyun Hu, Yuan Yuan, Guohua Liang and Chenwu Xu

    Citation: BMC Evolutionary Biology 2014 14:147

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  37. Content type: Research article

    The evolution of the coding exome is a major driving force of functional divergence both between species and between protein isoforms. Exons at different positions in the transcript or in different transcript ...

    Authors: Feng-Chi Chen, Trees-Juen Chuang, Hsuan-Yu Lin and Min-Kung Hsu

    Citation: BMC Evolutionary Biology 2014 14:145

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  38. Content type: Research article

    Selection pressure governs the relative mutability and the conservedness of a protein across the protein family. Biomolecules (DNA, RNA and proteins) continuously evolve under the effect of evolutionary pressu...

    Authors: Vineetha Mandlik, Sonali Shinde and Shailza Singh

    Citation: BMC Evolutionary Biology 2014 14:142

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  39. Content type: Research article

    NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where s...

    Authors: Syed Nabeel-Shah, Kanwal Ashraf, Ronald E Pearlman and Jeffrey Fillingham

    Citation: BMC Evolutionary Biology 2014 14:139

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  40. Content type: Research article

    Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique ...

    Authors: Kathryn B Walters-Conte, Diana LE Johnson, Warren E Johnson, Stephen J O’Brien and Jill Pecon-Slattery

    Citation: BMC Evolutionary Biology 2014 14:137

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  41. Content type: Research article

    The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellula...

    Authors: Wanlu Song, Yajuan Qin, Yan Zhu, Guangjun Yin, Ningning Wu, Yaxuan Li and Yingkao Hu

    Citation: BMC Evolutionary Biology 2014 14:124

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  42. Content type: Research article

    Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A ...

    Authors: Åke Strese, Anders Backlund and Cecilia Alsmark

    Citation: BMC Evolutionary Biology 2014 14:119

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  43. Content type: Research article

    Starch is the main source of carbon storage in the Archaeplastida. The starch biosynthesis pathway (sbp) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the pl...

    Authors: Odrade Nougué, Jonathan Corbi, Steven G Ball, Domenica Manicacci and Maud I Tenaillon

    Citation: BMC Evolutionary Biology 2014 14:103

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2017 Journal Metrics

  • Citation Impact
    3.027 - 2-year Impact Factor
    3.628 - 5-year Impact Factor
    1.16 - Source Normalized Impact per Paper (SNIP)
    1.656 - SCImago Journal Rank (SJR)

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