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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

Page 18 of 18

  1. Content type: Research article

    Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the ...

    Authors: Robert Boissy, Azad Ahmed, Benjamin Janto, Josh Earl, Barry G Hall, Justin S Hogg, Gordon D Pusch, Luisa N Hiller, Evan Powell, Jay Hayes, Susan Yu, Sandeep Kathju, Paul Stoodley, J Christopher Post, Garth D Ehrlich and Fen Z Hu

    Citation: BMC Genomics 2011 12:187

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  2. Content type: Research article

    Alu elements are the most abundant retrotransposable elements comprising ~11% of the human genome. Many studies have highlighted the role that Alu elements have in genetic instability and how their contribution t...

    Authors: Wensheng Zhang, Andrea Edwards, Wei Fan, Prescott Deininger and Kun Zhang

    Citation: BMC Genomics 2011 12:157

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  3. Content type: Research article

    Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomi...

    Authors: Robert HS Kraus, Hindrik HD Kerstens, Pim Van Hooft, Richard PMA Crooijmans, Jan J Van Der Poel, Johan Elmberg, Alain Vignal, Yinhua Huang, Ning Li, Herbert HT Prins and Martien AM Groenen

    Citation: BMC Genomics 2011 12:150

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  4. Content type: Research article

    Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular ch...

    Authors: Neha Potnis, Ksenia Krasileva, Virginia Chow, Nalvo F Almeida, Prabhu B Patil, Robert P Ryan, Molly Sharlach, Franklin Behlau, J Max Dow, MT Momol, Frank F White, James F Preston, Boris A Vinatzer, Ralf Koebnik, João C Setubal, David J Norman…

    Citation: BMC Genomics 2011 12:146

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  5. Content type: Research article

    Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, th...

    Authors: Zhixi Tian, Yanjun Yu, Feng Lin, Yeisoo Yu, Phillip J SanMiguel, Rod A Wing, Susan R McCouch, Jianxin Ma and Scott A Jackson

    Citation: BMC Genomics 2011 12:142

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  6. Content type: Research article

    The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagio...

    Authors: Francois Thiaucourt, Lucia Manso-Silvan, Woubit Salah, Valérie Barbe, Benoit Vacherie, Daniel Jacob, Marc Breton, Virginie Dupuy, Anne Marie Lomenech, Alain Blanchard and Pascal Sirand-Pugnet

    Citation: BMC Genomics 2011 12:114

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  7. Content type: Research article

    A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagno...

    Authors: Arong Luo, Aibing Zhang, Simon YW Ho, Weijun Xu, Yanzhou Zhang, Weifeng Shi, Stephen L Cameron and Chaodong Zhu

    Citation: BMC Genomics 2011 12:84

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  8. Content type: Research article

    The prevalence of invasive fungal infections (IFIs) has increased steadily worldwide in the last few decades. Particularly, there has been a global rise in the number of infections among immunosuppressed peopl...

    Authors: Ana Karina R Abadio, Erika S Kioshima, Marcus M Teixeira, Natalia F Martins, Bernard Maigret and Maria Sueli S Felipe

    Citation: BMC Genomics 2011 12:75

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  9. Content type: Research article

    Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important...

    Authors: Wang Minxiao, Sun Song, Li Chaolun and Shen Xin

    Citation: BMC Genomics 2011 12:73

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  10. Content type: Research article

    Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a...

    Authors: Urko M Marigorta, Oscar Lao, Ferran Casals, Francesc Calafell, Carlos Morcillo-Suárez, Rui Faria, Elena Bosch, François Serra, Jaume Bertranpetit, Hernán Dopazo and Arcadi Navarro

    Citation: BMC Genomics 2011 12:55

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  11. Content type: Research article

    The piRNA pathway operates in animal germ lines to ensure genome integrity through retrotransposon silencing. The Piwi protein-associated small RNAs (piRNAs) guide Piwi proteins to retrotransposon transcripts,...

    Authors: Philipp Berninger, Lukasz Jaskiewicz, Mohsen Khorshid and Mihaela Zavolan

    Citation: BMC Genomics 2011 12:46

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  12. Content type: Research article

    Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombinat...

    Authors: Svenja Sammler, Christoph Bleidorn and Ralph Tiedemann

    Citation: BMC Genomics 2011 12:35

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  13. Content type: Methodology article

    The dual concepts of pan and core genomes have been widely adopted as means to assess the distribution of gene families within microbial species and genera. The core genome is the set of genes shared by a grou...

    Authors: Andrey O Kislyuk, Bart Haegeman, Nicholas H Bergman and Joshua S Weitz

    Citation: BMC Genomics 2011 12:32

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  14. Content type: Research article

    Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands ...

    Authors: Luis Delaye, Carmen M González-Domenech, María P Garcillán-Barcia, Juli Peretó, Fernando de la Cruz and Andrés Moya

    Citation: BMC Genomics 2011 12:25

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  15. Content type: Research article

    Enzymes in the radical SAM (rSAM) domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. E...

    Authors: Daniel H Haft

    Citation: BMC Genomics 2011 12:21

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  16. Content type: Research article

    Bacterial taxonomy and phylogeny based on rrs (16S rDNA) sequencing is being vigorously pursued. In fact, it has been stated that novel biological findings are driven by comparison and integration of massive data...

    Authors: Vipin Chandra Kalia, Tanmoy Mukherjee, Ashish Bhushan, Jayadev Joshi, Pratap Shankar and Nusrat Huma

    Citation: BMC Genomics 2011 12:18

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  17. Content type: Research article

    Type A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically indistinguishable 150 kD protein that causes botul...

    Authors: Ping-Ke Fang, Brian H Raphael, Susan E Maslanka, Shuowei Cai and Bal Ram Singh

    Citation: BMC Genomics 2010 11:725

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  18. Content type: Research article

    Members of the makorin (mkrn) gene family encode RING/C3H zinc finger proteins with U3 ubiquitin ligase activity. Although these proteins have been described in a variety of eukaryotes such as plants, fungi, inve...

    Authors: Astrid Böhne, Amandine Darras, Helena D'Cotta, Jean-Francois Baroiller, Delphine Galiana-Arnoux and Jean-Nicolas Volff

    Citation: BMC Genomics 2010 11:721

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  19. Content type: Research article

    The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 ...

    Authors: Henriette O'Geen, Yu-Hsuan Lin, Xiaoqin Xu, Lorigail Echipare, Vitalina M Komashko, Daniel He, Seth Frietze, Osamu Tanabe, Lihong Shi, Maureen A Sartor, James D Engel and Peggy J Farnham

    Citation: BMC Genomics 2010 11:689

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  20. Content type: Research article

    Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detec...

    Authors: Shea N Gardner, Crystal J Jaing, Kevin S McLoughlin and Tom R Slezak

    Citation: BMC Genomics 2010 11:668

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  21. Content type: Methodology article

    Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing thes...

    Authors: Jeffrey Martin, Vincent M Bruno, Zhide Fang, Xiandong Meng, Matthew Blow, Tao Zhang, Gavin Sherlock, Michael Snyder and Zhong Wang

    Citation: BMC Genomics 2010 11:663

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  22. Content type: Research article

    The posterior genes of the HoxD cluster play a crucial role in the patterning of the tetrapod limb. This region is under the control of a global, long-range enhancer that is present in all vertebrates. Variation ...

    Authors: An Mannaert, Chris T Amemiya and Franky Bossuyt

    Citation: BMC Genomics 2010 11:658

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  23. Content type: Research article

    Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between ...

    Authors: Barbara Hutter, Matthias Bieg, Volkhard Helms and Martina Paulsen

    Citation: BMC Genomics 2010 11:649

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  24. Content type: Research article

    The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with to...

    Authors: Muhammad L Aslam, John WM Bastiaansen, Richard PMA Crooijmans, Addie Vereijken, Hendrik-Jan Megens and Martien AM Groenen

    Citation: BMC Genomics 2010 11:647

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  25. Content type: Research article

    In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translationa...

    Authors: Conrad von Mandach and Rainer Merkl

    Citation: BMC Genomics 2010 11:617

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  26. Content type: Research article

    Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for ne...

    Authors: Priscila VSZ Capriles, Ana CR Guimarães, Thomas D Otto, Antonio B Miranda, Laurent E Dardenne and Wim M Degrave

    Citation: BMC Genomics 2010 11:610

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  27. Content type: Research article

    The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has...

    Authors: Ming-Long Yuan, Dan-Dan Wei, Bao-Jun Wang, Wei Dou and Jin-Jun Wang

    Citation: BMC Genomics 2010 11:597

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  28. Content type: Research article

    Peroxide turnover and signalling are involved in many biological phenomena relevant to human diseases. Yet, all the players and mechanisms involved in peroxide perception are not known. Elucidating very remote...

    Authors: Krzysztof Pawłowski, Anna Muszewska, Anna Lenart, Teresa Szczepińska, Adam Godzik and Marcin Grynberg

    Citation: BMC Genomics 2010 11:590

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  29. Content type: Research article

    Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralog...

    Authors: Marit S Bratlie, Jostein Johansen, Brad T Sherman, Da Wei Huang, Richard A Lempicki and Finn Drabløs

    Citation: BMC Genomics 2010 11:588

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  30. Content type: Research article

    Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants exp...

    Authors: Federico Zambelli, Giulio Pavesi, Carmela Gissi, David S Horner and Graziano Pesole

    Citation: BMC Genomics 2010 11:534

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  31. Content type: Research article

    The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosup...

    Authors: Cecelia A Shertz, Robert J Bastidas, Wenjun Li, Joseph Heitman and Maria E Cardenas

    Citation: BMC Genomics 2010 11:510

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  32. Content type: Research article

    Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodo...

    Authors: Weerayuth Kittichotirat, Roger Bumgarner and Casey Chen

    Citation: BMC Genomics 2010 11:489

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