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Comparative genomics

Section edited by Graziano Pesole

This section incorporates all aspects of comparative genomic analysis including but not limited to: methods and applications for the analysis of comparative phylogenetic and genomic data.

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  1. Content type: Software

    The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to r...

    Authors: Thomas Bigot, Vincent Daubin, Florent Lassalle and Guy Perrière

    Citation: BMC Bioinformatics 2013 14:109

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  2. Content type: Research article

    Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already ident...

    Authors: Giulia Menconi, Giovanni Battaglia, Roberto Grossi, Nadia Pisanti and Roberto Marangoni

    Citation: BMC Bioinformatics 2013 14:102

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  3. Content type: Research article

    Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of t...

    Authors: Hsiu-Ling Chou, Chung-Tay Yao, Sui-Lun Su, Chia-Yi Lee, Kuang-Yu Hu, Harn-Jing Terng, Yun-Wen Shih, Yu-Tien Chang, Yu-Fen Lu, Chi-Wen Chang, Mark L Wahlqvist, Thomas Wetter and Chi-Ming Chu

    Citation: BMC Bioinformatics 2013 14:100

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  4. Content type: Methodology article

    A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relatio...

    Authors: Andrés Varón and Ward C Wheeler

    Citation: BMC Bioinformatics 2013 14:66

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  5. Content type: Methodology article

    For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its pur...

    Authors: Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk and Markus Göker

    Citation: BMC Bioinformatics 2013 14:60

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  6. Content type: Research article

    One of the major issues in the fight against infectious diseases is the notable increase in multiple drug resistance in pathogenic species. For that reason, newly acquired high-throughput data on virulent micr...

    Authors: Arkadiusz Gladki, Szymon Kaczanowski, Pawel Szczesny and Piotr Zielenkiewicz

    Citation: BMC Bioinformatics 2013 14:36

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  7. Content type: Methodology article

    Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting ...

    Authors: Yasin Bakış, Hasan H Otu, Nivart Taşçı, Cem Meydan, Neş’e Bilgin, Sırrı Yüzbaşıoğlu and O Uğur Sezerman

    Citation: BMC Bioinformatics 2013 14:20

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  8. Content type: Methodology article

    Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, S...

    Authors: Gabriel Cardona, Arnau Mir, Francesc Rosselló, Lucía Rotger and David Sánchez

    Citation: BMC Bioinformatics 2013 14:3

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  9. Content type: Methodology article

    Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are o...

    Authors: Melissa Pronold, Marzieh Vali, Roger Pique-Regi and Shahab Asgharzadeh

    Citation: BMC Bioinformatics 2012 13:336

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  10. Content type: Research article

    Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein ...

    Authors: Dong Seon Kim and Yoonsoo Hahn

    Citation: BMC Bioinformatics 2012 13:299

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  11. Content type: Research article

    Yeasts are a model system for exploring eukaryotic genome evolution. Next-generation sequencing technologies are poised to vastly increase the number of yeast genome sequences, both from resequencing projects ...

    Authors: Estelle Proux-Wéra, David Armisén, Kevin P Byrne and Kenneth H Wolfe

    Citation: BMC Bioinformatics 2012 13:237

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  12. Content type: Software

    The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database ex...

    Authors: Arno Meiler, Claudia Klinger and Michael Kaufmann

    Citation: BMC Bioinformatics 2012 13:223

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  13. Content type: Research article

    The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. S...

    Authors: David C Haws, Peter Huggins, Eric M O’Neill, David W Weisrock and Ruriko Yoshida

    Citation: BMC Bioinformatics 2012 13:210

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  14. Content type: Software

    Ongoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and web servers. This brings with it the challenge of...

    Authors: Eric Talevich, Brandon M Invergo, Peter JA Cock and Brad A Chapman

    Citation: BMC Bioinformatics 2012 13:209

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  15. Content type: Research article

    Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to combine the tw...

    Authors: Zhi-Zhong Chen, Lusheng Wang and Satoshi Yamanaka

    Citation: BMC Bioinformatics 2012 13:155

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  16. Content type: Software

    Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents...

    Authors: Bhakti Dwivedi, Robert Schmieder, Dawn B Goldsmith, Robert A Edwards and Mya Breitbart

    Citation: BMC Bioinformatics 2012 13:37

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  17. Content type: Research article

    A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite...

    Authors: Jike Cui, Todd F DeLuca, Jae-Yoon Jung and Dennis P Wall

    Citation: BMC Bioinformatics 2011 12:476

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  18. Content type: Research article

    Next generation sequencing (NGS) enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test several simple a...

    Authors: Jorge Barriuso, Jose R Valverde and Rafael P Mellado

    Citation: BMC Bioinformatics 2011 12:473

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  19. Content type: Methodology article

    Continuous time Markov chains (CTMCs) is a widely used model for describing the evolution of DNA sequences on the nucleotide, amino acid or codon level. The sufficient statistics for CTMCs are the time spent i...

    Authors: Paula Tataru and Asger Hobolth

    Citation: BMC Bioinformatics 2011 12:465

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  20. Content type: Research article

    Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between...

    Authors: Claire Lemaitre, Aurélien Barré, Christine Citti, Florence Tardy, François Thiaucourt, Pascal Sirand-Pugnet and Patricia Thébault

    Citation: BMC Bioinformatics 2011 12:457

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  21. Content type: Software

    Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif...

    Authors: John Antoniw, Andrew M Beacham, Thomas K Baldwin, Martin Urban, Jason J Rudd and Kim E Hammond-Kosack

    Citation: BMC Bioinformatics 2011 12:447

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  22. Content type: Software

    Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements i...

    Authors: Malay K Basu, Jeremy D Selengut and Daniel H Haft

    Citation: BMC Bioinformatics 2011 12:434

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  23. Content type: Methodology article

    A birth and death process is frequently used for modeling the size of a gene family that may vary along the branches of a phylogenetic tree. Under the birth and death model, maximum likelihood methods have bee...

    Authors: Liang Liu, Lili Yu, Venugopal Kalavacharla and Zhanji Liu

    Citation: BMC Bioinformatics 2011 12:426

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  24. Content type: Research article

    Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.

    Authors: Steven G Cresawn, Matt Bogel, Nathan Day, Deborah Jacobs-Sera, Roger W Hendrix and Graham F Hatfull

    Citation: BMC Bioinformatics 2011 12:395

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  25. Content type: Research article

    Machine learning is a powerful approach for describing and predicting classes in microarray data. Although several comparative studies have investigated the relative performance of various machine learning met...

    Authors: Jenny Önskog, Eva Freyhult, Mattias Landfors, Patrik Rydén and Torgeir R Hvidsten

    Citation: BMC Bioinformatics 2011 12:390

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  26. Content type: Software

    A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their h...

    Authors: Brian D Ondov, Nicholas H Bergman and Adam M Phillippy

    Citation: BMC Bioinformatics 2011 12:385

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  27. Content type: Research article

    Modern gene therapy methods have limited control over where a therapeutic viral vector inserts into the host genome. Vector integration can activate local gene expression, which can cause cancer if the vector ...

    Authors: Angela P Presson, Namshin Kim, Yan Xiaofei, Irvin SY Chen and Sanggu Kim

    Citation: BMC Bioinformatics 2011 12:367

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  28. Content type: Research article

    The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dep...

    Authors: Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia and Florencio Pazos

    Citation: BMC Bioinformatics 2011 12:363

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  29. Content type: Software

    The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Altho...

    Authors: Kashi V Revanna, Chi-Chen Chiu, Ezekiel Bierschank and Qunfeng Dong

    Citation: BMC Bioinformatics 2011 12:316

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  30. Content type: Methodology article

    Etiologic studies of cancer increasingly use molecular features such as gene expression, DNA methylation and sequence mutation to subclassify the cancer type. In large population-based studies, the tumor tissu...

    Authors: Cyril Rakovski, Daniel J Weisenberger, Paul Marjoram, Peter W Laird and Kimberly D Siegmund

    Citation: BMC Bioinformatics 2011 12:284

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  31. Content type: Research article

    Fused genes are important sources of data for studies of evolution and protein function. To date no service has been made available online to aid in the large-scale identification of fused genes in sequenced g...

    Authors: Hannah MW Salim, Amanda M Koire, Nicholas A Stover and Andre RO Cavalcanti

    Citation: BMC Bioinformatics 2011 12:279

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  32. Content type: Research article

    Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, an...

    Authors: Jiajie Zhang, Amir Madany Mamlouk, Thomas Martinetz, Suhua Chang, Jing Wang and Rolf Hilgenfeld

    Citation: BMC Bioinformatics 2011 12:248

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  33. Content type: Methodology article

    This paper is devoted to distance measures for leaf-labelled trees on free leafset. A leaf-labelled tree is a data structure which is a special type of a tree where only leaves (terminal) nodes are labelled. T...

    Authors: Jakub Koperwas and Krzysztof Walczak

    Citation: BMC Bioinformatics 2011 12:204

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  34. Content type: Research article

    The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems.

    Authors: Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer and Alain Viari

    Citation: BMC Bioinformatics 2011 12:193

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    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
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