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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: Methodology

    In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree w...

    Authors: Guilherme P. Telles, Graziela S. Araújo, Maria E. M. T. Walter, Marcelo M. Brigido and Nalvo F. Almeida

    Citation: BMC Bioinformatics 2018 19:172

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  2. Content type: Research Article

    Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding...

    Authors: Vassily Lyubetsky, Roman Gershgorin and Konstantin Gorbunov

    Citation: BMC Bioinformatics 2017 18:537

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  3. Content type: Research Article

    With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and c...

    Authors: Oluwatosin Oluwadare and Jianlin Cheng

    Citation: BMC Bioinformatics 2017 18:480

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  4. Content type: Software

    During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatran...

    Authors: Peng Zhai, Longshu Yang, Xiao Guo, Zhe Wang, Jiangtao Guo, Xiaoqi Wang and Huaiqiu Zhu

    Citation: BMC Bioinformatics 2017 18:434

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  5. Content type: Software

    Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotate...

    Authors: Joseph Guhlin, Kevin A. T. Silverstein, Peng Zhou, Peter Tiffin and Nevin D. Young

    Citation: BMC Bioinformatics 2017 18:367

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  6. Content type: Research Article

    Biomarker detection presents itself as a major means of translating biological data into clinical applications. Due to the recent advances in high throughput sequencing technologies, an increased number of met...

    Authors: Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin and Jan Suchodolski

    Citation: BMC Bioinformatics 2017 18:328

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  7. Content type: Methodology Article

    In phylogenetics, we often seek to reconcile gene trees with species trees within the framework of an evolutionary model. While the most popular models for eukaryotic species allow for only gene duplication an...

    Authors: Jennifer Rogers, Andrew Fishberg, Nora Youngs and Yi-Chieh Wu

    Citation: BMC Bioinformatics 2017 18:292

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  8. Content type: Research Article

    Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological chal...

    Authors: Rasha E. Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat and Benjamin Audit

    Citation: BMC Bioinformatics 2017 18:209

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  9. Content type: Research Article

    The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolv...

    Authors: José Santos and Ángel Monteagudo

    Citation: BMC Bioinformatics 2017 18:195

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  10. Content type: Research article

    Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and...

    Authors: Malik Yousef, Waleed Khalifa, İlhan Erkin Acar and Jens Allmer

    Citation: BMC Bioinformatics 2017 18:170

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  11. Content type: Software

    Guide Picker (https://​www.​deskgen.​com/​guide-picker/​) serves as a meta tool for designing CRISPR experiments by presenting ten different guide RNA scori...

    Authors: Soren H. Hough, Kris Kancleris, Leigh Brody, Neil Humphryes-Kirilov, Joseph Wolanski, Keith Dunaway, Ayokunmi Ajetunmobi and Victor Dillard

    Citation: BMC Bioinformatics 2017 18:167

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    The Erratum to this article has been published in BMC Bioinformatics 2017 18:202

  12. Content type: Research Article

    Transcriptional gene regulation is a fundamental process in nature, and the experimental and computational investigation of DNA binding motifs and their binding sites is a prerequisite for elucidating this pro...

    Authors: Martin Nettling, Hendrik Treutler, Jesus Cerquides and Ivo Grosse

    Citation: BMC Bioinformatics 2017 18:141

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  13. Content type: Software

    Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribut...

    Authors: Diego Pasqualin, Marcos Barbeitos and Fabiano Silva

    Citation: BMC Bioinformatics 2017 18:123

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  14. Content type: Methodology article

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes...

    Authors: James C. Wilgenbusch, Wen Huang and Kyle A. Gallivan

    Citation: BMC Bioinformatics 2017 18:85

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  15. Content type: Software

    Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical me...

    Authors: Yasir Rahmatallah, Boris Zybailov, Frank Emmert-Streib and Galina Glazko

    Citation: BMC Bioinformatics 2017 18:61

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

    Social Media Impact
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