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. Research Article

    Multi-scale structural community organisation of the human genome

    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...

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

    BMC Bioinformatics 2017 18:209

    Published on: 11 April 2017

  2. Software

    Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments

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

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

    BMC Bioinformatics 2017 18:167

    Published on: 14 March 2017

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

  3. Research article

    MicroRNA categorization using sequence motifs and k-mers

    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...

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

    BMC Bioinformatics 2017 18:170

    Published on: 14 March 2017

  4. Software

    SFREEMAP - A simulation-free tool for stochastic mapping

    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...

    Diego Pasqualin, Marcos Barbeitos and Fabiano Silva

    BMC Bioinformatics 2017 18:123

    Published on: 22 February 2017

  5. Methodology article

    Visualizing phylogenetic tree landscapes

    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...

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

    BMC Bioinformatics 2017 18:85

    Published on: 2 February 2017

  6. Software

    GSAR: Bioconductor package for Gene Set analysis in R

    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...

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

    BMC Bioinformatics 2017 18:61

    Published on: 24 January 2017

  7. Software

    iGC—an integrated analysis package of gene expression and copy number alteration

    With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional anal...

    Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu and Eric Y. Chuang

    BMC Bioinformatics 2017 18:35

    Published on: 14 January 2017

  8. Database

    GTB – an online genome tolerance browser

    Accurate methods capable of predicting the impact of single nucleotide variants (SNVs) are assuming ever increasing importance. There exists a plethora of in silico algorithms designed to help identify and priori...

    Hashem A. Shihab, Mark F. Rogers, Michael Ferlaino, Colin Campbell and Tom R. Gaunt

    BMC Bioinformatics 2017 18:20

    Published on: 6 January 2017

  9. Methodology Article

    PERGOLA: fast and deterministic linkage mapping of polyploids

    A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creatio...

    Fabian Grandke, Soumya Ranganathan, Nikkie van Bers, Jorn R. de Haan and Dirk Metzler

    BMC Bioinformatics 2017 18:12

    Published on: 4 January 2017

  10. Methodology article

    Integrating mean and variance heterogeneities to identify differentially expressed genes

    In functional genomics studies, tests on mean heterogeneity have been widely employed to identify differentially expressed genes with distinct mean expression levels under different experimental conditions. Va...

    Weiwei Ouyang, Qiang An, Jinying Zhao and Huaizhen Qin

    BMC Bioinformatics 2016 17:497

    Published on: 6 December 2016

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:89

  11. Methodology Article

    A statistical model for the analysis of beta values in DNA methylation studies

    The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variable...

    Leonie Weinhold, Simone Wahl, Sonali Pechlivanis, Per Hoffmann and Matthias Schmid

    BMC Bioinformatics 2016 17:480

    Published on: 22 November 2016

  12. Methodology article

    InDel marker detection by integration of multiple softwares using machine learning techniques

    In the biological experiments of soybean species, molecular markers are widely used to verify the soybean genome or construct its genetic map. Among a variety of molecular markers, insertions and deletions (In...

    Jianqiu Yang, Xinyi Shi, Lun Hu, Daipeng Luo, Jing Peng, Shengwu Xiong, Fanjing Kong, Baohui Liu and Xiaohui Yuan

    BMC Bioinformatics 2016 :1312

    Published on: 2 November 2016

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