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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: Research article

    Transcription factor binding site (TFBS) loss, gain, and reshuffling within the sequence of a regulatory element could alter the function of that regulatory element. Some of the changes will be detrimental to ...

    Authors: Mario A. Flores and Ivan Ovcharenko

    Citation: BMC Bioinformatics 2018 19:316

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  2. Content type: Methodology article

    Reproducibility of hits from independent CRISPR or siRNA screens is poor. This is partly due to data normalization primarily addressing technical variability within independent screens, and not the technical d...

    Authors: Costa Bachas, Jasmina Hodzic, Johannes C. van der Mijn, Chantal Stoepker, Henk M. W. Verheul, Rob M. F. Wolthuis, Emanuela Felley-Bosco, Wessel N. van Wieringen, Victor W. van Beusechem, Ruud H. Brakenhoff and Renée X. de Menezes

    Citation: BMC Bioinformatics 2018 19:301

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  3. Content type: Software

    Changes in spatial chromatin interactions are now emerging as a unifying mechanism orchestrating the regulation of gene expression. Hi-C sequencing technology allows insight into chromatin interactions on a ge...

    Authors: John C. Stansfield, Kellen G. Cresswell, Vladimir I. Vladimirov and Mikhail G. Dozmorov

    Citation: BMC Bioinformatics 2018 19:279

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  4. Content type: Software

    While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use case...

    Authors: Stephen D. Shank, Steven Weaver and Sergei L. Kosakovsky Pond

    Citation: BMC Bioinformatics 2018 19:276

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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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

  16. 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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  17. 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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  18. 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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  19. 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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  20. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:35

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  21. Content type: Software

    The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS plat...

    Authors: Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert and Reinhard Ullmann

    Citation: BMC Bioinformatics 2017 18:19

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  22. Content type: Database

    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...

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

    Citation: BMC Bioinformatics 2017 18:20

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  23. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:12

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  24. Content type: Methodology Article

    Feature selection, aiming to identify a subset of features among a possibly large set of features that are relevant for predicting a response, is an important preprocessing step in machine learning. In gene ex...

    Authors: Milos Radovic, Mohamed Ghalwash, Nenad Filipovic and Zoran Obradovic

    Citation: BMC Bioinformatics 2017 18:9

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  25. Content type: Methodology article

    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...

    Authors: Weiwei Ouyang, Qiang An, Jinying Zhao and Huaizhen Qin

    Citation: BMC Bioinformatics 2016 17:497

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

  26. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2016 17:480

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  27. Content type: Methodology article

    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...

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

    Citation: BMC Bioinformatics 2016 :1312

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  28. Content type: Software

    Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for t...

    Authors: Jorge Álvarez-Jarreta and Eduardo Ruiz-Pesini

    Citation: BMC Bioinformatics 2016 17:436

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  29. Content type: Research Article

    Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be described by a tree but is instead a direct...

    Authors: Hussein A. Hejase and Kevin J. Liu

    Citation: BMC Bioinformatics 2016 17:422

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  30. Content type: Research article

    Perfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between a...

    Authors: Lev I. Rubanov, Alexandr V. Seliverstov, Oleg A. Zverkov and Vassily A. Lyubetsky

    Citation: BMC Bioinformatics 2016 17:385

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  31. Content type: Research Article

    Studies exploring the potential of Chaos Game Representations (CGR) of genomic sequences to act as “genomic signatures” (to be species- and genome-specific) showed that CGR patterns of nuclear and organellar D...

    Authors: Rallis Karamichalis, Lila Kari, Stavros Konstantinidis, Steffen Kopecki and Stephen Solis-Reyes

    Citation: BMC Bioinformatics 2016 17:313

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  32. Content type: Software

    With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an effi...

    Authors: Achal Rastogi, Omer Murik, Chris Bowler and Leila Tirichine

    Citation: BMC Bioinformatics 2016 17:261

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  33. Content type: Research Article

    Random forests have often been claimed to uncover interaction effects. However, if and how interaction effects can be differentiated from marginal effects remains unclear. In extensive simulation studies, we i...

    Authors: Marvin N. Wright, Andreas Ziegler and Inke R. König

    Citation: BMC Bioinformatics 2016 17:145

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  34. Content type: Methodology Article

    Gene set analysis (GSA) aims to evaluate the association between the expression of biological pathways, or a priori defined gene sets, and a particular phenotype. Numerous GSA methods have been proposed to ass...

    Authors: Huey-Miin Hsueh and Chen-An Tsai

    Citation: BMC Bioinformatics 2016 17:74

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  35. Content type: Methodology article

    Success in genome-wide association studies and marker-assisted selection depends on good phenotypic and genotypic data. The more complete this data is, the more powerful will be the results of analysis. Nevert...

    Authors: A. Xavier, William M. Muir and Katy M. Rainey

    Citation: BMC Bioinformatics 2016 17:55

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  36. Content type: Research article

    One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree...

    Authors: Vassily Lyubetsky, Roman Gershgorin, Alexander Seliverstov and Konstantin Gorbunov

    Citation: BMC Bioinformatics 2016 17:40

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


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