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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

    With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic r...

    Authors: Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam and Eve Syrkin Wurtele

    Citation: BMC Bioinformatics 2019 20:440

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  2. Content type: Research article

    Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant da...

    Authors: Hamid Bagheri, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin and Hridesh Rajan

    Citation: BMC Bioinformatics 2019 20:436

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  3. Content type: Software

    Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata represent...

    Authors: Ben C. Stöver, Sarah Wiechers and Kai F. Müller

    Citation: BMC Bioinformatics 2019 20:402

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  4. Content type: Research article

    Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated.

    Authors: Kaining Hu, Kai Xu, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Yidan Ouyang and Jinxing Tu

    Citation: BMC Bioinformatics 2019 20:354

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  5. Content type: Software

    Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis...

    Authors: Daniel G. Piqué, Grasiella A. Andriani, Elaine Maggi, Samuel E. Zimmerman, John M. Greally, Cristina Montagna and Jessica C. Mar

    Citation: BMC Bioinformatics 2019 20:336

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  6. Content type: Database

    The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio reri...

    Authors: Joseph Brown, Aaron R. Phillips, David A. Lewis, Michael-Andres Mans, Yvonne Chang, Robert L. Tanguay, Elena S. Peterson, Katrina M. Waters and Susan C. Tilton

    Citation: BMC Bioinformatics 2019 20:255

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  7. Content type: Methodology article

    An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with respect to a chosen taxonomic level, which delimits the position of t...

    Authors: Davide Heller, Damian Szklarczyk and Christian von Mering

    Citation: BMC Bioinformatics 2019 20:228

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  8. Content type: Software

    When designing an epigenome-wide association study (EWAS) to investigate the relationship between DNA methylation (DNAm) and some exposure(s) or phenotype(s), it is critically important to assess the sample si...

    Authors: Stefan Graw, Rosalyn Henn, Jeffrey A. Thompson and Devin C. Koestler

    Citation: BMC Bioinformatics 2019 20:218

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  9. Content type: Methodology article

    A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk mul...

    Authors: Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti and Giulio Caravagna

    Citation: BMC Bioinformatics 2019 20:210

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  10. Content type: Software

    Log-linear and multinomial modeling offer a flexible framework for genetic association analyses of offspring (child), parent-of-origin and maternal effects, based on genotype data from a variety of child-paren...

    Authors: Miriam Gjerdevik, Astanand Jugessur, Øystein A. Haaland, Julia Romanowska, Rolv T. Lie, Heather J. Cordell and Håkon K. Gjessing

    Citation: BMC Bioinformatics 2019 20:165

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  11. Content type: Methodology article

    Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have be...

    Authors: Daehong Kwon, Jongin Lee and Jaebum Kim

    Citation: BMC Bioinformatics 2019 20:147

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  12. Content type: Software

    A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine des...

    Authors: Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach and Amjad Ali

    Citation: BMC Bioinformatics 2019 20:123

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  13. Content type: Research article

    Previous cancer genomics studies focused on searching for novel oncogenes and tumor suppressor genes whose abundance is positively or negatively correlated with end-point observation, such as survival or tumor...

    Authors: Minzhe Zhang, Tao Wang, Rosa Sirianni, Philip W. Shaul and Yang Xie

    Citation: BMC Bioinformatics 2019 20:13

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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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

  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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

2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
    1.374 - SCImago Journal Rank (SJR)


    Social Media Impact
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