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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.

Page 1 of 5

  1. Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content analysis of genomes at different phylogenetic levels (isolates, species). These tools rel...

    Authors: Hatice Akarsu, Lisandra Aguilar-Bultet and Laurent Falquet

    Citation: BMC Bioinformatics 2019 20:621

    Content type: Software

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  2. Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and ...

    Authors: Ross Mawhorter and Ran Libeskind-Hadas

    Citation: BMC Bioinformatics 2019 20:612

    Content type: Methodology Article

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  3. Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for it...

    Authors: Emma Persson, Mateusz Kaduk, Sofia K. Forslund and Erik L. L. Sonnhammer

    Citation: BMC Bioinformatics 2019 20:523

    Content type: Research article

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  4. 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

    Content type: Software

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Software

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Software

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  9. 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

    Content type: Database

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  10. 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

    Content type: Methodology article

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  11. 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

    Content type: Software

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  12. 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

    Content type: Methodology article

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  13. 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

    Content type: Software

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  14. 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

    Content type: Methodology article

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  15. 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

    Content type: Software

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  16. 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

    Content type: Research article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Methodology article

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  19. 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

    Content type: Software

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  20. 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

    Content type: Software

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  21. 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

    Content type: Methodology

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  22. 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

    Content type: Research Article

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  23. 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

    Content type: Research Article

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  24. 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

    Content type: Software

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  25. 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

    Content type: Software

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  26. 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

    Content type: Research Article

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  27. 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

    Content type: Methodology Article

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  28. 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

    Content type: Research Article

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  29. 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

    Content type: Research Article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Software

    Published on:

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

  32. 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

    Content type: Research Article

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  33. 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

    Content type: Software

    Published on:

  34. 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

    Content type: Methodology article

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  35. 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

    Content type: Software

    Published on:

  36. 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

    Content type: Software

    Published on:

  37. 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

    Content type: Database

    Published on:

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)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

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