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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. Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using C...

    Authors: Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra and Gianvito Urgese

    Citation: BMC Bioinformatics 2021 22:360

    Content type: Software

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  2. Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large genomic datasets is crucial to analyze their...

    Authors: Léa Pradier, Tazzio Tissot, Anna-Sophie Fiston-Lavier and Stéphanie Bedhomme

    Citation: BMC Bioinformatics 2021 22:349

    Content type: Methodology article

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  3. Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insi...

    Authors: Jake L. Weissman, Sonia Dogra, Keyan Javadi, Samantha Bolten, Rachel Flint, Cyrus Davati, Jess Beattie, Keshav Dixit, Tejasvi Peesay, Shehar Awan, Peter Thielen, Florian Breitwieser, Philip L. F. Johnson, David Karig, William F. Fagan and Sharon Bewick

    Citation: BMC Bioinformatics 2021 22:306

    Content type: Research article

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  4. Testing for differential abundance of microbes in disease is a common practice in microbiome studies. Numerous differential abundance (DA) testing methods exist and range from traditional statistical tests to ...

    Authors: Zachary D. Wallen

    Citation: BMC Bioinformatics 2021 22:265

    Content type: Research article

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  5. Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of ant...

    Authors: Xiao Liang, Kyle Akers, Ishi Keenum, Lauren Wind, Suraj Gupta, Chaoqi Chen, Reem Aldaihani, Amy Pruden, Liqing Zhang, Katharine F. Knowlton, Kang Xia and Lenwood S. Heath

    Citation: BMC Bioinformatics 2021 22:117

    Content type: Software

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  6. Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortiu...

    Authors: Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, Michael P. Snyder and Euan A. Ashley

    Citation: BMC Bioinformatics 2021 22:85

    Content type: Methodology article

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  7. Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and expe...

    Authors: Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler and Jianlin Cheng

    Citation: BMC Bioinformatics 2021 22:38

    Content type: Software

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  8. High-throughput sequencing has increased the number of available microbial genomes recovered from isolates, single cells, and metagenomes. Accordingly, fast and comprehensive functional gene annotation pipelin...

    Authors: Carlos A. Ruiz-Perez, Roth E. Conrad and Konstantinos T. Konstantinidis

    Citation: BMC Bioinformatics 2021 22:11

    Content type: Software

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  9. Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, suc...

    Authors: You Tang, Zhuo Li, Chao Wang, Yuxin Liu, Helong Yu, Aoxue Wang and Yao Zhou

    Citation: BMC Bioinformatics 2020 21:461

    Content type: Software

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  10. The problem of assessing associations between multiple omics data including genomics and metabolomics data to identify biomarkers potentially predictive of complex diseases has garnered considerable research i...

    Authors: Haileab Hilafu, Sandra E. Safo and Lillian Haine

    Citation: BMC Bioinformatics 2020 21:283

    Content type: Methodology article

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  11. The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a m...

    Authors: Kitsuchart Pasupa, Wanthanee Rathasamuth and Sissades Tongsima

    Citation: BMC Bioinformatics 2020 21:216

    Content type: Methodology Article

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  12. Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite...

    Authors: Michael Gruenstaeudl and Nils Jenke

    Citation: BMC Bioinformatics 2020 21:207

    Content type: Software

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  13. Compared to the many uses of DNA-level testing in clinical oncology, development of RNA-based diagnostics has been more limited. An exception to this trend is the growing use of mRNA-based methods in early-sta...

    Authors: Hersh D. Ravkin, Ofer Givton, David B. Geffen and Eitan Rubin

    Citation: BMC Bioinformatics 2020 21:196

    Content type: Research article

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  14. The Sackin indexS of a rooted phylogenetic tree, defined as the sum of its leaves’ depths, is one of the most popular balance indices in phylogenetics, and Sackin’s paper (Syst Zool 21:225–6, 1972) is usually cit...

    Authors: Tomás M. Coronado, Arnau Mir, Francesc Rosselló and Lucía Rotger

    Citation: BMC Bioinformatics 2020 21:154

    Content type: Research Article

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  15. DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations wi...

    Authors: Joshua J. Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas and Brock C. Christensen

    Citation: BMC Bioinformatics 2020 21:108

    Content type: Methodology article

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  16. The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don’t code for proteins, yielding a need to infer evolutionary history of sequen...

    Authors: Kun Gao and Jonathan Miller

    Citation: BMC Bioinformatics 2020 21:48

    Content type: Methodology article

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  17. Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with ge...

    Authors: Dan Jiang, Cong Xin, Jinhua Ye, Yingbo Yuan and Ming Fang

    Citation: BMC Bioinformatics 2019 20:731

    Content type: Software

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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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

    Published on:

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