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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: Methodology Article

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for com...

    Authors: Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron and Krister M. Swenson

    Citation: BMC Bioinformatics 2016 17:30

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  2. Content type: Research Article

    Branch lengths are an important attribute of phylogenetic trees, providing essential information for many studies in evolutionary biology. Yet, part of the current methodology to reconstruct a phylogeny from g...

    Authors: Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel J. P. Douzery and Fabio Pardi

    Citation: BMC Bioinformatics 2016 17:23

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  3. Content type: Methodology Article

    In genome-wide association studies (GWAS) for complex diseases, the association between a SNP and each phenotype is usually weak. Combining multiple related phenotypic traits can increase the power of gene sea...

    Authors: James J. Yang, Jia Li, L. Keoki Williams and Anne Buu

    Citation: BMC Bioinformatics 2016 17:19

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  4. Content type: Research Article

    Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach sear...

    Authors: Thu-Hien To, Edwin Jacox, Vincent Ranwez and Celine Scornavacca

    Citation: BMC Bioinformatics 2015 16:384

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  5. Content type: Software

    Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α– & β–diversity. Feature subset selection – a sub-field ...

    Authors: Gregory Ditzler, J. Calvin Morrison, Yemin Lan and Gail L. Rosen

    Citation: BMC Bioinformatics 2015 16:358

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  6. Content type: Software

    Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to...

    Authors: Saulo Alves Aflitos, Edouard Severing, Gabino Sanchez-Perez, Sander Peters, Hans de Jong and Dick de Ridder

    Citation: BMC Bioinformatics 2015 16:352

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  7. Content type: Research article

    GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain Gm...

    Authors: Magdalena A. Machnicka, Katarzyna H. Kaminska, Stanislaw Dunin-Horkawicz and Janusz M. Bujnicki

    Citation: BMC Bioinformatics 2015 16:336

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  8. Content type: Methodology article

    Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent ...

    Authors: Jose Alfredo Samaniego Castruita, Marie Lisandra Zepeda Mendoza, Ross Barnett, Nathan Wales and M Thomas P. Gilbert

    Citation: BMC Bioinformatics 2015 16:232

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  9. Content type: Research article

    Transcriptional regulation is normally based on the recognition by a transcription factor of a defined base sequence in a process of direct read-out. However, the nucleic acid secondary and tertiary structure ...

    Authors: David C Whitley, Valeria Runfola, Peter Cary, Liliya Nazlamova, Matt Guille and Garry Scarlett

    Citation: BMC Bioinformatics 2014 15:288

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  10. Content type: Methodology article

    Microarray technology, as well as other functional genomics experiments, allow simultaneous measurements of thousands of genes within each sample. Both the prediction accuracy and interpretability of a classif...

    Authors: Osama Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad Khan, Metodi V Metodiev and Berthold Lausen

    Citation: BMC Bioinformatics 2014 15:274

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  11. Content type: Software

    Dominance effect may play an important role in genetic variation of complex traits. Full featured and easy-to-use computing tools for genomic prediction and variance component estimation of additive and domina...

    Authors: Chunkao Wang, Dzianis Prakapenka, Shengwen Wang, Sujata Pulugurta, Hakizumwami Birali Runesha and Yang Da

    Citation: BMC Bioinformatics 2014 15:270

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  12. Content type: Research article

    Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserv...

    Authors: Joseph MEX Lucas, Matthieu Muffato and Hugues Roest Crollius

    Citation: BMC Bioinformatics 2014 15:268

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  13. Content type: Database

    The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing ...

    Authors: Lia Di, Pedro E Pagan, Daniel Packer, Che L Martin, Saymon Akther, Girish Ramrattan, Emmanuel F Mongodin, Claire M Fraser, Steven E Schutzer, Benjamin J Luft, Sherwood R Casjens and Wei-Gang Qiu

    Citation: BMC Bioinformatics 2014 15:233

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  14. Content type: Research article

    With the help of epigenome-wide association studies (EWAS), increasing knowledge on the role of epigenetic mechanisms such as DNA methylation in disease processes is obtained. In addition, EWAS aid the underst...

    Authors: Simone Wahl, Nora Fenske, Sonja Zeilinger, Karsten Suhre, Christian Gieger, Melanie Waldenberger, Harald Grallert and Matthias Schmid

    Citation: BMC Bioinformatics 2014 15:232

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  15. Content type: Software

    Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical...

    Authors: Todd H Oakley, Markos A Alexandrou, Roger Ngo, M Sabrina Pankey, Celia K C Churchill, William Chen and Karl B Lopker

    Citation: BMC Bioinformatics 2014 15:230

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  16. Content type: Software

    Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship betwee...

    Authors: Neda Zamani, Görel Sundström, Jennifer RS Meadows, Marc P Höppner, Jacques Dainat, Henrik Lantz, Brian J Haas and Manfred G Grabherr

    Citation: BMC Bioinformatics 2014 15:227

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  17. Content type: Research article

    Whole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down to single nucleotide resolution. Several studies ...

    Authors: Egor Dolzhenko and Andrew D Smith

    Citation: BMC Bioinformatics 2014 15:215

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  18. Content type: Methodology article

    Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued ...

    Authors: Benedict Paten, Daniel R Zerbino, Glenn Hickey and David Haussler

    Citation: BMC Bioinformatics 2014 15:206

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  19. Content type: Software

    Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is...

    Authors: José Ignacio Lucas-Lledó, David Vicente-Salvador, Cristina Aguado and Mario Cáceres

    Citation: BMC Bioinformatics 2014 15:163

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  20. Content type: Research article

    Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard co...

    Authors: Leo van Iersel, Steven Kelk, Nela Lekić and Celine Scornavacca

    Citation: BMC Bioinformatics 2014 15:127

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  21. Content type: Research article

    Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily r...

    Authors: Birte Kehr, Kathrin Trappe, Manuel Holtgrewe and Knut Reinert

    Citation: BMC Bioinformatics 2014 15:99

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  22. Content type: Research article

    A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino ...

    Authors: Dawit Nigatu, Attiya Mahmood and Werner Henkel

    Citation: BMC Bioinformatics 2014 15:80

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  23. Content type: Software

    Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Anal...

    Authors: Zhuohui Gan, Jianwu Wang, Nathan Salomonis, Jennifer C Stowe, Gabriel G Haddad, Andrew D McCulloch, Ilkay Altintas and Alexander C Zambon

    Citation: BMC Bioinformatics 2014 15:69

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  24. Content type: Research article

    Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains pattern...

    Authors: Nicholas J Hudson, Laercio R Porto-Neto, James Kijas, Sean McWilliam, Ryan J Taft and Antonio Reverter

    Citation: BMC Bioinformatics 2014 15:66

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  25. Content type: Research article

    Evidence suggests that common complex diseases may be partially due to SNP-SNP interactions, but such detection is yet to be fully established in a high-dimensional small-sample (small-n-large-p) study. A numb...

    Authors: Jianwei Gou, Yang Zhao, Yongyue Wei, Chen Wu, Ruyang Zhang, Yongyong Qiu, Ping Zeng, Wen Tan, Dianke Yu, Tangchun Wu, Zhibin Hu, Dongxin Lin, Hongbing Shen and Feng Chen

    Citation: BMC Bioinformatics 2014 15:62

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  26. Content type: Research article

    Genes located in the same chromosome region share common evolutionary events more often than other genes (e.g. a segmental duplication of this region). Their evolution may also be related if they are involved ...

    Authors: Yao-ban Chan, Vincent Ranwez and Celine Scornavacca

    Citation: BMC Bioinformatics 2013 14:332

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  27. Content type: Software

    Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computat...

    Authors: Mehmood Alam Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren and Lars Arvestad

    Citation: BMC Bioinformatics 2013 14:334

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  28. Content type: Software

    Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling,...

    Authors: Wellington S Martins, Welton C Carmo, Humberto J Longo, Thierson C Rosa and Thiago F Rangel

    Citation: BMC Bioinformatics 2013 14:324

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  29. Content type: Software

    As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods for cluster analysis have become necessary. We have developed an au...

    Authors: Manon Ragonnet-Cronin, Emma Hodcroft, Stéphane Hué, Esther Fearnhill, Valerie Delpech, Andrew J Leigh Brown and Samantha Lycett

    Citation: BMC Bioinformatics 2013 14:317

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  30. Content type: Research article

    Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biolo...

    Authors: Jaehee Kim, Robert Todd Ogden and Haseong Kim

    Citation: BMC Bioinformatics 2013 14:310

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  31. Content type: Software

    Dynamic visualisation interfaces are required to explore the multiple microbial genome data now available, especially those obtained by high-throughput sequencing — a.k.a. “Next-Generation Sequencing” (NGS) — tec...

    Authors: Pierre Lechat, Erika Souche and Ivan Moszer

    Citation: BMC Bioinformatics 2013 14:277

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  32. Content type: Software

    PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—pe...

    Authors: Joel Sjöstrand, Lars Arvestad, Jens Lagergren and Bengt Sennblad

    Citation: BMC Bioinformatics 2013 14:209

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  33. Content type: Methodology article

    In the past decade, bioinformatics tools have matured enough to reliably perform sophisticated primary data analysis on Next Generation Sequencing (NGS) data, such as mapping, assemblies and variant calling, h...

    Authors: Alireza Hadj Khodabakhshi, Anthony P Fejes, Inanc Birol and Steven JM Jones

    Citation: BMC Bioinformatics 2013 14:167

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  34. Content type: Software

    Scientists rarely reuse expert knowledge of phylogeny, in spite of years ofeffort to assemble a great “Tree of Life” (ToL). A notableexception involves the use of Phylomatic, which provides tools togenerate custo...

    Authors: Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab…

    Citation: BMC Bioinformatics 2013 14:158

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  35. Content type: Methodology article

    Complex traits may be defined by a range of different criteria. It would result in a loss of information to perform analyses simply on the basis of a final clinical dichotomized affected / unaffected variable.

    Authors: Chen Suo, Timothea Toulopoulou, Elvira Bramon, Muriel Walshe, Marco Picchioni, Robin Murray and Jurg Ott

    Citation: BMC Bioinformatics 2013 14:151

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  36. Content type: Research article

    With the advancement of next-generation sequencing and transcriptomics technologies, regulatory effects involving RNA, in particular RNA structural changes are being detected. These results often rely on RNA s...

    Authors: James WJ Anderson, Ádám Novák, Zsuzsanna Sükösd, Michael Golden, Preeti Arunapuram, Ingolfur Edvardsson and Jotun Hein

    Citation: BMC Bioinformatics 2013 14:149

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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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