Scope Guidelines
Genome analysis
This category includes: Genome assembly, genome and chromosome annotation, gene finding, alternative splicing, EST analysis and comparative genomics.
We will consider algorithms and applications in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method.
Sequence analysis
This category includes: Multiple sequence alignment, sequence searches and clustering; prediction of function and localisation; novel domains and motifs; prediction of protein, RNA and DNA functional sites and other sequence features.
We will consider algorithms and applications in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method. Papers that analyse existing sequence data will only be considered if novel biological insight is obtained.
Phylogenetics
This category includes: novel phylogeny estimation procedures for molecular data including nucleotide sequence data, amino acid data, SNPs, etc., simultaneous multiple sequence alignment and phylogeny estimation, using phylogenetic approaches for any aspect of molecular sequence analysis (see Sequence Analysis scope), models of evolution, assessments of statistical support of resulting phylogenetic estimates, comparative biological methods, coalescent theory, population genetics, approaches for comparing alternative phylogenies, approaches for testing and/or mapping character change along a phylogeny.
We will consider algorithms, applications, databases, data repositories, and representation tools in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real or simulated biological data with a preference towards the combination of both approaches. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method. Papers that analyse existing sequence data will only be considered if novel biological insight is obtained.
Structural Bioinformatics
This category includes: New methods and tools for structure prediction, analysis and comparison; new methods and tools for model validation and assessment; new methods and tools for docking; models of proteins of biomedical interest; protein design; structure based function prediction.
We will consider algorithms, applications and databases in any of the above areas relating to Protein, RNA or DNA. We will consider papers related to new methods for organizing structural information, and for its representation. Small improvements or modifications of existing algorithms will generally not be suitable. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Papers that report three-dimensional models of macromolecules, molecular dynamics simulations and docking results will only be published if they provide valuable insight into biological problems. Descriptions of repositories of automatically generated models will only be published if it can be demonstrated that they provide significant advantages over existing ones.
Gene Expression
This category includes a wide range of applications relevant to the high-throughput analysis of expression of biological quantities, including microarrays (nucleic acid, protein, array CGH, genome tiling, and other arrays), EST, SAGE, MPSS, and related technologies, proteomics and mass spectrometry. Approaches to data analysis to be considered include statistical analysis of differential gene expression; expression-based classifiers; methods to determine or describe regulatory networks; pathway analysis; integration of expression data; expression-based annotation (e.g., Gene Ontology) of genes and gene sets, and other approaches to meta-analysis.
We will consider novel algorithms and applications in the above areas that constitute significant advances. Applications (including databases and web resources) will only be considered if significantly innovative. Measures of significance include anticipated impact on broad community and replacement of heuristics with principled approaches. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Development in areas with established approaches, such as normalization or classification, must represent a conceptual advance and show more than marginal improvement over existing methods.
Development in areas with established approaches, such as normalization or classification, must represent a conceptual advance and show more than marginal improvement over existing methods. For more detail on the journal's policy in this area please see Editorial at http://bioinformatics.oxfordjournals.org/cgi/content/full/25/6/701
Genetics and Population Analysis
This category includes: Segregation analysis, linkage analysis, association analysis, map construction, population simulation, haplotyping, linkage disequilibrium, pedigree drawing, marker discovery, power calculation, genotype calling.
We will consider algorithms and applications in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method. We consider statistical methodology only when there is significant bioinformatics content such as new algorithms or software. We do not consider software that implements methods recently published elsewhere by the same authors.
Systems Biology
This category includes whole cell approaches to molecular biology. Any combination of experimentally collected whole cell systems, pathways or signaling cascades on RNA, proteins, genomes or metabolites that advances the understanding of molecular biology or molecular medicine will be considered. Interactions and binding within or between any of the categories will be considered including protein interaction networks, regulatory networks, metabolic and signaling pathways. Detailed analysis of the biological properties of the systems are of particular interest.
We will consider algorithms, applications, databases, data repositories, and visualization and representation tools in any of the above areas. Systems for the simulation of dynamics and/or spatial behaviour will be also considered. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. The inclusion of experimental data is very much encouraged.
Data and Text Mining
This category includes: New methods and tools for extracting biological information from text, databases and other sources of information. Description of tools to organize, distribute and represent this information. New methods for inferring and predicting biological features based on the extracted information. The submission of databases and repositories of annotated text, computational tools and general methodology for the work in this area are encouraged, provided that they have been previously tested.
The journal requires that methods, systems and data to be made public. Strong emphasis should be placed on the biological applicability of the methods and the application to realistic biological scenarios. The main interest of the journal is the application to problems in molecular biology, but we also encourage submissions related with the relation between molecular and other type of data such as clinical, epidemiological, evolutionary, genomics, and others. Combination of information extraction technologies from heterogeneous sources and the combination with various computational approaches is also encouraged. The journal is not primarily interested in publishing analysis related with the sociological aspects of publications. The use of standard data sets for the evaluation of the methods is strongly advised, as well as the comparison with previous methods using common data sets.
Databases and Ontologies
This category includes: Curated biological databases, data warehouses, eScience, web services, database integration, biologically-relevant ontologies.
We will consider applications in any of the above areas. Descriptions of databases will not be published if they have been previously described unless there have been substantial changes or enhancements that represent a fundamental change in the database. We encourage Application Notes describing programmatic interfaces to biological data and services.
