Summary of Bioinformatics Journals

 

Summary of Bioinformatics Journals

Or more precisely, journals where bioinformatics articles can appear:

from  http://www.cs.ucr.edu/~vladimir/lib/journals.html

Name	2008	2007	2006	2005	Publisher
Biochemistry	3.379	3.368			American Chemical Society
Bioinformatics	4.328	5.039	4.894	6.019	Oxford University Press
BMC Bioinformatics	3.78	3.49	3.62	4.96	BioMed Central
BMC Genomics	3.93	4.18	4.03	4.09	BioMed Central
BMC Molecular Biology	2.81	3.37			BioMed Central
BMC Systems Biology	3.71				BioMed Central
Briefings in Bioinformatics	4.627	4.415	24.370		Oxford University Press
Briefings in Functional Genomics & Proteomics					Oxford University Press
Computational Biology and Chemistry		1.653	2.135	2.196	Elsevier
The EMBO Journal	8.295	7.45	8.175	10.053	European Molecular Biology Organization (EMBO)
Genome Biology	6.153	6.59	7.17	9.71	BioMed Central
Genome Research	10.176				Cold Spring Harbor Laboratory Press
Human Molecular Genetics	7.249	7.806	8.099	7.764	Oxford University Press
IEEE/ACM Transactions on Computational Biology and Bioinformatics	1.866				IEEE
The International Journal of Biostatistics					The Berkeley Electronic Press
Journal of Bioinformatics and Computational Biology					World Scientific Publishing
Journal of Biomedical Informatics	1.924	2.000	2.346	2.388	Elsevier
Journal of Computational Biology	1.563			2.446	Mary Ann Liebert
Journal of Molecular Biology	4.146	4.472	4.890	5.229	Elsevier
Journal of Molecular Modelling		1.669			Springer
Journal of Proteome Research	5.684	5.615			American Chemical Society
Metabolic Engineering		3.444		2.484	Elsevier
Molecular Systems Biology	12.243	9.954			European Molecular Biology Organization (EMBO), Nature Publishing Group
Nature	31.434			27.074	Nature Publishing Group
Nature Biotechnology	22.297				Nature Publishing Group
Nature Genetics	30.259			28.543	Nature Publishing Group
Nature Structural Biology	10.987			8.738	Nature Publishing Group
Nucleic Acids Research	6.878	6.954	6.317	7.552	Oxford University Press
OMICS: A Journal of Integrative Biology	3.167				Mary Ann Liebert
PLoS Biology	12.683	13.5			Public Library of Science
PLoS Computational Biology	5.895	6.2	4.9		The International Society for Computational Biology, Public Library of Science
PLoS Genetics	8.883	8.7			Public Library of Science
Proceedings of the National Academy of Sciences	9.380	9.598		10.520	National Academy of Sciences
Protein Engineering	2.787	2.662		3.605	Oxford University Press
Protein Science	3.115	3.135		4.806	The Protein Society, Cold Spring Harbor Laboratory Press
Proteins: Structure, Function, and Bioinformatics	3.419	4.297		5.162	Wiley Interscience
Proteomics	4.586	5.479			Wiley Interscience
Science	28.103			21.911	AAAS
Statistical Applications in Genetics and Molecular Biology	1.773				The Berkeley Electronic Press
Structure	5.397	5.2			Cell Press
Trends in Biochemical Sciences	14.101		13.9	17.217	Cell Press
Trends in Biotechnology	6.624		7.8	3.606	Cell Press
Trends in Genetics	8.659		9.9	10.446	Cell Press

Bioinformatics

Scope:

• Genome analysis
• Sequence analysis
• Phylogenetics
• Structural bioinformatics
• Gene expression
• Genetic and population analysis
• Systems biology
• Data and text mining
• Databases and ontologies

Formats:

• Original Papers (up to 7 pages; this is approx. 5000 words)
• Discovery Notes(up to 4 pages, this is approx. 3000 words)
• Application Notes (up to 2 pages; this is approx. 1300 words or 1000 words plus one figure)
• Reviews (3-8 pages)
• Letters to the Editor

BMC Bioinformatics

Scope:

• all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology

Formats:

• Research article
• Database
• Methodology article
• Software

BMC Genomics

Scope:

• all aspects of gene mapping, sequencing and analysis, functional genomics, and proteomics

Formats:

• Research article
• Database
• Methodology article
• Software

Briefings in Bioinformatics

Scope:

• DNA sequencing
• expression profiling
• alignment methods
• gene expression studies
• protein profiles and HMMs
• metabolic and signalling pathways
• structure and function prediction
• mapping
• microarrays

Formats:

• Review articles (2000-5000 words)
• Opinion articles (500-1000 words)
• Letters to the Editors (500-1000 words)
• Software and website reviews (500-1000 words)
• Book reviews (500-1000 words)

Briefings in Functional Genomics & Proteomics

Scope:

• microarray technology
• gene and protein expression profiling
• differential display
• electrophoresis
• genotyping
• transgenic systems
• mutation screens
• protein spectrometry
• comparative genomics
• phage display
• combinatorial libraries

Formats:

• Review articles (2000-5000 words)
• Opinion articles (500-1000 words)
• Letters to the Editors (500-1000 words)
• Software and website reviews (500-1000 words)
• Book reviews (500-1000 words)

Computational Biology and Chemistry

Scope:

• biomolecular sequence analysis
• molecular evolution
• molecular genetics (functional genomics and proteomics)
• theory and practice of either biology-specific or chemical-biology-specific modeling
• structural biology of nucleic acids and proteins (including computer-assisted predictions of folding)

Formats:

• research papers
• brief communications
• software notes
• review articles
• book review articles

The EMBO Journal

Scope:

• Development (mechanisms of developmental processes, investigated at a molecular level)
• Immunology (molecular mechanisms underlying innate and adaptive immunity in all organisms)
• Neuroscience (molecular aspects of differentiation, (patho)physiology and (dys)function of the nervous system)
• Plant Biology (molecular studies focusing on unicellular and multicellular autotrophic organisms)
• Structural Biology (multi-dimensional structures and dynamics of biological macromolecules)
• Genomic & Computational Biology (large-scale analysis of genomes and their expression, modelling of biological processes at all levels of molecular organisation)
• Genome Stability & Dynamics (processes involved in repair, recombination and replication of genomes)
• Chromatin & Transcription (nuclear and chromosomal architecture, epigenetics, transcription and its regulation)
• RNA (splicing, modification, folding, stability and catalytic activity of RNA)
• Proteins (translation, protein folding, post-translational modification and degradation of proteins)
• Cellular Metabolism (bioenergetics, anabolic/catabolic processes studied at the molecular level)
• Signal Transduction (mechanisms involved in sending, receiving and integrating biological signals)
• Cell Cycle (mechanisms regulating the division cycle of eukaryotic and prokaryotic cells)
• Differentiation & Death (molecular studies on cellular differentiation processes and cell death)
• Membranes & Transport (structure and function of cellular membranes and compartments, trafficking and transport of (macro)molecules)
• Cell & Tissue Architecture (cytoskeleton, extracellular matrix, cell polarity, migration and adhesion)
• Microbiology & Pathogens (molecular biology of viruses, bacteria, and unicellular or multicellular pathogens)
• Molecular Biology of Disease (molecular mechanisms underlying human or other diseases, cancer)

Formats:

Genome Biology

Scope:

• molecular, cellular, organismal or population biology studied from a genomic perspective
• genomics
• proteomics
• bioinformatics
• genomic methods (including structure prediction)
• computational biology
• sequence analysis (including large-scale and cross-genome analyses)
• comparative biology and evolution

Formats:

• Reviews
• Short reports on relevant papers, websites and meetings
• News, comment and editorials
• Primary research articles
• Preprint depository
• Supplements

Genome Research

Scope:

• gene discovery
• comparative genome analyses
• molecular and human evolution
• informatics
• genome structure and function
• proteomics
• technological innovations and applications
• statistical and mathematical methods
• cutting-edge genetic and physical mapping and DNA sequencing
• systems biology
• other reports that present data where sequence information is used to address biological concerns

Formats:

• Articles
• Letters
• Methods
• Resource reports
• Review articles
• Commentaries
• Perspectives

Human Molecular Genetics

Scope:

• the molecular basis of human genetic disease
• developmental genetics
• cancer genetics
• neurogenetics
• chromosome and genome structure and function
• gene therapy
• mouse and other models of human diseases
• functional genomics
• computational genomics

Formats:

• Articles
• Reviews

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Scope:

• algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology
• development and testing of effective computer programs in bioinformatics
• development and optimization of biological databases
• important biological results that are obtained from the use of these methods, programs, and databases

Formats:

• research articles

The International Journal of Biostatistics

Scope:

• biostatistical models and methods
• statistical theory
• original applications of statistical methods, for important practical problems arising from the biological, medical, public health, and agricultural sciences

Formats:

Journal of Bioinformatics and Computational Biology

Scope:

Formats:

• original research articles (technical presentations of new assertions, discoveries and tools, intended for a narrower specialist community)
• expository tutorial papers
• review papers
• short, critical comments on technical issues associated with the analysis of cellular information

Journal of Computational Biology

Scope:

• genomics
• mathematical modeling and simulation
• distributed and parallel biological computing
• designing biological databases
• pattern matching and pattern detection
• linking disparate databases and data
• new tools for computational biology
• relational and object-oriented database technology for bioinformatics
• biological expert system design and use
• reasoning by analogy, hypothesis formation and testing by machine
• management of biological databases

Formats:

• Mini-Review/News/Perspectives (typically 2-4 pages long)
• Reviews
• Papers
• Communications (typically 2 pages long; this section is for communications too brief for a full paper)
• Software, Hardware, and Book Reviews (these reviews will usually be commissioned by the Editor-in-Chief or the Editorial Board, but a short (1-2 page) outline can be sent to the Editor-in-Chief unsolicited. Typical reviews will be one or two typeset pages, with a maximaximum of three figures)

Journal of Molecular Biology

Scope:

• Genes: Epression, replication and recombination, sequence organization and structure, genetics of eukaryotes and prokaryotes.
• Viruses and Bacteriophages: Genetics, structure, growth cycle.
• Cells and Development: Developmental biology, organelle structure and function, motility, transport and sorting of macromolecules, energy transfer, growth control.
• Proteins, Nucleic Acids and other Biologically Important Macromolecules: Molecular structure, physical chemistry, molecular engineering, macromolecular assembly and enzymology.

Formats:

• Communications (brief papers that make a specific well-documented point. In general, no more than four figures and tables. The text will be continuous, with technical and methological detail printed in the legend to the tables and figures.)
• Articles (no longer than 15 printed pages with no more than 10 figures and four tables.)
• Reviews (sharply focused and balanced accounts of progress in fields of interest to the general reader. No longer than 12 printed pages and with no more than 12 figures and tables. Authorship is normally by invitation: an Editor should be consulted in advance by anyone wishing to submit an unsolicited Review.)

Journal of Molecular Modelling

Scope:

• Life Science Modeling
  • Computer-aided molecular design
  • Rational drug design, de novo ligand design, receptor modeling and docking
  • Cheminformatics, data analysis, visualization and mining
  • Computational medicinal chemistry
  • Homology modeling
  • Simulation of peptides, DNA and other biopolymers
  • Quantitative structure-activity relationships (QSAR)
  • Quantitative structure-property relationships (QSAR) and ADME-modeling
  • Modeling of biological reaction mechanisms
  • Combined experimental/computational studies in which calculations play a major role
• Materials Modeling
  • Classical or quantum mechanical modeling of materials
  • Modeling mechanical and physical properties
  • Computer-based structure determination of materials
  • Catalysis-modeling
  • Modeling zeolites, layered minerals etc.
  • Modeling catalytic reaction mechanisms and computational catalysis optimization
  • Polymer modeling
  • Nanomaterials, fullerenes and nanotubes
  • Modeling stationary phases in separation science
• New Methods
  • New classical modeling techniques and parameter sets
  • New quantum mechanical techniques, including ab inito DFT and semiempirical MO-methods, basis sets etc.
  • New hybrid QM/MM techniques
  • New computer-based methods for interpreting experimental data
  • New visualization techniques
  • New statistical methods for treating biopolymers
  • New software and new versions of existing software
  • New techniques for simulating environments or solvent
• Computational Chemistry
  • Classical and quantum mechanical modeling of chemical structures and reactions
  • Molecular recognition
  • Modeling sensors
  • New desktop modeling software and techniques
  • Theories of chemical structure and reactions
  • Neural nets and genetic algorithms in chemistry

Formats:

Metabolic Engineering

Scope:

• Metabolic Control Analysis
• Biological Transport
• Computer Simulation
• Genetics & Genetic Engineering
• Nuclear Magnetic Resonance
• Biotechnology
• Algorithms
• Bioinformatics
• Biological Networks
• Biomedical Engineering
• Enzyme Kinetics
• Pathway Engineering
• Signal Transduction

Formats:

Molecular Systems Biology

Scope:

• Proteomics
• Metabolomics
• Functional genomics
• Structural genomics
• Transcriptomics
• Computational biology
• Bioinformatics
• Theoretical biology
• Synthetic biology

Formats:

Nucleic Acids Research

Scope:

• chemistry
• computational biology
• genomics
• molecular biology
• nucleic acid enzymes
• RNA
• structural biology

Formats:

The first issue of each year is devoted to biological databases, and an issue in July is devoted to papers describing web-based software resources of value to the biological community.

OMICS: A Journal of Integrative Biology

Scope:

• Physical mapping and sequencing
• Gene and protein expression
• Peptide identifications
• Bacterial coding capabilities
• Developments in plant research
• Spectral analysis methods

Formats:

PLoS Computational Biology

Scope:

• All aspects of computational biology applied to different and integrated biological scales, from molecules and cells to patient populations and ecosystems

Formats:

• research articles
• reviews
• perspectives
• tutorials

Protein Science

Scope:

• structure of proteins and strategies of determining protein structure by chemical, biophysical, and recombinant methods
• peptides
• protein domains
• protein folding and molecular dynamics
• novel isolation procedures
• enzyme action and regulation
• interactions of proteins with nucleic acids, lipids, ligands, and other proteins
• receptor-mediated signal transduction and other trans-membrane phenomena
• the functions of proteins in replication, supramolecular assembly, immune reactions, development, and other biological processes
• protein trafficking, synthesis, and sorting
• recognition, localization and signaling of proteins
• results of protein-centered work involving sequencing, modification, and mass spectrometry
• cDNA, mutagenesis, and cloning
• computational analysis
• isolation and characterization
• thermodynamics and hydrodynamics
• kinetics
• equilibrium phenomena

Formats:

• original research papers
• reviews
• book reviews

Proteins: Structure, Function, and Bioinformatics

Scope:

• new experimental or computational approaches for interpreting and understanding data from biophysical chemistry
• structural studies of proteins and macromolecular assemblies
• alterations of protein structure and function engineered through techniques of molecular biology and genetics
• functional analyses under physiologic conditions
• interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates
• synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function

Formats:

• full-length reports
• short communications (usually not more than 4 printed pages)
• prediction reports

Structure

Scope:

• Atomic resolution analysis
• X-ray crystallography
• Nuclear magnetic resonance spectroscopy
• Computational analyses, simulations, and predictions
• Electron microscopy
• Neutron scattering
• Hydrodynamics
• X-ray absorption spectroscopy
• Biochemical studies
• Biophysical analyses
• Fluorescence energy transfer
• Design, construction, and analysis of novel protein and RNA structures
• Catalytic activities
• Medium- to low-resolution structural analysis
• Single-molecule analysis
• Small-angle X-ray scattering
• Emerging methods in structure determination

Formats:

• Research articles
• Technical advances
• Ways & means
• Matters arising

Trends in Biotechnology

Scope:

• molecular biotechnology
• gene transfer and expression
• applied microbiology
• environmental biotechnology
• fermentation and bioprocessing
• rDNA therapeutics and vaccines
• plant biotechnology
• patenting and regulatory issues

Formats:

• reviews
• opinions
• research focus
• letters (no more than 700 words long with a maximum of 12 references and one figure)