Journals in Bioinformatics and computational biology
Journals in Bioinformatics and computational biology
- ISSN: 0020-7519
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International Journal for Parasitology
Sponsored by the Australian Society for ParasitologyThe International Journal for Parasitology publishes the results of original research in all aspects of basic and applied parasitology, including all the fields covered by its Specialist Editors, and ranging from parasites and host-parasite relationships of intrinsic biological interest to those of social and economic importance in human and veterinary medicine and agriculture. Original research includes the development of novel and innovative concepts and ideas, as well as experimental and observational science that raises new hypotheses.We do not publish new genome sequences and assemblies alone without new and significant insight into the biology of the parasite, the parasite-host relationship or mechanisms of pathogenesis. Because of its breadth of discipline coverage, the aims and significance of all contributions should be made clear to readers who are not expert in the particular subject of papers. In applied parasitology, it will tend to favour contributions of broader significance to the subject rather than narrow, highly specialised applications. The principal form of publication is the full length paper which contains substantial results from a major program of research. The Journal also provides a medium for the publication of shorter, but complete, papers reporting highly significant original findings, as Succinctus articles. It also publishes Thematic Issues incorporating papers on a topical theme and commissions papers with emphasis on shorter, focussed Reviews of topical issues and strategically important subjects. The Journal encourages critical comment and debate on matters of current controversy in parasitology via "Current Opinions".The International Journal for Parasitology has also launched two specialist, open access titles you are welcome to submit to:International Journal for Parasitology: Parasites and WildlifeInternationa... Journal for Parasitology: Drugs and Drug Resistance
- ISSN: 0304-4165
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Biochimica et Biophysica Acta: General Subjects
BBA General Subjects invites submissions of original research, hypothesis-driven studies, and reviews that address topics in biochemistry and biophysics. Manuscripts should present significant advancements in our understanding of molecular mechanisms and be of broad scientific interest to a wide audience. Interdisciplinary studies are encouraged. Descriptive studies without biochemical or biophysical mechanistic evidence and insights are discouraged. Preferred topics areBiomedicine: Fundamental and emerging topics in biochemistry/biophys... with potential medical implicationsNanobiol... Nanoparticles, nanotoxicology, nanomedicine; the topics are not limited to formulation of nanoparticles but investigate mechanism of action on cell types or animal models.Omics: Genomics, proteomics, lipidomics, glycomics, bioinformatics experimentally addressing a defined biological question; descriptive bioinformatics studies that rely solely on publicly available data without experimental validation are discouraged.Chemical biology: Chemical compounds, drug mechanisms, synthesis of novel compounds, click chemistryStructural biology: Crystallography, NMR, multimeric proteins, protein dynamics, nucleic acidsNovel complexes: Nucleic acids, pure natural compounds, synthetic compounds, protein complexes, nucleic acid derivativesCellular signaling: Receptor signaling, protein phosphorylation cascades, phosphatases, secondary messengers, transcription regulation, gene expressionGlycobiolo... Sugar metabolites and metabolism, glycosylated proteins, membrane protein, glycosylation, glycomicsMicrobiolog... Fundamental and applied microbiology, emphasizing biochemical and biophysical aspects and mechanistic insights into infection and disease, as well as the mechanism of action of antimicrobials; manuscripts on clinical aspects such as treatment outcomes, clinical trials, and patient management are not suitable for this journal. Redox biology: Redox switches, glutathione and thioredoxin systems, oxygen and nitrogen radical species, superoxide, hydrogen peroxide, hydroxyl radical, nitric oxide, peroxides, hypoxia, redox regulation of transcription factorsNeurobiology: Neuronal growth factors and nerve signaling, glial cells, autonomic and central nervous systemsStem cells: Differentiation, stem cell isolation and cultivation, growth factorsAdvanced molecular imaging technologies: This may include both biochemical and biophysical approaches.Plant biology: Specific emphasis on molecular plant sciences with mechanistic details and their applications through plant biotechnologyMechani... characterization of compounds having biochemical importance and general interest (drug leads, toxicants, nutrients, and metabolites)BBA General Subjects does not consider studies on the biological effects of crude extracts of natural sources, natural extracts, or traditional medicine unless the exact active molecules are identified and singularly characterized and their mechanism of action is experimentally evaluated.
- ISSN: 2405-4712
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Cell Systems
For more information go to http://www.cell.com/... Cell Systems was established in 2015 to provide a home at Cell Press for elegant work that addresses fundamental questions in systems biology. "Systems biology," as we broadly define it, is work that develops a rigorous understanding of any biological phenomenon where one plus one does not apparently equal two. Disciplines in the physical sciences have met this challenge for a long time, and we've found that our strongest papers tend to apply quantitative, inference-based approaches taken in physics, engineering, mathematics, and computer science to salient biological questions.We believe it's our responsibility to ensure that the next generation of scientists can begin their work on solid ground. Accordingly, we focus our review process on validity and scientific acuity, rather than more subjective feelings and opinions. We also believe that scientific transparency is of paramount importance. A study's structure and presentation should be candid and forthright (e.g. it should ensure fair comparisons; it should either use non-arbitrary cut-offs or clearly explained arbitrary cut-offs that do not affect outcomes; its data visualization choices should promote objective understanding; its limitations should not be obscured). Fundamentally good scientific practice also demands that studies be repeatable. We encourage authors to make their code and data FAIR?that is findable, accessible, interoperable, and reusable, as defined by the NIH data commons. Although it is too early to formally require that all studies we publish be FAIR, we consider that requirement annually.As editors, we hold ourselves to the same standards of transparency but also recognize that living up to those standards requires constant effort. Like all journals, Cell Systems is a work in progress. A collection of editorials that document our thoughts and their evolution can be found here. We are always happy to talk to you.Visit the Cell Press website for more information about Cell System- http://www.cell.com/...
- ISSN: 0167-7012
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Journal of Microbiological Methods
The Journal of Microbiological Methods publishes Research, Review and Short Communication articles on novel, state-of-the-art, and significantly improved methodologies in microbiology. Innovative, validated applications of existing methods that advance the field are also welcome. JMM considers research on all types of microorganisms including protozoa, fungi, bacteria, and viruses. Data must clearly support method interpretation and utility.The scope includes, but is not limited to:· Environmental, Agricultural & Ecological Microbiology: Applied and environmental microbiology, microbial ecology and diversity, soil/sediment/geomic... microbiomes, rumen microbiology, and methods for extreme environments including space missions.· Genetics, Molecular & Cellular Microbiology: Microbial genetics, genomics, molecular microbiology, physiology, ultrastructure, imaging, high-throughput sequencing, omics technologies (metabolomics, metagenomics, proteomics, transcriptomics), bioinformatics, and mathematical modeling.· Clinical, Medical, Veterinary & Public Health Microbiology: Diagnostics, clinical and veterinary microbiology, public health, sero-diagnostics, immunology, typing, and microbial identification.· Microbial Interactions & Pathogenesis: Host-pathogen interactions, microbiome interactions, plant-microbe relationships, parasitology, and mycology.· Virology: Innovative approaches for virus detection, isolation, quantification, and characterization, including molecular techniques, cell culture assays, viral genomics, imaging technologies, and high-throughput screening methods.· Technological Advances & Method Development: Bioassays, biosensors biochemical methods, sampling techniques, robotics, and radioisotope applications in microbiology.· Food Microbiology: Studies on the role of microorganisms in food production, preservation, spoilage, and foodborne illnesses. · Industrial Microbiology: Explores the industrial applications of microorganisms, such as in the production of pharmaceuticals, enzymes, and biofuels. We invite proposals for review articles and special issues on emerging microbiological methods driving scientific progress.
- ISSN: 1532-0464
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Journal of Biomedical Informatics
The premier methodology journal in the fieldThe Journal of Biomedical Informatics (JBI) is the premier methodology journal in the field of biomedical informatics. JBI publishes research on new methodologies and techniques that have general applicability and form the basis for the evolving science of biomedical informatics. Papers should focus on a real-world biomedical or clinical problem, develop a novel approach to address the problem, and evaluate its appropriateness in comparison to the current state-of-the-art (SoA) methods. Involvement of healthcare professionals in motivating the work and evaluation of results is expected.Focus Areas and Topics of InterestJBI seeks to publish papers that make a conceptual contribution to the field, typically by describing an innovation in methodology or technique or by discussing substantive generalizable lessons that have been learned in the context of an informatics project. When a methodological contribution has a theoretical basis, that theory is an appropriate emphasis for papers as well. Research papers may also present a novel "method of methods" explaining how to apply the existing methods to a space of biomedical problems that share unique characteristics influencing the choice of methods.JBI publishes papers on a wide range of informatics topics. However, across these topics, papers must build on deep understanding and utilization of medical domain knowledge and should consider pragmatic translation for clinical care or applications. Topics of interest include (but are not limited to) clinical decision support, patient safety, natural language processing, artificial intelligence and machine learning, knowledge representation for healthcare, translational bioinformatics, clinical research informatics, and clinical informatics. Additional considerations for papers in the areas of translational bioinformatics, machine learning, security and privacy are provided below. Irrespective of the topic, papers must focus on novel informatics methods and its comparison to the current approaches.Manuscrip... can be submitted in the following categories: original research, methodological review, commentaries, special communication, letters to the editor, book reviews, and editorials (see additional details on each of these categories below). Given the international readership of JBI, country-specific health systems or approaches will be considered only if they offer generalizable lessons that are relevant to the broader readership, regardless of their country, language, culture, or health system.Specific considerations for manuscripts in certain topical areas have also been provided in recent editorials.If you are considering an article with a focus on translational bioinformatics , please read this editorial. Biologic discoveries based on the use of routine informatics techniques may be important biologic contributions, but are not suitable for JBI. In addition, please note that JBI publishes bioinformatics papers only if they deal with issues in translational (human) science (e.g., translational bioinformatics papers).If you are considering an article describing a new machine learning approach, please read this editorial. Machine learning papers would be considered only if the methods that are introduced demonstrate substantial novelty and advancement beyond the current SoA and their evaluation is sound and includes an assessment of the potential of the method to be used in clinical practice. For example, submissions reporting publishing marginally SoA findings without an in-depth analysis or discussion of how the methods are potentially generalizable (or applicable in a wider setting) would not be considered. Novel and important clinical problems addressed by existing machine learning methods may warrant Special Communication papers if their discussion includes novel insights or lessons learned for future research in such domains.Authors considering an article on biomedical privacy and security, please read this editorial. To be considered, the privacy and security methods that are introduced should demonstrate substantial novelty and advancement beyond the SoA, should be specific to the biomedical informatics domain, and their practical application and/or likely real-world usefulness in the biomedical domain.Please also note that papers related to signal processing, imaging, medical devices, or communication networks are generally considered outside the scope of the journal. To be considered, such papers must introduce novel informatics methods that build on deep understanding and utilization of medical domain knowledge and should be translatable into applications. Papers on such topics should focus on information processing and management or knowledge-based approaches.Please also consult the editorial that explains where to direct Artificial Intelligence in Medicine-related manuscripts for peer review and possible publication, considering the different scope of the three Elsevier medical informatics journals: JBI, Artificial Intelligence in Medicine, and Intelligence-based Medicine.
- ISSN: 0014-4894
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Experimental Parasitology
The main focus of Experimental Parasitology is experimental approaches to investigating different aspects of parasitology, including, but not limited to, those encompassed by molecular tools, cell biology, and immunology. The journal predominantly publishes Original Research Papers in which experimentation is used to investigate the physiological, metabolic, immunological, biochemical, nutritional, and chemotherapeutic aspects of parasites and host-parasite relationships. In addition, the journal welcomes Method Papers that describe new approaches to such investigations and Review Articles (short reviews, full reviews, and systematic reviews) that provide critical evaluation of published articles on a theme within the scope of the journal. Furthermore, the journal is open to publishing special issues or meeting reports within the themes of the journal. Please contact the editors for further information. See our Guide for Authors for further information on the different paper types accepted by Experimental Parasitology.
- ISSN: 1476-9271
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Computational Biology and Chemistry
Computational Biology and Chemistry publishes high quality full-length articles and review articles in all areas of computational life sciences. It covers a very wide range of areas of research, including:Nucleic Acid and Protein Sequence ResearchMolecular EvolutionMolecular Genetics (Functional Genomics and Proteomics)Biology-S... Modeling Theory and PracticeChemical-Bio... Modeling Theory and PracticeStructural Biology of Nucleic Acids and ProteinsBioinformati... BiologyEcologyComput... PharmacologyComputat... Molecular BiophysicsMetabolism... EngineeringEpidemiol... GeneticsInnovative AI methodologies for biological data, biomolecular modelling and machine learning modelsGiven their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
- ISSN: 1570-9639
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Biochimica et Biophysica Acta: Proteins and Proteomics
BBA Proteins and Proteomics covers protein structure conformation and dynamics; protein folding; protein-ligand interactions; enzyme mechanisms, models and kinetics; protein physical properties and spectroscopy; and proteomics and bioinformatics analyses of protein structure, protein function, or protein regulation.The journal no longer considers manuscripts dealing with binding of compounds such as drugs or drug analogues to circulatory proteins such as serum albumin. These studies are better accommodated in journals dealing with drug design and development.Manuscri... must advance our insights into the molecular and mechanistic properties of proteins. Computational studies must generally be validated or complemented by experimental studies. Studies only consisting of computational work will not be considered unless they provide new theoretical insight that allows us to better understand or reinterpret surprising or unexpected experimental data.Comparative proteomics studies are generally not considered for review unless they provide specific insights into the structural and/or functional properties of individual proteins. Proteomics studies must also address properties of individual proteins and should as far as possible be validated by direct investigations of relevant identified proteins.Concise and comprehensive reviews of recent developments are considered for publication. However, authors are strongly advised to consult one of the Executive Editors before starting a review.Please see our Guide for Authors for information on article submission. If you require any further information or help, please visit our Support Center
- ISSN: 2452-3100
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Current Opinion in Systems Biology
Current Opinion in Systems Biology is a new review journal that aims to provide specialists with a unique and educational platform to keep up-to-date with the expanding volume of information published in the field of Systems Biology. It publishes polished, concise and timely reviews and opinion articles. In addition to describing recent trends, the authors are encouraged to give their subjective opinion on the topics discussed. As this is such a broad discipline, we have determined themed sections each of which is regularly reviewed.The following areas will be covered by Current Opinion in Systems Biology: • Genomics and Epigenomics • Gene Regulation • Metabolic Networks • Cancer and Systemic Diseases • Mathematical Modelling • Big Data Acquisition and Analysis • Systems Pharmacology and Physiology • Synthetic Biology • Stem Cells, Development, and Differentiation • Systems Biology of Model Organisms • Systems Immunology and Host-Pathogen Interaction • Systems Ecology and EvolutionSection Editors, who are major authorities in the field, are appointed by the Editors in Chief of the journal. They divide their sections into a number of topics, ensuring that the field is comprehensively covered and that all issues of current importance are emphasised. Section Editors commission reviews from authors on each topic that they have selected and arrange for the peer review process. The papers are reviewed by 2 independent reviewers.ReviewsAut... write short review articles in which they present recent developments in their subject, emphasizing the aspects that, in their opinion, are most important. In addition, they provide short annotations to the papers that they consider to be most interesting from all those published in their topic over the previous year.Opinion ArticlesAuthoritativ... opinion articles that provide an in-depth background and personal, well reasoned perspective on current, relevant as well as controversial topics within the themes of the journal will be written by the Editor-in-Chief and / or invited by the Editor-in-Chief.Edit... OverviewSection Editors write a short overview at the beginning of the section to introduce the reviews and to draw the reader's attention to any particular interesting developments.Invited authors are encouraged to visit our Guide for Authors for information on article submission.
- ISSN: 0166-6851
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Molecular and Biochemical Parasitology
Molecular and Biochemical Parasitology provides a medium for rapid publication of investigations of the molecular biology and biochemistry of parasitic protozoa, fungi, helminths and ectoparasites, including molecular interactions between parasites and their definitive and intermediate hosts and their vectors. This includes emerging or neglected eukaryotic pathogens.The main subject areas covered are:• The structure, biosynthesis, degradation, properties and function of parasite biomolecules - DNA, RNA, proteins, lipids, carbohydrates and small molecular-weight substances. This includes molecules of intermediary metabolism and bioenergetics. host-parasite relationships particularly as related to specific parasite molecules. • The response of host organisms to infection, and the response of host cells to intracellular parasites. Included are studies on the detailed molecular mechanisms of anti-parasitic immune responses, parasite immune evasion, and host-pathogen signalling pathways.• “Omics” technologies and systems biology, including genomics, transcriptomics, proteomics, metabolomics, and epigenomics of parasites and the host’s response to infection.• Vector-parasite relationships at the molecular level; this includes molecular studies on arthropod vectors that transmit parasites, especially those focusing on vector-parasite interactions, vector immunity, and vector control strategies.• Structural studies of parasite proteins and their interactions. • Drug target characterization and the mode of action of antiparasitic drugs; mechanisms of drug resistance; novel therapeutics including natural products, synthetic compounds, and vaccine candidates. Please note that studies that are restricted to in silico docking of compounds or other purely computational approaches will not be accepted in the absence of some experimental validation.• Analysis of variation in parasite populations relevant to genetic exchange, pathogenesis, drug and vaccine target characterization, and drug resistance; please note that genetic variation data must be supported by phenotypic/experimen... data showing the effect of the variation, and that papers reporting solely on allele frequencies in specific regions will not be accepted.• Parasite protein trafficking, organelle and membrane biogenesis, and cellular structure especially with reference to the roles of specific molecules• Parasite programmed cell death, development, and cell division at the molecular level• Parasitic disease diagnostics, especially molecular diagnostics, biomarkers, and biosensors for parasite detection and disease monitoring.•Microbio... of parasites, symbiotic relationships, and how microbiota influence parasite development and pathogenicity.• Environmental molecular parasitology, including studies linking molecular parasitology with ecological and environmental factors influencing parasite transmission, adaptation, and evolution.• Methods reports - descriptions of novel or newly-optimized methods with broad applicability to molecular and biochemical parasitologyPapers will only be accepted for publication if they fall within these areas, if they contain original and complete work of high scientific quality, and if they are well presented and clearly written in scientific English. Papers solely confirming the conserved functions of genes previously studied in other organisms will not be considered. We welcome short communications documenting a succinct but clear and important advance.