Systems Medicine Resources: (updated january 30, 2008)
If you have any questions or suggestions please contact Jesper at +46 703 282989 or jesper@karlavagen90.se
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Model Databases
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Broad Institute - Data
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Broad Institute - Software
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Other Genomics Analysis tools
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Network reconstruction algorithms
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Disease related tools and initiatives
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Other Resources
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Journals
Model Databases
Broad Institute - Data
Broad Institute - Software
Other Genomics Analysis tools
- Cytoscape (Visualization and integration of networks - Trey Ideker)
- Gaggle (dataintegration - open-source Java software environment which combine the capabilities of different and forthcoming analysis tools to create a data exploration and analysis environment - Hood Institute)
- Systems Biology Experiment Analysis Management System (Hood Institute)
- Ravi Iyengars lab software (edge library & network visualization)
Network reconstruction algorithms
- Genomica (Module analysis and visualization tool - Eran Segal)
- Gardner lab software tools (MNI Algorithm - ODE based, CLR algorithm - information based, NIR algorithm - ODE based)
- ARACNE (Based on information theory - a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems - Califano lab Columbia, New York)
- Seed gene algorithm (Local bayesian expansion around seed gene - Jose Pena, [download zip file, paper-pdf])
Disease related tools and initiatives
Other Resources
Journals (IF = Impact Factor as of 2005)
- Annals of Human Genetics, [Principal aim is to increase understanding of the biology of human variation, both in disease and in health. In recent years it has become apparent that the study of population genetics is extremely relevant to molecular pathology. The interaction of these fields can greatly increase our understanding of the generation and maintenance of variation in the human genome. Major topics covered include: Human genome variation - its evolution and implications for human biology. Interpretations of the current or future state of the human genome sequence are also welcomed. Human population genetics - including studies which elucidate human history, our understanding of chromosome evolution, and the geographic distribution of particular diseases, worldwide. Will consider studies on primate populations. Statistical genetics - the application and improvement of mathematical approaches for analysis of genetic data, including linkage and association mapping of genes and QTLs. Welcomes papers focussing on more general bioinformatic approaches. Genetics of common multifactorial diseases and other complex traits and QTLs - in general we expect these to be human but relevant animal models will also be considered. Mendelian disorders and their molecular pathology. Focus is on human, but animal models or in vitro work may also be considered. Pharmacogenetics - the potential application of human genetic variation in response to drugs and other chemicals.]
- Annual Review of Genomics and Human Genetics
- Applied Bioinformatics
- ATVB (IF=7,053)
- Bioinformatics (IF = 6.019) [New developments in genome bioinformatics and computational biology. Shorter papers: Discovery Notes reports biologically interesting discoveries using computational methods. Application Notes explore the applications used for experiments]
- BMC Bioinformatics (IF=4.96) [All aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology]
- BMC Cardiovascular Disorder
- BMC Genomics (IF =4,092) [All aspects of gene mapping, sequencing and analysis, functional genomics, and proteomics]
- BMC Systems Biology
- Briefings in Functional Genomics and Proteomics, [Reviews the techniques, protocols and approaches in genome and proteome research. The journal aims to provide a centralised resource for researchers in the fields of genomics and proteomics as well as give guidance to scientists new to these areas. Papers range in scope and depth from the introductory level to specific details of protocols and analyses encompassing bacterial, plant, animal and human data. Detailed subject areas covered by the journal include: microarray technology, gene and protein expression profiling, differential display, electrophoresis, genotyping, transgenic systems, mutation screens, protein spectrometry, comparative genomics, phage display and combinatorial libraries.]
- Briefings in Bioinformatics [Reviews for the users of databases and analytical tools of contemporary genetics and molecular biology. Practical help and guidance to the non-specialist. Introductory level papers to specific details of protocols and analyses encompassing bacterial, plant, animal and human data. Subject areas covered include: DNA sequencing, expression profiling, alignment methods, gene expression studies, protein profiles and HMMs [Hidden Markov Models], metabolic and signalling pathways, structure and function prediction, mapping and microarrays]
- Bulletin of Mathematical Biology [Bioresearch at the junction of computational, theoretical and experimental biology. Research Areas Include: Developmental Biology, Ecology, Epidemiology, Immunology, Molecular Biology, Morphology, Neurobiology, Pharmacology, Physiology, Population Biology, Sequence Comparison, Official publication of the Society for Mathematical Biology]
- Cellular Immunology
- Circulation (IF =11,632)
- Circulation Research (IF =9,408)
- Current Bioinformatics
- Current Genomics, [Human and functional genomics.]
- Current Opinion in Biotechnology (IF =6,898)
- Current Protocols in Bioinformatics, [Using and building biological databases, functional domains, homologies, finding genes, modeling structure from sequence, inferring evolutionary relationships, analyzing expression patterns, analyzing molecular interactions, assembling sequences, comparing large sequence sets, protein identification from mass spec, analyzing RNA sequence and structure.]
- FEBS Journal [FEBS Journal is dedicated to the rapid publication of full-length research papers and reviews in all areas of the molecular life sciences. The broad aims and scope include the growing points of bioinformatics, genomics and proteomics, molecular cell biology and the molecular biology of disease, systems biology and nanoscience. Reviews, minireviews and meeting reports cover a wide range of topics. ]
- FEBS Letter (IF=3.4) [is one of the world's leading journals in biochemistry and is renowned both for its quality of content and speed of production. Bringing together the most important developments in the molecular biosciences, FEBS Letters provides an international forum for Minireviews, hypotheses and research letters that merit urgent publication.]
- Gene, [Structural, functional, and evolutionary aspects of genes, chromatin, chromosomes and genomes.]
- Genes and Immunity, Nature Publishing, 1999- [Emphasizes studies which demonstrate genetic, genomic or functional variation in the immune system, and assist our understanding of how the basic control over the immune system varies between individuals both in health and disease. The emerging role for genes outside the MHC will be of particular interest.]
- Genome Biology (IF=9.71) [Dissemination, discussion and critical review of information about all areas of biology informed by genomic research. Key objectives are to provide a guide to the rapidly developing resources and technology in genomics and its impact on biological research, to publish large datasets and extensive results that are not readily accommodated in traditional journals, and to help establish new standards and nomenclature for post- genomic biology.]
- Genomics (IF= 3.840) [All facets of human and mouse genetic analysis. The scope of the journal is broad, and studies of other species that provide important insights into gene function in human and mouse will be considered Functional genomics, identification of genes involved in disease and complex traits, novel gene discovery, higher order genome organization, chromosome structure, and functional genetic bases for human diversity are suitable. Manuscripts describing new technologies and methods and application of gene and genome analysis, including robotic and high-throughput strategies, are encouraged. The editors also encourage submission of manuscripts describing transgenic and gene modification mouse models, especially as they apply to human disease.]
- Genome Research (IF =10,139) [Genome studies in all species, and presents research that provides or aids in genome- based analyses of biological processes. The journal represents a nexus point where genomic information, applications, and technology come together with biological information to create a more global understanding of all biological systems. Novel reports on gene discovery, comparative genome analyses, proteomics, evolution studies, informatics, genome structure and function, technological innovations and applications, statistical and mathematical methods, cutting- edge genetic and physical mapping and DNA sequencing, and other reports that present data where sequence information is used to address biological concerns. Complete data sets are presented electronically on the journal's web site.]
- Human Molecular Genetics, [All aspects of human molecular genetics, including: 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. Also publishes research on other model systems for the analysis of genes, especially when there is an obvious relevance to human genetics.]
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- IET Systems Biology [IET Systems Biology (formerly IEE Proceedings Systems Biology) covers intra- and inter-cellular dynamics, using systems- and signal-oriented approaches. Papers that analyse genomic data in order to identify variables and basic relationships between them are considered if the results provide a basis for mathematical modelling and simulation of cellular dynamics. Manuscripts on molecular and cell biological studies are encouraged if the aim is a systems approach to dynamic interactions within and between cells.
- Genomics, transcriptomics, proteomics, metabolomics, cells, tissue and the physiome
- Molecular and cellular interactions; gene, cell and protein function
- Networks and pathways
- Metabolism and cell signalling
- Dynamics, regulation and control
- Systems, signals, and information
- Experimental data analysis
- Mathematical modelling, simulation and theoretical analysis
- Biological modelling, simulation, prediction and control
- Methodologies, databases, tools and algorithms for modelling and simulation ]
- In Silico Biology:International Journal on Computational Molecular Biology [Data acquisition, development, and applications of theoretical / mathematical / computational tools onto biological systems rather than on the description of new algorithms. Systematic compilations of biological as well as computational results from various sources, evaluation of original experimental data with biocomputational tools, WWW-online resources for experimental scientist]
- International Journal of Approximate Reasoning (IF =0,959)
- International Journal of Bioinformatics Research and Applications
- Journal of the American College of Cardiology (IF =9,2)
- Journal of Biological Chemistry (IF =5,854)
- Journal of Computational Biology (IF =2,446) [Analysis, management, and visualization of cellular information at the molecular level. Includes 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, and management of biological databases.]
- Journal of Lipid Research (IF =3,909)
- Journal of Machine Learning Research (IF =4,027, ranked as No 1 in computer science)
- Journal of Mathematical Biology, [Mathematical modelling and reasoning to the understanding of biological systems and the explanation of biological phenomena. Biologically inspired problems of a mathematical nature. Biological insight as a result of mathematical analysis or identify and open up challenging new types of mathematical problems that derive from biological knowledge (in the form of data, or theory, or simulation results). Biofluids, cell biology, physiology, neurobiology and behaviour, development, ecology, population biology, genetics and evolution, epidemiology, immunology, molecular biology, DNA and protein structure and function. It is understood that research in mathematical biology may rely on advanced computational methods and visualization tools, more traditional analytical and stochastic approaches. Official journal of the European Society for Mathematical and Theoretical Biology.]
- Lancet (IF =23,878)
- Mathematical Biosciences, [ Formulation, analysis and solution of mathematical models in the biosciences. Serves both mathematicians involved in solving model equations or in reaching conclusions that are testable in the real world, and biologists who are interested in forming mathematical models of biological processes and systems]
- Mathematical Medicine and Biology, [Articles with a significant mathematical content addressing topics in medicine and biology. Papers exploiting modern developments in applied mathematics are particularly welcome. The biomedical relevance of mathematical models should be demonstrated clearly and validation by comparison against experiment is strongly encouraged. Contributions relevant to any area of the life sciences welcomed, including: biomechanics, biophysics, cell biology, developmental biology, ecology and the environment, epidemiology, immunology, infectious diseases, neuroscience, pharmacology, physiology, population biology]
- Nature (IF =29,273)
- Nature Biotechnology (IF =22,738)
- Nature Cell Biology, [All areas of cell biology, encouraging those that shed light on the molecular mechanisms responsible for fundamental cell biological processes. Scope is broad and includes the following areas (not listed in order of preference): Membrane traffic and protein sorting, Cell adhesion and migration, Signal transduction, Proteolysis, Apoptosis, Organisation of the nucleus and nuclear transport, Developmental biology, Cell cycle and cell division, Cytoskeletal dynamics and molecular motor function, Transcription and chromatin, Cell cycle, DNA replication and repair, Cellular mechanisms of neurobiology, immunology and human disease (provided that the primary focus is on general processes of cell biology), Microbiology, Plant cell biology, Stem cells. ]
- Nature Genetics (IF= 25,797) [Particular emphasis on genetic mechanism through studies on human traits and model organisms (including mouse, yeast, C. elegans, Drosophila and zebrafish). Also features New Technology articles. Our aim is to publish results of exceptional significance, originality and relevance not just to geneticists but to the scientific community at large.]
- Nature Medicine (IF =28,878)
- Nature Molecular Systems Biology
- Nature Reviews Drug Discovery (IF=18.775)
- Nature Review Genetics (IF=19.211) [Scope includes: Genomics (genome projects, genome sequencing, bioinformatics), Functional genomics (transcript profiling, mutant screens, bioinformatics), Evolutionary genetics (evo- devo, comparative genomics, population genetics, phylogenetics), Technology (new techniques, experimental strategies, therapy, applied genetics and genomics, computational biology), Multifactorial genetics (complex disease, disease susceptibility/ resistance, association studies, technology), Disease (disease gene identification, relationship between genotype and phenotype, molecular pathology of genetic disease), Chromosome biology (DNA elements, telomeres, centromeres, mobile elements, artificial chromosomes, chromosome stability), Epigenetics (DNA methylation, histone modification, chromatin structure, imprinting, chromatin remodeling), Developmental biology (reproductive technology, patterning, differentiation, evo- devo), Gene expression (DNA elements, LCRs, insulators, enhancers, silencers, broad perspectives on gene regulation) ]
- Nature Review Molecular Cell Biology (IF=29.85) [Scope includes: Chromosome biology (chromosome structure, chromatin, transposons), Nucleic- acid metabolism (DNA repair, recombination and replication), Gene expression (transcription, splicing, RNA stability, translation, circadian rhythms), Nuclear transport (import and export of molecules to and from the nucleus), Protein structure and metabolism (structure- function relationships, quality control, post- translational modifications, folding, translocation, degradation), Membrane dynamics (membrane organization, endocytosis, exocytosis, organelle biogenesis), Bioenergetics (photosynthesis, respiration, organelle biochemistry), Cell signalling (signalling cascades, ion channels, gap junctions), Cell growth and division (cancer, cell cycle, cytokinesis), Cytoskeletal dynamics (cell motility, molecular motors, actin, microtubules, intermediate filaments), Cell adhesion (adhesion molecules, extracellular matrix), Developmental cell biology (asymmetric cell division, stem- cell biology, developmental signalling, differentiation), Cell death (apoptosis, necrosis), Cellular microbiology (host- pathogen interactions), Plant cell biology.]
- New England Journal of Medicine (IF=44,016)
- Nucleic Acid Research (IF=7.552) [First issue of each year is a guide to databases. Physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. RNA, molecular biology, chemistry, genomics, computational biology and structural biology.]
- Omics[Covers genomics (the quantitative study of genes, regulatory and noncoding sequences), transcriptomics (RNA and gene expression), proteomics (protein expression), and metabolomics (metabolites and metabolic networks). The Journal explores advances in the era of post-genomic biology and medicine, including pharmacogenomics (the quantitative study on how genetics affects hosts' responses to drugs), and physiomics (physiological dynamics and functions of whole organisms). Integrative, quantitative, experimental, and computational approaches bring new knowledge, novel methods, and innovative technologies to engender a better understanding of complex biological systems and processes.]
- Pattern Recognition Letters (IF=1,138)
- Physiological Genomics, [Wide variety of studies from human and from informative model systems with techniques linking genes and pathways to physiology, from prokaryotes to eukaryotes. Encourages the submission of research that links genes to cell replication, development, metabolic function, cell signal transduction and intracellular signaling pathways, tissue and organ function, and whole organism function and the utilization of approaches ranging from expression profiling, assays for molecular interactions, natural and directed gene alteration, selective breeding studies, gene identification, and the assessment of gene/ environment interaction and new computational approaches, integrative models, and image analysis predictive of gene function.]
- PLoS Biology (IF=14,672) [We believe there is a global need for greater access to scientific and medical information and that open- access journals can meet this need by removing subscription barriers to the written scientific record. Our goal, however, is not simply to provide a free online journal. Our goal is to create a potent scientific and public resource. As more open-access articles become available, we and many others will be working to develop new tools for integrating, interlinking, organizing, searching, and annotating this expanding collection of information. We invite the community to share these tools as they become available on our site, as well as to propose tools, links, and techniques that would make this treasury of scientific information more useful.]
- PLoS Computational Biology
- PLoS Genetics
- PLoS Medicine (IF=8,389)
- Proceedings of National Academy of Science (IF =10,231)
- Science (IF = 30,927)
- Trends in Genetics (IF =12,047) [Aspects of current research in genetics, developmental biology and genomics. Reviews that synthesise for a non- specialist readership current topics in these fields. Perspective articles, in which novel hypotheses are discussed, and comment pieces, which feature key recent developments in genetics. Genome Analysis section, a forum for original observations concerning the function, organisation and evolution of genomes.]
- Trends in Molecular Medicine (IF =5,505)