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Physiological Genomics journal announces a major restructuring

BETHESDA, Md. (September 18, 2012)Propelled by rapid growth in the field, Physiological Genomics, a specialty journal of the American Physiological Society (APS;, announced today that it was undergoing a major change in its editorial policy.

The journal will continue to operate under the name Physiological Genomics, but will dramatically increase the scope of papers accepted to include contributions in the areas of genomics, systems biology, biomarkers, and emerging technologies.

Andy Greene, Editor-in-Chief of the journal, said "We felt there was a need for a journal that welcomes contributions in the area of emerging technologies and their application to physiology. By combining our historic expertise in 'omics approaches with the expertise in the systems level thinking that is shared by physiologists, we will help anchor these technologies to physiological applications and serve as a link between the APS and other scientists working at the leading edge of 'omics fields."

The "new" journal has ten separate Sections, each having a Section Editor and a group of Editorial Board members. The journal will be actively recruiting very high quality manuscripts in each of the sections. The new sections will be:

  • Nutrient Gene Interaction (Juan Loor, Section Editor): This section focuses on manuscripts that utilize genome-enabled technologies and cellular/tissue physiological measures to understand the effects of nutrients on human, animal, and cellular function through alterations of the epigenome, genome, proteome, and/or metabolome. Studies in humans and animals focused on the link between genetic variation and nutrition with implications to physiological outcomes in susceptible groups are also welcomed. This section is particularly interested in publishing manuscripts that illustrate the opportunities for advancing the understanding of nutritional mechanisms using systems approaches in mammalian species and cell culture models.

  • Biomarkers (Rick Paules, Section Editor): This section will present a forum for innovative scientific studies that integrate genomic, proteomic and metabolomic approaches with studies of complex physiological regulatory processes to gain a systems biology insight into complex pathways and networks controlling homeostatic and pathophysiologic states. One outcome of such studies might be the development of novel biomarkers of disease states, adverse responses, beneficial responses, exposures, or therapeutic responses.

  • Regulation of Gene Expression (Jason Mills and Andy Greene, co-Section Editors): This section focuses on manuscripts that use existing or novel high-throughput technologies to study, at the systems level, how gene products (RNA, protein) change in abundance during pathophysiology and/or development. Manuscripts typical of this section would describe experiments generating and analyzing lists of genes and studies of how those genes combine to regulate: differentiation of a particular cell type; cellular, tissue, or organ response to toxic/pathogenic agents; adaptation to environmental stresses. Also relevant are studies of the upstream mechanisms that regulate levels and function of those gene products, for example: how a transcription factor regulates multiple targets or how factors can regulate translation or post-translational modification of multiple proteins.

  • MicroRNA (Chandan Sen and Mingyu Liang, co-Section Editors): This section focuses on manuscripts that address all aspects of microRNA research including basic biology and translational and clinical studies. In addition, the section will entertain submission of work addressing all aspects of post-transcriptional gene silencing, technologies related to microRNA analyses, as well as bioinformatics relevant to microRNA research.

  • Model Organisms (Julian Dow, Section Editor): This section covers genetic models, from mouse to yeast. These organisms frequently lead the way in new techniques or integration of data modalities, because of the advantages that made them models in the first place: sequenced genomes, powerful technologies for forward and reverse genetics, and an extraordinary wealth of experimentation and data. However, physiological study of such organisms has often lagged behind larger, classical physiological models. This section welcomes papers that explore new technologies or data that may be of general interest, and which address physiological questions in these organisms in a genomic context.

  • Omics Technologies and Applications (Aoy Mitchell, Section Editor): This section focuses on manuscripts that utilize or improve upon existing omic technologies and are focused on advancing clinical and translational applications. Omic disciplines include, but are not limited to, genomics, transcriptomics, and proteomics. Submissions utilizing omic methods and technologies as a discovery tool and for modeling are also encouraged.

  • Computational Algorithms and Tools (Bruce Aronow, Section Editor): This section focuses on the generation of databases, analysis tools, or large scale analyses carried out from new or established datasets that generate hypotheses into the structure and function of physiological systems at the sub cellular or organismal level. The integration of multi-scale knowledge and data is strongly encouraged including the analysis of gene expression, epigenetics, physiological function, pathological states, and drug and small molecule effects as a function of genetic and environmental and epigenetic state alterations. The use of biological network representations is strongly encouraged.

  • Systems Biology of Cell State Regulation (Hilary Coller, Section Editor): This section focuses on manuscripts that use genomic, metabolomic, proteomic and other high-throughput approaches to understand and compare cell states as well as cell and molecular biological approaches to understand the regulation cell state transitions. Manuscripts that increase our understanding of the processes through which stem cells and progenitors differentiate into committed progeny, the commitment cell death programs such as apoptosis and necrosis, aging, and the transition between proliferation and cell cycle arrest are welcome. Comparisons among cells in the same and different cellular states in different tissues and species can also provide information on the essential qualities of specific cell states and would be considered in this section.

  • Molecular Genetics of Complex Traits (Bina Joe, Section Editor). This section invites manuscripts describing (a) Linkage, association, substitution or positional mapping and epigenetic studies in any species; (b)Validation studies of candidate genes using genetically-engineered mutant model organisms; (c) Studies focused on epistatis and gene-environment interactions; (d) Analysis of the functional implications of genomic sequence variation and aim to attach physiological or pharmacogenomic relevance to alterations in genes or proteins; (e) Studies of DNA copy number variants, non-coding RNA, genome deletions, insertions, duplications and other single nucleotide polymorphisms and their relevance to physiology or pharmacology in humans or model organisms, in vitro or in vivo; and (f) Theoretical approaches to analysis of sequence variation.

All sections welcome full length Original Research Communications, Innovative Methodologies submissions, Short Critical Review articles, full length Comprehensive Review articles, as well as Letters to the Editor.

The APS, with its established track record as a leading publisher and its unique strength in physiological and disease applications, provides a natural home for this twice-monthly published journal. Authors will benefit from the robust journal activities including very rapid review (average time to decision is less than 23 days, 14 days to online publication), high visibility and impact (papers publicized on journal website, monthly newsletters, Facebook, Twitter, 2011 impact factor 3.368,) , and author services (connection to nomenclature services, pre-publication annotation of data for submission to data resources and repositories, as well as video and other alternative content as part of the embedded content).

According to Greene, the journal will begin accepting submissions in the new categories immediately. He added. "We hope authors will join us in this exciting new phase in the life of Physiological Genomics by submitting their best relevant work to one of our sections."


Contact: Donna Krupa
American Physiological Society

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