Network Medicine

Network Medicine is a premier open access, peer-reviewed journal focused on interdisciplinary approaches to exploiting the power of big data by applying network science and systems thinking to medicine. Network Medicine yields major breakthroughs towards mechanism-based re-definitions of diseases for high-precision diagnostics and treatments, proof-of-concept trials, confirmatory trials, pharmacoepidemiology.

Network Medicine is the premier open access, peer-reviewed journal focused on interdisciplinary approaches to exploiting the power of big data by applying network science and systems thinking to medicine. Network Medicine yields major breakthroughs towards mechanism-based re-definitions of diseases for high-precision diagnostics and treatments.

Network Medicine publishes high quality basic science, translational, and clinical research in the form of original research articles, comprehensive review articles, mini-reviews, rapid communications, brief reports, technology reports, hypothesis articles, perspectives, and letters to the editor. The Journal publishes under the Creative Commons Attribution 4.0 (CC BY) license to ensure broad dissemination and participation. All articles submitted to Network Medicine are rapidly reviewed and published online within 4-5 weeks after acceptance. Network Medicine is fully NIH-, HHMI- and Wellcome Trust compliant.

Network Medicine coverage includes:

  • Network science applied to Medicine
  • Mechanism-based disease definitions, diagnostics and therapies
  • Network medicine and network pharmacology
  • Multiscale modeling and medical simulation
  • Multiscale medical data science and computing
  • Virtual patient repositories and data analytics platforms
  • Big data analytics in precision medicine
  • Clinical validation of systems medicine approaches (including quali-quantitative methods)
  • Multiscale approaches, e.g. translational and qualitative research and psycho-sociological variables
  • Implementing systemic management in medicine in organizations and integrated healthcare networks
  • Educational and training articles in systems medicine and network medicine methodologies for clinicians

Audience: Biomedical researchers and cell biologists; multi-omics biotechnology researchers; network scientists; systems biologists; precision medicine (nutrigenomics, pharmacogenomics) scientists; bioinformaticians and computational biologists; clinicians, medical doctors, nurses, healthcare professionals; industry scientists (pharma, diagnostics); regulatory, government and policymakers; scholars in global health, among others.

 

Network Medicine e-ISSN:  2941-251X

Published by ScienceOpen GmbH, Berlin

 

 

Editors

 

Harald H.H.W. Schmidt, MD, PhD, PharmD, Professor of Pharmacology, Chairman Department of Pharmacology and Personalised Medicine, Maastricht University

Jan Baumbach, PhD, Professor and Director of the Institute for Computational Systems Biology, University of Hamburg, Germany

David B. Blumenthal, PhD,  Professor of Biomedical Network Science, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg

Markus List, PhD, Big Data in BioMedicine, Chair of Experimental Bioinformatics, School of Life Sciences, Technical University of Munich, Germany

Albert-Laszlo Barabasi, PhD, Northeastern University, Boston, MA, USA

Joseph Loscalzo, MD, PhD, Harvard University, Boston, MA, USA

Paolo Parini, PhD, Professor/senior physician, Department of Laboratory Medicine, and Department of Medicine, Karolinska Institutet, and International and National Affairs Department, Karolinska University Hospital

Christina Kiel, PhD, Principal Investigator, UCD School of Medicine

Ana Casas, PhD, Jun.-Prof. Dr., Department of Pharmacology & Personalised Medicine, Faculty of Health, Medicine & Life Science, Maastricht University

Martin Schäfer, PhD, Junior group leader, IEO Research Istituto Europeo di Oncologia

Kristina Tammimies, PhD, Principal researcher, Karolinska Institute

Dominik Heider, PhD, Head of Department, Philipps-Universität Marburg

Emre Guney, PhD, CTO, Head of Discovery and Data Science, STALICLA

Silvia Regina Rogatto, PhD, Professor, University of Southern Denmark 

Martina Kutmon, PhD, Assistant Professor, Maastricht University

Alejandro Rodríguez González, PhD, Full Professor, Principal Investigator of Medical Data Analytics Laboratory (MEDAL). Centro de Tecnologia Biomedica (CTB) & Escuela Técnica Superior de Ingenieros Informáticos (ETSIINF). Universidad Politécnica de Madrid. Spain.

Kimberly Glass, PhD, Assistant Professor, Channing Division of Network Medicine, Harvard Medical School, Boston MA, USA.

 

 

Submission of Manuscripts

 

All manuscripts must be submitted online through the "Submit a manuscript" button on this website. First time users will have to register at this site and will need an ORCID ID. Registration is free but mandatory. Registered authors can keep track of their articles after logging into the site. If you experience any problems, please contact info@scienceopen.com.
A manuscript will be reviewed for possible publication with the understanding that it is being submitted to Network Medicine alone at that point in time and has not been published anywhere, simultaneously submitted, or already accepted for publication elsewhere. Manuscripts that have been previously posted as preprints in DrugRxiv, BioRxiv, MedRxiv, arXiv and related preprint repositories will be considered for publication. The journal expects that authors would authorize one of them to correspond with the journal for all matters related to the manuscript. All manuscripts received are duly acknowledged. On submission, editors review all submitted manuscripts initially for suitability. Manuscripts with insufficient originality, serious scientific or technical flaws, or lack of a significant message are rejected before proceeding with formal peer-review.
Manuscripts that have met basic requirements and are within the scope of Network Medicine will be sent to two or more expert reviewers for evaluation. Manuscripts may be returned to the authors for major or minor revision after a first round of peer review.
Manuscripts finally accepted for publication are copy edited for grammar, punctuation, print style, and format and are tagged in XML mark-up language. Page proofs are sent to the corresponding author as PDF for review and approval. The corresponding author is expected to return the corrected proofs within 5-7 working days. Articles will be finally published with a Crossref Digital Object Identifier (DOI) as part of the permanent scientific record. Articles may only be removed through a formal retraction.

Authorship Criteria

Authorship credit should be based only on substantial contributions to each of the three components mentioned below: 

  1. Concept and design of study or acquisition of data or analysis and interpretation of data;
  2. Drafting the article or revising it critically for important intellectual content; and
  3. Final approval of the version to be published.

Participation solely in the acquisition of funding or the collection of data does not justify authorship. General supervision of the research group is not sufficient for authorship. Each contributor should have participated sufficiently in the work to take public responsibility for appropriate portions of the content of the manuscript.

Conflicts of Interest/ Competing Interests

All authors of must disclose any and all conflicts of interest they may have with publication of the manuscript or an institution or product that is mentioned in the manuscript and/or is important to the outcome of the study presented. Authors should also disclose conflict of interest with products that compete with those mentioned in their manuscript.

Manuscript requirements

Manuscripts may be written in any standard program including Word, GoogleDocs and LaTeX. You can find a LaTeX template here. Authors will upload a pdf for peer review. Upon submission of revised manuscripts authors will also be requested to describe the changes made in the Revision Notes section and to submit a pdf version with tracked changes. Only after final acceptance of a manuscript will the author be requested to submit Word or LaTeX files for typesetting.

There are no strict formatting requirements, but all manuscripts should follow the basic structure for reporting scientific research below. The manuscript should be submitted as a pdf file.

Structure

The manuscript should include: Title page (title, authors, affiliations, contact, abstract, keywords (up to 10), conflict of interest statement), acknowledgments (Funder); Main text (introduction, materials and methods, results, discussion, figures with captions, tables with captions), References.

There are no word limits for submissions but manuscripts should be concise and well-written.

Title Page This page should include

  1. Article title
  2. Type of manuscript (original article, case report, review article, Letter to editor, etc.) title of the manuscript, names and affiliations of all authors/ contributors.
  3. Authors. The names and affiliations of all authors as well as the name, address, e-mail of the corresponding author, who is responsible for communicating with the other authors about revisions and final approval of the proofs.
  4. Author contributions. A description of work done by each author.
  5. Conflicts of Interest of each author/ contributor. A statement of financial or other relationships that might lead to a conflict of interest.
  6. Data availability statement
  7. Code availability statement
  8. Acknowledgements, if any. One or more statements should specify 1) contributions that need acknowledging but do not justify authorship, such as general support by a departmental chair; 2) acknowledgments of technical help; and 3) acknowledgments of financial and material support, which should specify the nature of the support. This should be included in the title page of the manuscript and not in the main article file.
  9. Registration number in case of a clinical trial and where it is registered (name of the registry and its URL)

Methods section

Describe your experiment in as much detail as required for another researcher to reproduce your results. Use RRIDs (https://www.rrids.org/) to identify your research resources such as strains of organisms or antibodies. If a brand name is cited, supply the manufacturer's name and address (city and state/country).Follow all best practice reporting standards (e.g. the NIHMDAR, and ARRIVE). If AI or machine learning was used provide an AIMe registry link (https://aime-registry.org). All submissions will undergo a scientific rigor check performed by SciScore( https://www.sciscore.com/) that analyses the methods section for compliance.

Use standardized nomenclature for species-specific gene and protein names (see GenecardsMGI Nomenclature pageHUGO Gene Nomenclature Committee, or equivalent resources).

Data and Code

Refer to the Network Medicine Data Policy. Whenever possible follow the follow the FAIR (findable, accessible, interoperable, and reusable) data principles. You are strongly encouraged make your materials, data, protocols, code and scripts, available to readers in a public repository upon publication with exceptions for legal, ethical or logistical reasons. If you do not have requirements or support to publish data in an institutional or subject specific repository, search the DataCite Repository Finder  for appropriate repositories.Whenever possible data should be cited in the references section following the guidelines of the Joint Declaration of Data Citation Principles.

Tables

  • Tables should be black and white/greyscale only and formatted as simply as possible for best accessibility. See some guidelines here: https://www.w3.org/WAI/tutorials/tables/
  • Tables should be self-explanatory and should not duplicate textual material.
  • Number tables consecutively in the order of their first citation in the text and supply a brief title for each.
  • Place explanatory matter in footnotes, not in the heading.
  • Explain in footnotes all non-standard abbreviations that are used in each table.

Figures

  • Figures should be numbered consecutively according to the order in which they have been first cited in the text.
  • To support the visually impaired, this journal includes Alt Text (alternative text), a short piece of text tagged to your figure to describe for readers contents of the image. This text can be used by screen readers to make the object accessible to people that cannot read or see the object.  Add Alt Text using Microsoft Word tools or as a separate figure caption. Further information on Alt Text for images can be found here: https://www.w3.org/WAI/tutorials/images/.
  • It is the responsibility of authors/ contributors to obtain permissions for reproducing any copyrighted material. A copy of the permission obtained must accompany the manuscript.
  • High resolution images may be requested upon acceptance of the manuscript.

References

References should be complete with DOI numbers if possible. The Journal uses the “Vancouver” numbering style and same reference style as PLOS (for those working with Paperpile, Endnote or other reference management systems). Journal name abbreviations should be those found in the National Center for Biotechnology Information (NCBI) databases. Examples of the format are listed below.

Source

Format

Published articles

Aubé J. Drug repurposing and the medicinal chemist. ACS Med Chem Lett. 2012;3: 442–444. doi:10.1021/ml300114c  

 

Stalidzans E, Zanin M, Tieri P, et al. Mechanistic modeling and multiscale applications for precision medicine: Theory and practice. Network and Systems Medicine. 2020;3: 36–56. doi:10.1089/nsm.2020.0002  

 

Books

Cavalla D. Drug repurposing. London: Royal Society of Chemistry; 2022. doi:10.1039/9781839163401

 

Book chapters

Avram S, Curpan R, Oprea TI. Cheminformatics data mining and modeling for drug repurposing. In: Cavalla D, editor. Drug repurposing. London: Royal Society of Chemistry; 2022. pp. 129-146. doi:10.1039/9781839163401-00129

 

Deposited articles (preprints, e-prints, or arXiv)

Pouromran F, Lin Y, Kamarthi S. Automatic pain recognition from Blood Volume Pulse (BVP) signal using machine learning techniques. arXiv:2303.10607 [Preprint]. 2023 [cited 2023 Feb 3]. doi:10.48550/arXiv.2303.10607  

New media (blogs, web sites, or other written works)

Jasini K. Introducing the Drug Repurposing Research Collection by REPO4EU. 2023 Jan 24 [cited 24 March 2023]. In: ScienceOpen Blogs [Internet]. Berlin: ScienceOpen 2013. Available from: https://blog.scienceopen.com/2023/01/introducing-the-drug-repurposing-research-collection-by-repo4eu/

Masters' theses or doctoral dissertations

Sharma J. Drug repurposing & adverse event prediction through EHR knowledge graph completion. Master Thesis, Universität Freiburg. 2022. Available from: https://publica.fraunhofer.de/handle/publica/418000

 

Croset S. Drug repositioning and indication discovery using description logics. PhD Thesis, University of Cambridge. 2014. doi:10.17863/CAM.15985

 

Databases and repositories (Figshare, arXiv)

Melamed R. Drug Indication Predictions; 2023 [cited 2023 Feb 3]. Database: figshare [Internet]. doi:10.6084/m9.figshare.21926400.v1

 

 

Submission of a revised manuscript 

The revised version of the manuscript should be submitted online in a manner similar to that used for submission of the manuscript for the first time. When submitting a revised manuscript, contributors are requested to include a point by point response to the reviewer comments and describe the changes made. In addition, they are expected to mark the changes as underlined or colored text in the article and submit this “Tracked changes” version along with their revised manuscript.

Publication schedule

The journal publishes articles on its website immediately on acceptance and follows a continuous publishing schedule.

 

Publication Policy

 

Articles will be published Open Access under the terms of the Creative Commons Attribution License (CC-BY 4.0 License) which permits use, distribution and reproduction in any medium, provided that the work is properly cited.

This journal Network Medicine is generously funded through the European Project REPO4EU and there are currently no fees or article processing charges (APCs) associated with publishing in the journal.

 

 

Data / Code Policy

 

By publishing in the journal authors are required to make research data available to editors and reviewers, and to readers. For all research data deposition in repositories is required. For all papers, the decision to publish will be affected by whether or not authors share their research data.

Required

  • Data sharing via repositories for all research data
  • Data availability statements
  • Data sharing on request
  • Data citation

Optional / Encouraged

  • Prepare and share Data Management Plans

Feature

Text

Definition of research data

This policy applies to the research data that would be required to verify the results of research reported in articles published in the journal. Research data include data produced by the authors (“primary data”) and data from other sources that are analysed by authors in their study (“secondary data”).

Research data includes any recorded factual material that are used to produce the results in digital and non-digital form. This includes tabular data, code, images, audio, documents, video, maps, raw and/or processed data.

Definition of exceptions

Research data that are not required to verify the results reported in articles are not covered by this policy.

This policy does not require public sharing of quantitative or qualitative data that could identify a research participant (“personal data”) unless participants have consented to data release. The policy also does not require public sharing of other sensitive data, such as the locations of endangered species. Personal or sensitive data must be shared in a secure or controlled access way, in agreement with the Editors. Methods for sharing sensitive or personal data include:

  • Deposition of research data in an approved controlled access repositories and sharing metadata publicly about the research data
  • Anonymisation or deidentification of data before public sharing

In these cases the procedures and conditions for accessing your research data must be included in your manuscript.

Embargoes

Embargoes on data sharing are not permitted.

Supplementary materials

Sharing research data as supplementary information files is not permitted. The journal will require authors to deposit these in an approved repository as a condition of publication.

Data/Code repositories

Research data and code must be shared via data repositories. Please see https://repositoryfinder.datacite.org/ for help finding research data repositories. The journal will require authors to deposit these in an approved repository as a condition of publication.

Data citation

The journal requires authors to cite any publicly available research data in their reference list, and will verify this as a condition of publication. References to datasets (data citations) must include a persistent identifier (such as a DOI). Citations of datasets, when they appear in the reference list, should include the minimum information recommended by DataCite and follow journal style.

Data licensing

The journal encourages research data to be made available under open licences that permit reuse freely. The journal does not enforce particular licenses for research data, where research data are deposited in third party repositories. The publisher of the journal does not claim copyright in research data.

Researcher/ author support

Questions about complying with this policy should be sent to info@scienceopen.com.

Data availability statements

The journal requires authors to include in any articles that report results derived from research data to include a Data availability statement. The provision of a Data availability statement that is compatible with the journal’s research data policy will be verified as a condition of publication. Data availability statements must include information on where data supporting the results reported in the article can be found including, where applicable, hyperlinks to publicly archived datasets analysed or generated during the study. Where research data are not publicly available, a persistent link to a metadata record or landing page for the data should be provided. Any conditions for accessing the data must be stated in the manuscript.

Data formats and standards

The journal encourages authors to share research data using data formats and standards recognised by their research community. Please see FAIRsharing.org for more information on established data sharing formats and standards.

The journal prefers research data to be shared in open file formats – those that do not require proprietary software to access - where possible. For example, tabular data should be shared as CSV files rather than XLS files.

Mandatory data sharing (all papers)

The journal requires that all research data that support articles published in the journal, except those covered by the “Definition of exceptions”, must be available in public repositories.

Research data and peer review

Peer reviewers are encouraged to consider a manuscript’s Data Availability Statement (DAS), where applicable. They should consider if the authors have complied with the journal’s policy on the availability of research data, and whether reasonable effort has been made to make the data that support the findings of the study available for replication or reuse by other researchers. For the Data availability statement, reviewers should consider:

  • Has an appropriate DAS been provided?
  • Is it clear how a reader can access the data?
  • Where links are provided in the DAS, are they working/valid?
  • Where data access is restricted, are the access controls warranted and appropriate?
  • Where data are described as being included with the manuscript and/or supplementary information files, is this accurate?

For the data files, where available, reviewers should consider:

  • Are the data in the most appropriate repository?
  • Were the data produced in a rigorous and methodologically sound manner?
  • Are data and any metadata consistent with file format and reporting standards of the research community?
  • Are the data files deposited by the authors complete and do they match the descriptions in the manuscript?
  • Do they contain personally identifiable, sensitive or inappropriate information?

Data Management Plans

The journal encourages authors to prepare Data Management Plans before conducting their research and encourages authors to make those plans available to editors, reviewers and readers who wish to assess them.

 

 

Each manuscript submission will be undergo an automated check for scientific rigor performed by SciScore and will reviewed by a least two subject experts in a single-blind workflow. Manuscripts that have been previously posted as preprints may submit open reviews of the preprint for consideration by the editorial team. Reviewers have the option of posting their reviews publicly on the ScienceOpen platform after an  article has been published.

All material presented must be acquired according to ethical standards and approved by legally appropriate ethical committee(s).

We encourage authors to be aware of standardised reporting guidelines when preparing their manuscripts:

  • Case reports - CARE
  • Diagnostic accuracy - STARD
  • Observational studies - STROBE
  • Randomized controlled trial - CONSORT
  • Systematic reviews, meta-analyses - PRISMA
  • Animal research / In vivo experiments - ARRIVE

In all cases of publication ethics the journal will refer to the Committee on Publication Ethics (COPE) guidelines: https://publicationethics.org/

Reporting research that involves human subjects or data requires a declaration that the investigations were carried out following the rules of the Declaration of Helsinki (https://www.wma.net/what-we-do/medical-ethics/declaration-of-helsinki/). Approval from the institutional review board (IRB) or other appropriate ethics committee must be obtained before undertaking the research to confirm the study meets national and international guidelines. A statement including the project identification code, date of approval, and name of the ethics committee or institutional review board must be included as ‘Institutional Review Board Statement’ article. For example: "All subjects gave their informed consent for inclusion before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of XXX (Project identification code)." The privacy rights of human subjects must always be observed.

Reporting research that involves animals required a statement that authors have the relevant approval for their study from an appropriate ethics committee and/or regulatory body before the work starts. The ethical statement provides editors, reviewers and readers with assurance that studies have received this ethical oversight. Authors are responsible for complying with regulations and guidelines relating to the use of animals for scientific purposes. Authors should ensure that they follow the ARRIVE guidelines for reporting animal research.

The manuscript should follow the Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals and aim for the inclusion of representative human populations (sex, age and ethnicity) according to those recommendations. The terms sex and gender should be used correctly. Additionally, when studies describe groups by race, ethnicity, gender, disability, disease, etc., explanation regarding why such categorization was needed should be clearly stated in the article.

 

 

Author Agreement

 

Open Access Publishing Agreement

By submitting my manuscript to the journal Network Medicine published by REPO4EU (hereafter the ‘Publisher’) and managed by ScienceOpen, I herewith grant permission to the Publisher to publish my article upon editorial acceptance under the following publishing agreement.

I hereby confirm that this is my original work and that

  • I own sole copyright in this work
  • And/or I have obtained permission from all other Authors to execute this Agreement on their behalf if necessary

And that the work

  • Has never been published before.

I understand that in granting this consent I am granting to the Publisher the Rights to publish under a Creative Commons CC-BY 4.0 license the Contribution in the English language in digital form; moral rights will be retained by the original Author/s and copyright will be held by the Author.

I agree to this Publishing Agreement, consent to execution and delivery of the Publishing Agreement electronically and agree that confirming my consent electronically during the manuscript submission process with an electronic signature shall be given the same legal force as a handwritten signature.

Terms of Use

  1. The Contribution will be made Open Access under the terms of the Creative Commons Attribution License (CC-BY 4.0 License) which permits use, distribution and reproduction in any medium, provided that the Contribution is properly cited.
  2. The Journal (and Publisher) reserves the right to require changes to the Contribution as a condition of its acceptance. The Journal (and Publisher) reserves the right, notwithstanding acceptance, not to publish the Contribution if for any reason such publication would in the reasonable judgment of the Journal (and Publisher), result in legal liability or violation of journal ethical practices. If the Journal (or Publisher) decides not to publish the Contribution, the Author is free to submit the Contribution to any other journal from any other publisher.
  3. As above, the final Contribution will be made Open Access under the terms of the CC-BY license. Reproduction, posting, transmission or other distribution or use of the final Contribution in whole or in part in any medium by the Author as permitted by this Agreement requires a citation to the Journal suitable in form and content as follows: (Title of Contribution, Author, Journal Title and Volume/lssue, Digital Object Identifier (DOI), Date). Links to the final published Contribution should be provided following the guidance below on best practice.

Retained Rights

The Author retains all proprietary rights in addition to copyright, such as patent rights in any process, procedure or article of manufacture described in the Contribution.

Author's Representations

The Author(s) certify that they have participated sufficiently in the intellectual content, conception and design of this work or the analysis and interpretation of the data (when applicable), as well as the writing of the manuscript, to take public responsibility for it and have agreed to have their name listed as a contributor. The Author(s) believe the manuscript represents valid work. Neither this manuscript nor one with substantially similar content under their authorship has been published or is being considered for publication elsewhere, with the exception of online posting as a preprint. If requested by the editors, the Author(s) will provide the data/information or will cooperate fully in obtaining and providing the data/information on which the manuscript is based, for examination by the editors or their assignees. Financial interests, direct or indirect, that exist or may be perceived to exist for individual contributors in connection with the content of this paper have been disclosed in a "Conflicts of Interest" statement in the manuscript. Sources of outside support of the project are named in the Acknowledgements section.

Use of Information

The Author(s) acknowledges that, during the term of this Agreement and thereafter (for as long as necessary), the Publisher and the Journal may process the Author’s personal data, including storing or transferring data outside of the country of the Contributor’s residence, in order to communicate with the Author(s) and that the Publisher has a legitimate interest in processing the Author(s)’ personal data. By entering into this Agreement, the Author(s) agree to the processing of personal data (and, where applicable, confirms that the Author has obtained the permission from all other authors to process their personal data). The Publisher and the Journal shall comply with all applicable laws, statutes and regulations relating to data protection and privacy and shall process such personal data.

 

Collection Information