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4D Nucleome Project - Publication Policy

Version 1.0 - 15 November 2016

4D Nucleome Publication, Data Release, and Software Sharing Policies distinguish two release tiers:

  • Tier 1 concerns release to network members
  • Tier 2 concerns release to the public

This policy will be reviewed and, if necessary, updated on a semi-annual basis.

Rationale: To disseminate research outcomes quickly and to facilitate collaboration and coordination of research within the network.

This document describes the 4DN network policy for sharing manuscripts, from the planning stage through submission to a journal. All manuscripts resulting from 4D Nucleome-funded activities (i.e. manuscripts acknowledging 4DN support) are subject to this policy.

This policy encourages the open sharing of information within the network. In keeping with this principle, sharing of manuscript drafts and solicitation of feedback by network members before submission is strongly encouraged. Information shared internally (Tier 1) must be treated as confidential, and may not shared outside of the network.

It is the sole responsibility of network members to take appropriate steps to protect any intellectual property rights to their work and to follow any relevant rules of their institutions. A process to request an exception or an extension for compliance with the policy that may be required to protect intellectual property rights is detailed below.

The corresponding author is responsible for compliance with this policy, which includes updates of the manuscript tracking system when the status of a manuscript changes (draft to submitted, submitted to published, etc.), corrections, or retractions after publication. Authors of published manuscripts should notify the OH so that the manuscript can be included in the list of network publications and updated accordingly.

Tier 1: Internal sharing of planned manuscripts

  • The manuscript tracking system will be used to share information about planned manuscripts and analyses with other network members, in order to foster collaboration and coordination, and minimize overlap.
  • Currently, the manuscript tracking system is part of the network wiki: The manuscript tracking system time stamps abstracts and manuscripts that are shared with the network.
  • In order to stimulate collaboration and coordination with other network members, planned manuscripts should be entered into the manuscript tracking as early in the process as is reasonably possible.
  • Any information shared via the manuscript tracking system is considered to be a private communication, with the understanding that the information contained in such documents is not intended for public use, and will be kept confidential.

Tier 2: Rapid public sharing of submitted manuscripts

  • Preprints of submitted manuscripts must be shared with the public via an appropriate public preprint server (such as bioRxiv, arXiv, ChemRxiv) prior to, or concurrently with the time of submission to a journal, unless an exception or extension was granted by the 4DN Steering Committee.
  • Co-submissions to public preprint servers should be coordinated among network members when appropriate. The manuscript tracking system should be updated with a link to the preprint, once it becomes available.
  • Exceptions or extensions may be requested in cases where sharing of preprints is not allowed due to legal requirements related to the protection of intellectual property, or when the target journal does not allow preprints to be shared prior to publication.
  • Requests for exception or extension should be made via email to the NIH voting member (Dr. Judy Mietz with a CC to Dr. Lisa Chadwick ( Requests should explain why an exception or extension from the preprint policy is required, and should be supported by sufficient documentation from the institutional technology transfer office of the PI, or from the targeted journal. Such requests should be made well in advance of submission to a journal, in order to allow time for consideration by the Steering Committee.

Other Considerations

Citation of Preprints: The network acknowledges that public preprints are considered publications for all practical purposes by network members, and should be cited and credited like papers. Preprints establish priority in the field, can be included in progress reports, CVs, and lists of publications.

Open Access: Publications must at a minimum comply with the NIH Public Access policy ( In order to maximize the impact of the efforts of the network, authors should make strong efforts to publish their work using open access policies whenever possible.

Related Work: We encourage network members to share information about planned or submitted manuscripts even if the work is not funded by the network but related to the mission of the 4D Nucleome project.


Policy Working Group - Grantees

Co-Chairs: Nils Gehlenborg, Leonid Mirny

Stephanie Alexander, Ewan Birney, Job Dekker, Larry Gerace, Mike Levine, Timothée Lionnet, Chuck Murry, Shankar Subramaniam, Huimin Zhao

Policy Working Group - Program Staff

Iddil Bekirov, Olivier Blondel, Lisa Chadwick, Lisa Postow

Additional comments provided by William Noble, Andrew Belmont, Hanspeter Pfister, Sonja Hess, Erez Lieberman Aiden, Jay Shendure, Arjun Raj, Jennifer Cremins, Joan Politz Ritland, Burak Alver, and Dave Gilbert.


  • Version 1.0 - 15 November 2016
    • Approved by voting members of the Steering Committee.
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