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As the publishing landscape shifts towards open access, many researchers have questions about how to navigate new NIH policies. (Credit: Tada Images/Shutterstock)

The NIH Public Access Policy, which went into effect on July 1, 2025, has a noble goal: to make publicly funded research available to everyone as soon as it’s published in a peer-reviewed journal.

But as the publishing landscape slowly shifts towards open access, many researchers are finding themselves between a rock and a hard place. That’s because while the NIH requires the embargo-free deposit of NIH-funded articles into PubMed Central (PMC) immediately after publication, many scientific journals have embargo policies that require authors to keep their findings under wraps for as long as a year—and the journals often own the copyright.

So what is a scientist who wants to stay in the good graces of both federal funders and private publishers to do?

The information experts at Rockefeller’s Markus Library have ideas. Since the new rules began, University Librarian Matthew Covey and his team have been offering detailed guidance, resources, lectures, tips, and tools to help Rockefeller researchers navigate the new open access terrain.

“We really want people to be aware of what’s going on so that they don’t fall out of compliance and risk any future funding,” says Covey.

Here are some of the most important steps Covey recommends authors should take—and a couple of pitfalls to avoid.

Consider publishing in an open access journal

This is the most obvious choice, and it offers the most options. While some journals are fully open access by design, many are so-called hybrid journals, which offer both traditional embargo-limited publication as well as the option to publish open access. The catch is the article processing cost, or APC, which is the fee journals charge to publish a paper open access. For a top journal like Nature, this could run to nearly $13,000 for a single paper.

However, most journals have far lower APCs, and some—especially not-for-profit university publishers—charge less for institutions in many lower-income countries. Moreover, high-quality journals published by scientific societies generally keep their APCs low, and those fees help keep the lights on for the society and its members.

That the cost of APCs can be a barrier to expanding open access is something the NIH is well aware of. This past summer, it put out a public call for feedback on its proposal that no more than $2000 of any NIH grant could go towards an APC—and got more than 900 comments in response. Some were in support, and many were not.

The NIH plans to announce the APC limits this year.

Try amending your author contract with the publisher

Some publishers have adjusted their policies to allow for papers that weren’t published open access to be deposited in PMC without an embargo; those include AAAS/Science, JAMA, and Rockefeller University Press. But the largest publishers—Springer Nature, Elsevier, Wiley—have not, and instead their policy asks that authors pay the APC for open access.

However, that doesn’t mean that some journals aren’t open to negotiation, Covey says: “It’s possible to amend author agreements with publishers so that the author can retain copyright, eliminate the embargo, or otherwise adjust the contract so that they can be in compliance with NIH requirements.”

To help Rockefeller scientists in their negotiations, the library staff, in conjunction with the university’s Office of General Counsel, has drafted language that researchers can append to their author agreements. “People just have to ask us for it, and we’ll send it to them,” Covey says.

They’ve also solicited guidance from the copyright experts at Authors’ Alliance, which advances the interests of authors seeking to share their work widely while also protecting their rights. In October, the library hosted an online webinar with its executive director, Dave Hansen, who suggested an author addendum created by the open access advocacy group SPARC as another resource.

“It’s a really helpful tool to start a conversation with your publisher about retaining the rights that you need to comply with open access,” Hansen noted. “It’s especially good for smaller publishers who may have less well-developed policies around how to deal with authors who have NIH obligations.”

For more details, watch Hansen’s full presentation, which is available online to the Rockefeller community.

Publish for free in one of the nearly 5,000 journals Rockefeller has Read and Publish agreements with

Read and Publish agreements are an emerging tool in the transition to open access publishing. Typically, an institution pays a subscription fee to a journal or publisher that allows its members to read content, but these new agreements have the added benefit of allowing members to publish open access papers in them for free, without paying an APC (after a paper is accepted through the standard peer-review process).

Rockefeller University currently has Read and Publish agreements with the American Chemical Society, BioScientifica, Cambridge University Press, Cold Spring Harbor Laboratory Press, Company of Biologists, Institute of Physics, Microbiology Society, Oxford University Press, Portland Press (Biochemical Society Journals), Royal Society of Chemistry, Springer (minus Nature titles), and Wiley.

In all, there are nearly 5,000 journals to choose from. “We have many high-quality, highly respected publications,” Covey notes.

Don’t rely on journals to put your paper in PubMed Central

Journals have traditionally deposited papers into PMC on behalf of authors, but that practice is fading fast. “It’s important for people to not expect the system to function as it used to,” Covey notes. “Because of back-end system changes, publishers are no longer depositing papers as a matter of course, and if they do, they’re more aggressively asserting their author agreements by setting the terms of the embargo. These terms are unalterable, so if they set an embargo that’s incompatible with the NIH’s zero-embargo policy, the author won’t be in compliance. People have to be more proactive now about depositing their own work.”

The NIH has generally granted a three-month grace period from publication date to finalize a deposit into PMC via the NIH Manuscript Submission System, but he advises people to take action as fast as they can. “You don’t want to forget about it and run afoul of the rules,” he says. “We always recommend that people do it as soon as possible.”

Don’t assume a preprint is a workaround

While uploading a paper to BioRxiv seems like it could be a quick way to fulfill the terms of the NIH’s Public Access Policy, it isn’t.

“It would’ve been great if the NIH had allowed preprints to satisfy the public access requirements, but it didn’t do that. Once a paper is published in a journal, it must be put in PMC,” Covey says. “However, if NIH-funded research only appears as a preprint and is never published in a journal, that does fulfill the policy requirements.”

Reach out to Markus Library staff with questions

Rockefeller researchers can contact the library staff at any time for help at markuslibrary@rockefeller.edu.

“The best time to engage with us is early on in the planning phase of considering where to submit your work,” Covey says. “When we learn what your requirements are, we might be able to suggest suitable spots for your research.”