For years scientists have vied to have their research published in the most renowned peer-reviewed journals – with acceptance a guarantee of prestige and a crucial factor in influencing future funding and academic support for their work.

But now a Nobel Prize-winning biologist has accused some of the best known academic publishers of distorting the scientific process by promoting only the “flashiest” research in order to increase subscriptions.

Randy Schekman’s comments have sparked a debate about the future of scientific publishing between the big media houses who have dominated the field for years, and newer ‘open source’ internet publishers who are on a mission to open up scientific research.

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In an article, Professor Schekman, who on Tuesday jointly received the Nobel prize for physiology, said his lab would no longer send papers to the top-tier journals, Nature, Cell and Science. He is the editor of eLife, an online journal set up by the Wellcome Trust, which is a competitor to the other three.

“Because funding and appointment panels often use place of publication as a proxy for quality of science, appearing in these titles often leads to grants and professorships,” he wrote.

“The prevailing structures of personal reputation and career advancement mean the biggest rewards often follow the flashiest work, not the best. Those of us who follow these incentives are being entirely rational but we do not always best serve our profession’s interests, let alone those of humanity and society.”

Professor Schekman added that journals such as eLife should be given more weight by universities. “Just as Wall Street needs to break the hold of the bonus culture, which drives risk-taking that is rational for individuals but damaging to the financial system, so science must break the tyranny of the luxury journals,” he wrote.

“The result will be better research that better serves science and society.”

His comments elicited an irritated response from the big publishers. Philip Campbell, editor-in-chief at Nature, insisted they only selected research for publication on the basis of “scientific significance”.

“That in turn may lead to citation impact and media coverage, but Nature editors aren’t driven by those considerations, and couldn’t predict them even if they wished to do so,” he said.

But Professor Schekman appeared to receive the backing of Professor Peter Higgs, whose work in the 1960s led to the discovery of the Higgs Boson particle. Receiving his Nobel Prize on Tuesday, he said he doubted a similar breakthrough could be achieved today, due to the expectations on academics to collaborate and churn out papers.

“It’s difficult to imagine how I would ever have enough peace and quiet in the present sort of climate to do what I did in 1964,” he said, adding that he became “an embarrassment to the department when they did research assessment exercises” as he very rarely had things published.