The administrative building of the National Institutes of Health in Bethesda, Md. (J. Scott Applewhite/Associated Press)

During her time at the National Institutes of Health, Bibiana Bielekova has helped identify a treatment for multiple sclerosis. She has published 52 papers in peer-reviewed journals, some of them the most prestigious in her field. She has built an international reputation as a neuro-immunologist.

What Bielekova doesn’t have, at age 47, is tenure, the coveted guarantee of recognition, job security and freedom to pursue controversial ideas that is critical to long-term success in an academic career. She was not put forward as a candidate for the second time last year, despite a positive recommendation from a panel of outside experts who reviewed her qualifications.

In that way, she is also emblematic of women at NIH — the primary government biomedical research center — and elsewhere who have made little progress into the ranks of senior scientists.

Just 22 percent of the tenured research scientists at NIH are women, up from 19 percent in 2011, according to the institution. About 38 percent of the scientists now on the track toward tenure are women, up from 36 percent in 2011.

Bielekova, who has filed an Equal Employment Opportunity complaint against her institute’s director and two others, said women’s lagging prospects at NIH reflect gender bias, overt and unconscious, from the men who run the institution. She is supported by a body of research that leaves little doubt that bias is at least part of the problem.

Bibiana Bielekova, a neuro-immunologist, says “women are considered second-rate citizens” at NIH. (Courtesy of Bibiana Bielekova )

“It’s not negligence,” Bielekova said in a rare public discussion of tenure deliberations. “Women are considered second-rate citizens. They are fully aware that this is happening, the leadership. It’s happening with their blessing.”

NIH officials said they have spent years researching and trying to address gender imbalance in their ranks. They contend that more men than women apply for tenure-track jobs. Women who drop out of academia are mostly concerned about non-science issues: grueling hours, work-life flexibility, the desire to have children, and a shortage of female role models at NIH, to name a few, said Michael M. Gottesman, NIH’s deputy director for intramural research, and Hannah Valantine, NIH’s chief officer for scientific workforce diversity.

Women in academic careers face obstacles at every turn. They are paid less, promoted more slowly, earn less recognition and hold fewer leadership positions, according to the National Academy of Sciences. At NIH, there are 180 tenured women and 647 tenured men. “A woman looking at that would say that’s because the institution doesn’t want women,” Valantine acknowledged.

Sometimes NIH loses top women to another institution. “The women we offered jobs to weren’t dropping out of science,” said Story Landis, former director of the National Institute of Neurological Disorders and Stroke, where Bielekova works. “They were taking jobs elsewhere. We lost people to Stanford, Harvard, Northwestern.”

The drain of talent deprives research of the perspective women can bring and could hold back scientific progress, according to a panel of the National Academy of Sciences, which in 2007 reported on women in academic science and engineering.

“The consequences of not acting will be detrimental to the nation’s competitiveness,” the prestigious scholarly organization wrote.

The process of granting tenure is, by design, partly subjective, leaving considerable discretion to decision makers — generally senior department officials and the committees that decide a researcher’s fate. Intangibles count. Besides being a star, is the researcher a good mentor? A good colleague? Can he or she navigate the tricky roads of academia?

While tenure awards are supposed to be based largely on merit, it is widely acknowledged that personality conflicts, budget constraints, internal politics and other factors affect them.

“Tenure decisions are complicated, and not just about what you’ve published,” Landis said.

NIH notes that its tenure statistics are comparable to those of other academic medical centers, according to 2013-2014 data compiled by the Association of American Medical Colleges. At those medical schools, women also hold 22 percent of the tenured teaching jobs. Thirty percent of the new tenure awards went to women in 2013-2014, the same proportion as received them five years earlier.

Researchers have been examining the gender imbalance for decades, exposing a system that favors men.

“It is not lack of talent, but unintentional biases and outmoded institutional structures that are hindering the access and advancement of women,” the NAS panel wrote.

The U.S. research system developed when most scientists were men with spouses who did not work outside the home. “The system was developed by men for men and the way that their professional lives were structured,” said Shirley Malcom, director of education and human resources programs at the American Association for the Advancement of Science, who served on the panel.

And as women in many workplaces point out, qualities valued in men do not work for them. “Assertiveness and single-mindedness are stereotyped as socially unacceptable traits for women,” the NAS report concluded.

Or as one expert put it: “He is seen as an up-and-comer. She is seen as pushy.”

At NINDS, three women and 34 men hold tenured positions. “The numbers are terrible and we need to do better,” Director Walter J. Koroshetz said.

On the track toward tenure at NINDS, however, are six women and five men. Two of the six women are being put up for tenure this year and a third may be, he said.

Bielekova said she is not among them. When a board of experts in her field from research institutions around the country examined her work in September, it concluded that she “is an excellent physician scientist. Her international reputation is well-deserved, and strongly supports consideration for tenure,” according to a copy of their report that Bielekova gave to The Washington Post. The panel also called her “a productive mentor.”

The panel challenged one of Bielekova’s planned studies, saying the rationale for it “was perceived to be only modestly compelling.”

She said Koroshetz has told her that he will take as long as two more years to think about whether to nominate her for tenure, as allowed by NIH policy. That means it could be 10 years total before Bielekova comes up for formal review. She would have to leave NIH if she fails.

She filed her EEOC complaint in March. At one point, her attorney said, NIH offered to settle the case but without granting Bielekova tenure. She turned down the offer.

Specifically, Bielekova alleges retaliation and discrimination based on gender after what she describes as a “power struggle” following the retirement of her mentor, who was chief of the neuro-immunology branch. She said male scientists were provided numerous advantages in the aftermath and that she has been harmed by groundless accusations from male colleagues of unprofessional conduct. A male colleague from her branch, she said, was nominated for tenure at the same time that she was held back.

Koroshetz said he cannot discuss individual cases but makes his tenure decisions based on the institute’s overall programmatic needs, not gender. He said he has not seen gender bias but knows that women consider NIH a more difficult place to work than men do.

One NIH unit where tenured men and women can be found in almost equal numbers is the division of cancer epidemiology and genetics, part of the National Cancer Institute. Of the 49 tenured scientists there, 21 are women, said Stephen J. Chanock, the division’s director. Fourteen of the 24 people on the tenure track are women, he said.

The division has a long history of supporting researchers’ needs outside the workplace, Chanock said. But perhaps most important, epidemiologists who crunch data can work from home or elsewhere, flexibility they find very attractive, he said.

While the environment is competitive, “there isn’t the dictum that you really have to be there to succeed,” Chanock said.

Bielekova, who works long hours in the lab, is a native of Slovakia. She earned her medical degree there and did postgraduate work in the United States before arriving at NINDS in 1997, according to her curriculum vitae. She worked there until 2005, when she left to take a tenured position at the University of Cincinnati, but she returned in 2008 without tenure because, she said, the resources at NIH were superior for her goal of curing multiple sclerosis.

She knows that her decision to publicly discuss her tenure troubles could haunt the rest of her career, even if NIH ultimately awards it to her. But she said it’s time that women express publicly what they say privately.

“Women put their tails between their legs and they leave,” she said. “If they would fight, this would not be the case.”