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Top biotech analyst calls out Janet Yellen's comments

Did Fed Chair Janet Yellen catch something biotech's top analyst missed?

As a companion to Congressional testimony earlier this week, the Yellen-led Fed opined on stock valuations.

"Valuation metrics in some sectors do appear substantially stretched—particularly those for smaller firms in the social media and biotechnology industries, despite a notable downturn in equity prices for such firms early in the year," a report said.

Read More Yellen weighs in on US equities, debt

But a top-ranked biotech analyst took issue with the Federal Reserve's views.

"When I look at P/E ratios in biotech, I'm really asking the question, 'Are we in a bubble?' 'cause I think what the Fed perhaps – and I'm not a Fed observer – but I'm told what the Fed is looking for perhaps is signs of bubble," ISI Group's Mark Schoenbaum said Friday on CNBC's "Halftime Report."

"And on that, according to my data, I would argue that the answer is clearly no. Now, is biotech cheap? Is it a real steal here? That's a totally different debate."

Schoenbaum, named the No. 1 analyst in the biotech sector for the past nine years by Institutional Investor, published an analyst note that resembled an open letter to the Fed chair.

In it, he wrote: "Dr. Yellen — Thank you for sharing your thoughts recently on the biotech sector. … You stated that biotechnology valuations are 'stretched, with ratios of prices to forward earnings remaining high relative to historical norms.'"

Read More Bob Pisani: Yellen's 'stretched valuations' remark no surprise

As evidence, Schoenbaum included Russell 1000 data from biotech stocks dating back to 1978, "and my data show that the current ratio is roughly in line with the historical median and is approximately 40% below the peak.

"Please tell me what I'm missing, Dr. Yellen," he wrote.

Schoenbaum added that he had a "great deal of respect" for Yellen.

"However, we have a different view, perhaps, of the data on price-to-earnings ratios," he said.

Schoenbaum called biotech is "a large, large sector" with hundreds of companies, "most of which have no profits and no earnings. They're basically options vehicles based on a drug that will report data out in a few months. And certainly, in 2012 and 2013, it was an unprecedented bull run in biotech. For some of those stocks, there's probably too much optimism baked in.

Read More The cure for asset bubbles: Inflation

"But of course, in the giant universe of biotech stocks, you're going to find stocks that are overvalued and you're going to find some that are undervalued."

Schoenbaum added that he didn't see a bubble.

"Overall, I don't think the data suggest that we're in for a giant crash," he said.

By CNBC's Bruno J. Navarro.

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