The Federal Reserve, in a report accompanying Chair Janet Yellen's congressional testimony last week, expressed concern about biotechnology stock valuations.

But Mark Schoenbaum of ISI Group, ranked the No. 1 analyst for the biotech industry in each of the past nine years by Institutional Investor, took issue with that view.

As for the Fed report, it stated, "equity valuations of . . . biotechnology firms appear to be stretched, with ratios of prices to forward earnings remaining high relative to historical norms."

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Schoenbaum's response: "when I look at P/E [price-earnings] ratios in biotech, I'm really asking the question, are we in a bubble, because I think what the Fed . . . is looking for perhaps is signs of bubble," he tells CNBC.

"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."

In a commentary obtained by CNBC, Schoenbaum wrote, "my data show that the current [P/E] ratio is roughly in line with the historical median and is approximately 40 percent below the peak. Please tell me what I'm missing, Dr. Yellen."

Meanwhile, David Miller, manager of hedge fund Alpine BioVentures, writes in an article for Minyanville that while seasonality is no guarantee in the biotech sector, "if you look at a chart of biotech over the last decade, you'll see summer flattening or pullbacks enough times to recognize it's a thing you have to account for when managing a biotech portfolio."

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