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We have tracked the key short interest changes in the following biotech and emerging pharma companies: Alexion Pharmaceuticals Inc. (NASDAQ: ALXN), Amgen Inc. (NASDAQ: AMGN), Arena Pharmaceuticals Inc. (NASDAQ: ARNA), Biogen Idec Inc. (NASDAQ: BIIB), Celgene Corp. (NASDAQ: CELG), Dendreon Corp. (NASDAQ: DNDN), Gilead Sciences Inc. (NASDAQ: GILD), Illumina Inc. (NASDAQ: ILMN), Onyx Pharmaceuticals Inc. (NASDAQ: ONXX), Pharmacyclics Inc. (NASDAQ: PCYC), Regeneron Pharmaceuticals Inc. (NASDAQ: REGN), Vertex Pharmaceuticals Inc. (NASDAQ: VRTX) and VIVUS Inc. (NASDAQ: VVUS). We also tracked the iShares Nasdaq Biotechnology (NASDAQ: IBB) against the group.

The short interest in biotech stocks is mixed, judging by the short interest changes between the September 28 and October 15 settlement dates. There were notable swings in shares sold short from Biogen Idec, Gilead Sciences and VIVUS. Short interest also was mixed in the previous period.

Alexion Pharmaceuticals Inc. (NASDAQ: ALXN) short interest rose 2.5% between September 28 and Octber 15 to 5.16 million shares. Days to cover ticked back up above five.

Amgen Inc. (NASDAQ: AMGN) saw short interest grow 4.9% to 13.30 million shares. That was the highest number of shares since June.

Arena Pharmaceuticals Inc. (NASDAQ: ARNA) short interest shrank 0.5% to 47.44 million shares. That ended a streak of four consecutive increases. Short interest was 22% of the float.

Biogen Idec Inc. (NASDAQ: BIIB) shares sold short fell 9.6% to 1.68 million, its lowest level this year. Days to cover remains less than two. Short interest is less than 1% of the float.

Short interest in Celgene Corp. (NASDAQ: CELG) climbed 7.3% to 5.27 million shares. Days to cover remains just under two.

Dendreon Corp. (NASDAQ: DNDN) short interest increased 2.3% to 46.88 million shares. This was 31% of the float. Days to cover jumped to more than 15 from less than nine in the previous period.

Gilead Sciences Inc. (NASDAQ: GILD) short interest jumped 11.8% to 29.12 million shares. This followed a more than 26% increase in shares sold short in the previous period.

Illumina Inc. (NASDAQ: ILMN) saw short interest rise 2.2% to 28.37 million shares. That was the seventh consecutive period of increasing short interest. Short interest rose to 23.4% of the float.

Onyx Pharmaceuticals Inc. (NASDAQ: ONXX) shares sold short increased 2.1% to 6.10 million. The average daily volume was at its lowest level since March. Short interest was 9.5% of the float.

Pharmacyclics Inc. (NASDAQ: PCYC) short interest retreated 2.0% to 4.40 million shares. That was the lowest level this year. Days to cover doubled from the previous period to 12.

Regeneron Pharmaceuticals Inc. (NASDAQ: REGN) short interest rose about 4% to 5.18 million shares, essentially reversing the decline in the previous period. Short interest ticked up to 6.9% of the float.

Short interest in Vertex Pharmaceuticals Inc. (NASDAQ: VRTX) shrank 5.6% to 6.67 million shares. The average daily volume was at its highest since June.

VIVUS Inc. (NASDAQ: VVUS) short interest was 11.3% higher to 16.92 million shares. Days to cover rose to more than five. Short interest was 16.9% of the float.

To show how the sector has held up: the iShares Nasdaq Biotechnology (NASDAQ: IBB) ETF closed at $142.33 on the same date. Its current 52-week range is $92.15 to $148.54.

Trey Thoelcke