For those of you tracking the growing numbers of huge deals between the Bay Area’s formidable array of biotech companies and those gargantuan drug firms known as Big Pharma, here’s yet another:

Portola Pharmaceuticals of South San Francisco and New Jersey-based drug powerhouse Merck announced Thursday that they will collaborate on developing Portola’s anticoagulant drug candidate, betrixaban.

The payoff for Portola: a cool $50 million initially, with the possibility of $420 million more if certain milestones are met for getting the drug onto the market. In addition, Portola could earn double-digit royalties on worldwide sales of the drug, assuming the government approves its commercialization..

When Roche first began maneuvering to take complete control of Genentech, the air was thick with speculation that the Swiss drug giant’s plans would force out some of the South San Francisco company’s top talent.

Sure enough, upon completing the deal last month, Roche announced that Susan Desmond-Hellmann, Genentech’s president of product development, would give up that job midyear and thereafter be an adviser.

But Desmond-Hellmann has landed on her feet, though at somewhat of a pay cut. On Thursday was named chancellor of the University of California at San Francisco, effective Aug. 3.

A former medical intern and assistant professor at the university, she will earn $450,000 a year as chancellor. Her compensation at Genentech included $725,666 in base pay and $1.3 million in incentives other than stock-based compensation, according to UCSF.

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The $1.4 billion deal that Foster-City based Gilead Science’s announced March 12 to buy CV Therapeutics of Palo Alto has triggered a class-action shareholder lawsuit.

The legal action, which CV Therapeutics disclosed today in a filing with the U.S. Securities and Exchange Commission, was filed March 19 in Santa Clara County Superior Court by a group called Superior Partners. It accuses CV Therapeutics and its board of failing in their fiduciary duty to stockholders.

Among other claims, the suit alleges that CV Therapeutics’ board limited the number of potential buyers for the company and had a conflict of interest  because they will receive monetary compensation from the sale.

CV Therapeutics denied the claims.

Genitope, the beleaguered Fremont biopharmaceutical that halted development of its experimental MyVax treatment for non-Hodgkin’s lymphoma last March after the Food and Drug Administration said at least one more clinical trial was needed, saw its largest shareholder sell off its 8.1 million stake in the company for $1 on Wednesday, according to a regulatory filing made today.

CPMG, the Dallas-based investment firm, said in a filing Friday that it sold all 8,125,370 shares it controlled to Alan Powers for a total of $1. (And yes, we plugged that into a spreadsheet and got a per-share price of $0.00000012.)

Genitope shares were delisted from the Nasdaq market back in September, a move the company didn’t fight. In a filing that month, the company said it had cash and cash equivalents of approximately $1 million as of Aug. 31, and marketable securities worth an $476,000.

The company had sold or otherwise disposed of its equipment and vacated one of its two buildings in Fremont, saying it planned to vacate the second building “in the very near future”, leaving it with a “remaining rental obligation” of $97.9 million.

It was also down to a single employee, Chief Executive Dan Denney.

Aryx Therapeutics, the Fremont biopharamaceutical whose shares were slammed last July when Procter & Gamble pulled out of a partnership in developing Aryx’s drug to treat chronic constipation and abdominal pain, said today that it had raised $21.6 million through a private placement of about 9.6 million shares, along with the sale of warrants good on a potential 2.9 million additional shares.

The purchase price for the new shares was pegged at $2.20, the closing price for the stock the day before the announcement. Among the investors were existing stockholders, including entities affiliated with MPM Capital and OrbiMed Advisors, which already owned about 20 percent and 12 percent, respectively, of Aryx shares before the private placement. The warrants, which sold for 12.5 cents each, give the owners the right to buy shares of Aryx over the next five years for $2.64.

Aryx also released earnings for its third quarter, which were bolstered by  the last nonrefundable “upfront license fee” paid to it by P&G as a result of its termination of its collaboration agreement. Aryx said it had $33.8 million in cash and short-term investments as of Sept. 30, before today’s infusion, which will net the company $20.7 after agent fees are paid. Aryx says it now has “sufficient funds to finance operations through the first quarter of 2010 even in the absence of the completion of any corporate alliances for its programs.”

Shares of Aryx, which touched a 52-week low of $2.05 during trading on Tuesday, shot up about 30 percent in mid-day trading today. Prior to today they had lost nearly two-thirds of their value so far this year.

XenoPort of Santa Clara and its partner said Monday they withdrew their new drug application for Solzira, its time-released treatment of moderate-to-severe restless drug syndrome after the Food and Drub Administration asked for modifications to a study.

The news sent shares of XenoPort down $5.12, or 13 percent, to $34.44, although during the day they slumped even further, touching a 52-week low of $30.10 at one point.

The FDA specifically requested that the data in a single study be “reformatted”. The company’s partner in the drug study, GlaxoSmithKline, also said it will conduct a review of other “trial data set taking this input into account.”

Xenoport said that the withdrawal doesn’t relate “to the content” of new drug application and that GlaxoSmithKline intends to resubmit the application “quickly” once its work is complete.

In the meantime, Xenoport won’t receive a $23 million milestone payment associated with acceptance of the application by the FDA.

AP Pharma, the Redwood City specialty pharmaceutical company, has begun rationing its resources to ensure its survival “in response to the deterioration of the overall economic environment and the financial markets”, the company said in a release early Wednesday.

The steps include putting development activities on hold for all of its drug candidates except the one for treatment of chemotherapy-induced nausea and vomiting that recently completed its Phase 3 trial, along with a 35 percent reduction in its workforce. That translated into 18 layoffs that will cost the company an estimated $300,000 in fourth quarter charges.

“In light of the current economic uncertainties and volatile capital markets, we are taking these timely and meaningful actions to ensure the company’s ongoing viability,” said AP Pharma’s chief executive, Ronald Prentki, in a statement. “The decision to reduce our workforce was a difficult yet necessary one. On behalf of the A.P. Pharma Board of Directors, I would also like to express a sincere ‘thank you’ to our colleagues who are affected by this decision. We wish them well in their future professional endeavors.”

No word of any pay cut for Prentki, who makes $450,000 a year and has a bonus opportunity targeted at half that amount, and who also got a huge option grant when he joined the company back in July.

StemCells (Nasdaq:STEM), the Palo Alot biotech company, said Thursday that preclinical results for its product candidate HuCNS-SC, derived from human neural stem cells, were able to protect the retina from progressive degeneration when transplanted into lab rats.

“The HuCNS-SC cell has proven to have very robust survival, preserving vision in our rat model at time points beyond six months,” said Raymond Lund, a researcher and professor at the Casey Eye Institute at Oregon Health & Science University. “These data are very encouraging and suggest cell-based therapies for retinal degeneration can be a viable treatment approach.”

Shares of StemCells rose as much as 22 cents, or 22 percent, in Thursday trading after its news was released.

In a move to preserve cash, Maxygen said Wednesday it plans to cut its staff by 30 percent in the first quarter next year, a move that will leave it with some 65 employees when it is completed. The Redwood City biotechnology company said it will stage staggered terminations during the quarter beginning in January in both its operational and general-and-administrative departments. The company said it would provide “outplacement support and a severance package for each affected employee.”

Maxygen has also “retained the investment bank Lazard to assist in exploring strategic options, including a sale or disposition of one or more corporate assets, a strategic business combination, or other transactions.”

The company says it is scaling back its spending on its MAXY-G34 drug candidate, intended to treat chemotherapy-induced neutropenia, one of the most common side effects caused by chemotherapy that can quickly develop into a life-threatening situation. Maxygen said it will postpone Phase III manufacturing for the drug “until it identifies a partner who can share manufacturing costs.”

Affymetrix founder and chief executive Stephen P.A. Fodor (pictured) “will begin to transfer his CEO responsibilities to Kevin M. King, president of Affymetrix,” the company announced Wednesday afternoon. Fodor will assume a new role as full-time executive chairman of the company’s board. King will take over the top job on New Year’s Day.

The announcement comes on the heels of preliminary results released last week for its most recent quarter that estimated sales of about $75 million, down from the $91.5 million most analysts were expecting, an 18 percent miss. The company cited “increased competition for academic research funding and continued softness in industrial spending.”

Fodor founded Affymetrix to commercialize formulas he and his colleagues developed in the late 1980s that provide a platform for acquiring, analyzing and managing complex genetic information in order to improve the diagnosis, monitoring and treatment of disease.

Fodor, a native of Seattle, received his B.S. in Biology and M.S. in Biochemistry from Washington State University and his Ph.D. in Chemistry at Princeton University. From 1986 to 1989, he was a National Institutes of Health postdoctoral fellow at The University of California, Berkeley, working on time-resolved spectroscopy of bacterial and plant pigments.

In 2001, Fodor founded Perlegen, a Mountain View biotech company providing diagnostic tools to identify genetic differences and help understand human genetic variability.

Which brings to mind a quote from Mark Twain that Fodor used to end a talk he gave in 2004 at the In 2001, Fodor founded Perlegen, a Mountain View biotech company providing diagnostic tools to identify genetic differences and help understand human genetic variability.

Which brings to mind a quote from Mark Twain that Fodor used to end a commencement talk he gave in 2004 before the College of Chemistry at Cal:

“You are what your parents make you, but it’s your own fault if you stay that way.”