Three years have gone by since the region’s top biotech company was taken over by Eli Lilly, so it seemed like a good time to find out where all that talent migrated around the Northwest.

—Icos was once the great hope for Seattle biotech, but now three years have passed since the Bothell, WA-based company agreed to be sold to Eli Lilly for $2.3 billion. I wanted to find out where most of that scientific and business talent went in the wake of the mass layoffs that ensued, so I found a few Icosahedrons (as I’m told some of them like to be called) to help me put together a fascinating list of 270 alumni who have moved on to new opportunities.

—Seattle-based Trubion Pharmaceuticals (NASDAQ: TRBN) said this week that its co-founder and CEO, Peter Thompson, has resigned. He’ll be replaced on a temporary basis by Arch Venture Partners’ Steve Gillis while the company searches for a permanent replacement. I also recapped some of Trubion’s latest tribulations, to give a sense of what Thompson is leaving to his successor.

—Kirkland, WA-based OVP Venture Partners wanted a bigger piece of the original action in San Diego-based Fate Therapeutics, and now it grabbed some of that by leading a $30 million Series B venture round in the stem cell company. Carl Weissman, an OVP managing director and the CEO of Accelerator, will take a seat on Fate’s board as part of the deal.

—Seattle-based Oncothyreon (NASDAQ: ONTY) said it has decided to advance one of its experimental cancer drugs, PX-866, into mid-stage clinical trials next year. This is another sign of the company’s improving financial health, and its shift from cancer vaccines to cancer drugs, which I described in an in-depth feature earlier this year.

—Seattle-based NanoString Technologies earned a golden word of mouth endorsement this week from the Broad Institute of MIT and Harvard, which agreed to buy a couple of NanoString’s gene-expression tools to use them for a three-year research collaboration. Broad director Eric Lander, one of the big names in biology, said NanoString has “exciting” technology.

—People who work in Seattle’s global health cluster love to tell anecdotes about how certain projects can make a difference in people’s lives, but there hasn’t been as much effort to really catalog all the projects going on here and where they extend around the world. That was the goal of the Washington Global Health Alliance, a nonprofit led by Lisa Cohen, who wrote about it in this guest editorial. You can read more about the alliance in a profile I did of Cohen and her fledgling association in January.

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Seattle-based Oncothyreon (NASDAQ: ONTY) said it has decided to advance an experimental cancer drug into mid-stage clinical trials in the first half of 2010. The company plans to run two or more trials of PX-866, an oral pill made to block the PI3 Kinase pathway implicated in cancer cell growth. This shift in priorities, from cancer vaccines to cancer drugs which I profiled back in March, was applauded by analyst Simos Simeonidis at Rodman & Renshaw. “The company has not only been transformed into a well-run and very lean operation, but has literally been brought back from the brink of disaster,” Simeonidis wrote in a note to clients.

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Yesterday, we provided a rundown of the six hallmarks of a successful biotech company, according to Christopher Henney, the biotech pioneer who co-founded three of Seattle’s top biotechs—Immunex, Icos, and Dendreon. He made his remarks to an audience of about 100 investing professionals at the CFA Society meeting on Oct. 8 in Seattle.

Today, we follow up with the five red flags Henney advised investors to watch for when they evaluate biotech investments. Here’s what he singled out as warning signs:

—Top management without a scientific background. It’s not impossible for a biotech to succeed with a non-scientist at the helm, Henney said, but a smart investor must ask this non-scientific manager where the science comes from at the company. “The good answer would be, ‘It comes from my team of wonderful scientists who I recruited.’” A bad answer would be something like, “It comes from my scientific advisory board, which has two Nobel Laureates.” Henney added, “If you need to make an appointment to meet the guy who’s bringing you your science, then you don’t have much of a business.”

Henney wanted to make sure he wasn’t making a broadside attack against all non-scientific managers. One of his favorite biotech CEOs isn’t a scientist, but he adds, “You wouldn’t know it from talking to him.”

—No worries. An investor should ask what the management loses sleep over. “If they say, ‘I sleep like a baby,’ that’s a big red flag,” Henney said. All companies have their problems, and top management had better know them inside out.

—Hard-to-understand science. Ask the management to explain the science of their product in detail. “If they say something like the science is hard to explain, they can’t really explain it to you, that’s a big red flag.”

—Geographic remoteness. This provides some insight into Henney’s thinking on why two of the companies for whom he serves as chairman—Oncothyreon and AVI Biopharma—recently moved their headquarters from Edmonton, Canada, and Portland, OR, respectively, to the Seattle area. “You need a quorum of players,” Henney said. “You need access to talent, you need to be able to recruit people.” Seattle has more talent than the other places, and an ability to recruit more people, he said.

—Too many VCs. The board should be loaded with people that have experience running companies. “You shouldn’t have a board full of venture capitalists,” Henney said.

—Family members in key roles. “These aren’t family businesses. If you see a board dominated by siblings, or a couple of siblings in key management roles, I’d run, not walk.”

While those things might scare people away, Henney was hoping to drive home the message that investing in biotech actually isn’t that dangerous—if people know the right questions to ask. Despite the industry’s tough odds, he says he knows of people who make money in biotech year in and year out. He may have already been preaching to quite a few of the converted—I saw more than a few familiar biotech investors in the room—but Henney was hoping to light a spark for at least a few money managers to try their hand at something new.

“It’s a space that I wish more people would look at as an investment opportunity,” Henney said. “It can be really rewarding, and a lot of fun.”

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Seattle’s biotechnology industry is in significantly better financial shape than it was six months ago. The turnaround has been nothing short of amazing, thanks to a frantic run of dealmaking, cost-cutting, and remarkable clinical trial results that have made local companies some of the best-performing stocks this year on the NASDAQ.

Indeed, while our first analysis of the Northwest’s public life sciences companies, published last November, showed that six of 10 companies had less than a year’s worth of cash on hand at that point, only one—Seattle-based Northstar Neuroscience—actually folded.

And when we took a look at the most recent quarterly reports filed with the Securities and Exchange Commission by the 12 companies we’re following right now (11 of them public, one preparing for its IPO), we found that seven of them were actually in a stronger position at the end of June than they were at the start of the year. What’s more, three of the companies that were classified by this analysis as worse off (Seattle-based Trubion Pharmaceuticals and Targeted Genetics and Bothell, WA-based OncoGenex Pharmaceuticals) have recently struck partnerships or completed financings that aren’t yet reflected in the federal filings, but have clearly improved their financial futures.

Read on for a complete rundown of all 12 companies, listed in alphabetical order. To purchase a much expanded version of this report, in PDF format, click the “Add to Cart” button below. The expanded version, available for $95,* includes an assessment of each company’s financial position at the end of June compared to six months earlier, the projected length of time it can survive on its existing cash reserves, and an analysis of the strategic moves it has made to stay afloat in the current environment. Click here to see a sample entry. *Price is subject to change without notice.

We intend to repeat this analysis regularly to monitor the financial health of the life sciences companies we follow in San Diego, Seattle, and Boston. Please send feedback to editors@xconomy.com.

AVI Biopharma (NASDAQ: AVII)
Cash on hand: $20.2 million
Related Xconomy coverage:
“AVI Biopharma Bolts from Portland to Seattle to Tap Biotech Talent”
“AVI Biopharma Out to Reinvent Itself, Making RNA-based Drugs for Ebola and Other Nasty Things”
“Ebola Fighter AVI Biopharma Gears Up for Biodefense Contracts”

Cell Therapeutics (NASDAQ: CTIC)
Cash on hand: $12 million
Related Xconomy coverage:
“Cell Therapeutics Teeters on the Brink as Cash Runs Out on Promising Cancer Drugs”
“Cell Therapeutics Taps Stock Market Again, Seeks $40M or More”
“Cell Therapeutics Files Cancer Drug Application, In Nick of Time”
“Cell Therapeutics Lymphoma Drug Boosts Remissions, Shares Boom”
“Cell Therapeutics Reports Severe Cardiac Events in Drug Trial”
…Next Page »

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Quite a few publicly traded biotechs released quarterly financial statements this week, but we arranged some fascinating conversations with entrepreneurs and researchers to offset the necessary number-crunching.

—Seattle Genetics is having a breakout year, and one sure sign is that it has enrolled cancer patients in a clinical trial much faster than the industry norm. That was one big reason why the Bothell, WA-based biotech company (NASDAQ: SGEN) was able to sell 11 million new shares to investors this week, in an offering that raised a cool $118 million. Usually these offerings dilute the value of existing shares and drive down the stock price, but Seattle Genetics actually climbed 5 percent the following day.

—Amgen has spent five years researching biomarkers that might provide clues as to which cancer patients will respond to a drug, and which won’t. Much of the “personalized medicine” work, performed at research centers in Seattle and Cambridge, MA, was validated last week in the first big prospective clinical that showed patients with a normal form of the KRAS gene were more likely to benefit from taking panitumuab (Vectibix) than those with a mutated form.

—I had a fascinating conversation this week with Bonnie Ramsey, one of the world leaders in research and treatment of cystic fibrosis. Ramsey, who’s affiliated with Seattle Children’s Hospital and the University of Washington, talked in great depth about the surprising extent to which research has improved the outlook for CF patients over the past 30 years, and the significance of an emerging treatment from Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX).

—Stephen Friend is best known in Seattle as the founder of Rosetta Inpharmatics, and now he’s back in Seattle, dreaming big again. Friend described his vision, and progress during the early days, at the nonprofit genomics collaborative he’s leading called Sage Bionetworks.

—We published a couple of guest editorials this week that are of interest to biotechies. The first was from Jim Thomas, a vice president at Amgen in Seattle, on how he says lawmakers can provide a way for “biosimilars” to enter the marketplace without undermining incentives for companies like his to develop innovative new medicines. The next piece on national policy was from Ryo Kubota, CEO of Bothell, WA-based Acucela, who advised policymakers not to reform healthcare in any way that dampens the entrepreneurial spirit that makes America the best place for developing new drugs.

—Seattle-based Dendreon is starting to branch out across the U.S. map. The company (NASDAQ: DNDN) confirmed this week that it is planning to add two new manufacturing plants for its prostate cancer drug, sipuleucel-T (Provenge) in the greater Atlanta area, and in Orange County, CA. The company also reported that it had $287 million in cash and investments when the second quarter ended on June 30, helped along by a $227 million infusion it got from investors after Provenge passed its pivotal clinical trial in April.

—AVI Biopharma, the RNA-based drug developer that’s moving its headquarters from Portland, OR, to Bothell, WA, said it ended the second quarter with $20 million in cash. AVI (NASDAQ: AVII) has been strengthening its financial position for months, and predicted that it will pull together more funding this year from governments and other sources.

—Seattle-based Oncothyreon (NASDAQ: ONTY) said it ended June with $22.7 million in cash, which—hold on here for a double-take—was actually $3.5 million more than it had at the beginning of the year. The company has fattened up its balance sheet with another $14 million through a stock offering this month, giving it more breathing room in its quest to develop cancer drugs.

—The financial prospects looked a lot dimmer this week for Seattle-based Targeted Genetics (NASDAQ: TGEN). The gene therapy stalwart, which has been warning of its possible demise since May, said this week that it “must raise additional capital” if it is going to remain in business beyond the end of this month.

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Oncothyreon, the Seattle-based developer of cancer drugs, said today in its quarterly financial report that it had $22.7 million in cash and investments at the end of June, about $3.5 million more than it had at the beginning of the year. Earlier this month, it raised an additional $14 million through a stock offering—which is more than the $12 million total it expects to spend on operations for all of 2009. Oncothyreon (NASDAQ: ONTY) has been buoyed lately by clinical trial results that showed patients with lung cancer who took Oncothyreon’s Stimuvax treatment had long-term tumor responses with minimal side effects.

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The big news of the week was Microsoft’s sale of Razorfish to Publicis (see directly below), but there were a few other important deals in software, biotech, and energy.

—Microsoft’s online advertising subsidiary, Seattle-based Razorfish, was bought by French marketing firm Publicis for approximately $530 million, as Bob reported. The payment is expected to include cash and Publicis Groupe treasury shares. In addition, Microsoft and Publicis have entered into a five-year strategic alliance whereby Publicis clients can purchase display and search advertising from Microsoft on favorable terms. Microsoft (NASDAQ: MSFT) originally acquired Razorfish in its 2007 purchase of aQuantive.

—Bellevue, WA-based Confirma, a medical imaging software firm, has been acquired by Merge Healthcare, a Milwaukee, WI-based health IT provider, for about $22 million, as Eric reported. Merge will incorporate Confirma’s MRI software into its IT offerings for doctors.

—Vancouver, BC-based Tekmira (TSX: TKM) formed a two-year partnership with Cambridge, MA-based Alnylam Pharmaceuticals to develop new particles to deliver RNA-interference drugs to diseased cells deep in the body, as Ryan reported. Financial terms of the deal weren’t given. Alnylam is funding the research effort and has exclusive rights to new discoveries, while Tekmira can use the discoveries for some of its own RNAi treatment programs.

—Seattle-based EnerG2 won $21.3 million in federal stimulus funding from the U.S. Department of Energy to build a new manufacturing plant in Albany, OR. The University of Washington energy-storage spinout is developing nano-scale materials to make better ultracapacitors for electric and hybrid vehicles and other applications.

—A few more terms of the Microsoft-Yahoo search deal, in which Yahoo will use Bing as its search engine and will control ad sales for five years, were spelled out in a filing with the SEC. Microsoft (NASDAQ: MSFT) will pay Yahoo $50 million a year for three years to cover transition and implementation costs. It will also hire 400 Yahoo employees, plus another 150 to assist with the transition. Yahoo (NASDAQ: YHOO) can opt out of the deal if it isn’t approved within a year, or if Microsoft and Yahoo’s combined share of the search market dips below an undisclosed percentage.

—Seattle-based Oncothyreon (NASDAQ: ONTY), a developer of cancer drugs, raised $15 million by securing commitments from investors to buy new shares and warrants, as Luke reported. Last week, the company said a small group of lung cancer patients showed long-lasting responses after taking Stimuvax, the immune-boosting vaccine therapy Oncothyreon is co-developing with Germany-based Merck KGaA.

—Seattle-based WatchGuard Technologies, a network security company, acquired Toronto-based BorderWare Technologies, an e-mail and Web security firm, as Eric reported. Financial terms were not given. WatchGuard plans to use BorderWare’s technology to make its security software more comprehensive and competitive.

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Some of the lesser-known names in Seattle life sciences made some noise this week, just when we here at the Xconomy biotech desk thought things might slow down a tad in the dog days of summer.

—AVI Biopharma (NASDAQ: AVII), the Portland, OR-based maker of RNA-based therapies, is now getting a new tagline as the Bothell, WA-based maker of RNA-based therapies. This company, led by CEO Les Hudson and chairman Christopher Henney, decided to move its headquarters to the Seattle area to tap into this region’s deeper biotech talent pool as it advances drugs through clinical trials for Duchenne Muscular Dystrophy, Ebola and Marburg virus, and other tough-to-treat conditions.

—Seattle-based Dendreon (NASDAQ: DNDN) has one of the most avid fan bases in the biotech industry, but few people realize it has a low-key neighbor across the lake in Bothell, WA, that has also produced some very impressive results against prostate cancer this year. Scott Cormack, the CEO of OncoGenex Pharmaceuticals (NASDAQ: OGXI) told me this week in an exclusive feature that he’s fielding “competitive” partnership proposals from a number of Big Pharma companies that want a piece of its action.

—Sometimes you have to strike while the iron is hot in biotech, and that’s what Seattle-based Oncothyreon did this week. The company (NASDAQ: ONTY) said on Monday that some follow-up data suggests its immune-boosting therapy for lung cancer was able to generate long-term tumor responses without causing any serious side effects. This boosted the stock 26 percent on Monday. One day later, Oncothyreon CEO Bob Kirkman seized on the newfound demand for his shares by selling some more shares, and refilling the company coffers with $15 million.

—Scientists over at PATH, the Seattle-based nonprofit that works to improve health in poor countries, were pumped up about a new formula they developed that was shown to protect hepatitis B vaccine from getting damaged by hot or cold temperatures. This work, financed by the Bill & Melinda Gates Foundation, only adds one-tenth of a penny to the cost of a vaccine dose, and PATH says it ought to work just as well for a wide range of vaccines.

—Seattle-based ZymoGenetics (NASDAQ: ZGEN) said this week that second-quarter sales started to pick up, as expected, for its sole marketed product for surgical bleeding. The company reported $6 million in sales of recombinant thrombin (Recothrom), which puts it on pace to reach its full-year sales forecast of $25 million to $35 million.

—Buddhists and biotechies don’t usually go hand-in-hand, but this sort of unlikely alliance might yield some big future opportunities for biomedical entrepreneurs in mental health, according to Seattle’s Ben Shapiro. He’s the former executive vice president of worldwide research at Merck, who has been exposed to these ideas through serving on the board of the nonprofit Mind & Life Institute in Boulder, CO.

—Does the laid-back Northwest lifestyle keep this region from reaching its full potential as a dynamic hub of innovation and entrepreneurship? Janis Machala, the champion of startup creation at the UW TechTransfer office, stirred the pot last week with some thought-provoking comments about this idea at an event hosted by the Washington Biotechnology & Biomedical Association. This generated a lot of comments, many of them quite thoughtful, at the tail end of the story.

—Seattle-based Amnis, the maker of an instrument for high-speed imaging of cells, said it closed on the first $839,000 out of a $1.5 million round of financing. The company, which has seen rising demand for its second-generation product, raised the cash from CVF LLC, MedVenture Associates, and OrbiMed Capital, and angel investors.

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Oncothyreon (NASDAQ: ONTY), the Seattle-based developer of cancer drugs, said today it has raised $15 million by securing commitments from investors to buy new shares and warrants. The financing came one day after demand surged for Oncothyreon sales when it said a small group of lung cancer patients had long-lasting responses after taking Stimuvax, the immune-boosting vaccine therapy Oncothyreon is co-developing with Merck KGaA. Oncothyreon’s main business these days is actually in developing cancer drugs, not vaccines, as described in this March profile on Xconomy.

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Oncothyreon (NASDAQ: ONTY), the Seattle-based developer of cancer treatments, said today its Stimuvax therapy showed a long-lasting response and was well-tolerated in a long-term follow-up study. Ten of the 16 patients with non-small cell lung cancer, who were followed two to 8.2 years, were still alive as of April with no evidence of their disease spreading after they got Stimuvax. The treatment, being co-developed with Germany-based Merck KGaA, was well-tolerated during long-term use, researchers said. Data were presented Saturday at the World Conference on Lung Cancer in San Francisco.

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We had a smorgasbord of life sciences news this week, featuring updates on Northwest companies developing drugs, devices, vaccines, and scientific instruments.

—Cell Therapeutics has bet the company on pixantrone for non-Hodgkin’s lymphoma, and this week it hit one of its key goals for the year, by turning in its new drug application to the FDA before the end of June. The Seattle company (NASDAQ: CTIC) fell short in its bid to unload all of its $118.9 million in debt, instead getting rid of about $52.9 million of its liabilities.

—Seattle-based Targeted Genetics (NASDAQ: TGEN) has been in survival mode for some time now, and this week it said it will cut its staff down to as little as 10 to 15 employees. The company hopes the cuts will stretch its cash reserves into August, giving it enough time to close a deal to keep the company from closing its doors.

—Sanofi-Aventis CEO Chris Viehbacher traveled to Seattle last week for a global health meeting, and took time to offer a glimpse into his strategy to make the Paris-based drugmaker a bigger player in global health. He also shared his perspective on partnerships with biotech companies.

—Seattle-based Amnis shared its story of how it has rolled out a second-generation version of its sophisticated lab instrument, which combines properties of a microscope with a high-speed cell counter called a flow cytometer. Orders are building up, and this could be the company’s first full year of profitability after a decade in business, says CEO David Basiji.

—Oncothyreon (NASDAQ: ONTY), the Seattle-based developer of cancer drugs, said that its German partner, Merck KGaA, started up a pivotal trial of its immune-boosting therapy, Stimuvax. It’s the second big trial of this drug, which is already being tested against lung cancer. If it’s successful, Oncothyreon will stand to get royalties on product sales.

—AVI Biopharma (NASDAQ: AVII), the Portland, OR-based developer of RNA-based therapies, said it is working on a contract to develop swine flu drugs.

—Bothell, WA-based Mirabilis Medica told its story about how it is developing the first use of high-intensity therapeutic ultrasound waves to treat uterine fibroids, as a non-invasive alternative to surgery.

—MDRNA (NASDAQ: MRNA), the Bothell, WA-based developer of RNA interference drugs, gained full rights to a technology license from Denmark-based RiboTask to make its treatments more stable, and less likely to spark inflammation.

—Global health funding has quadrupled over the past two decades, and while a lot of this new money comes from foundations like the Bill & Melinda Gates Foundation, the biggest financier of this work is now the U.S. taxpayer, according to this intriguing new study from the University of Washington.

—Anthony Fauci, the head of the division of the National Institute of Allergy and Infectious Diseases, called for a transformative research agenda to fight tuberculosis, like the country did for HIV in the 1980s, during a stop last week at the Pacific Health Summit in Seattle.

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Oncothyreon, the Seattle-based developer of cancer drugs, said today that its partner, Germany-based Merck KGaA, has started a pivotal clinical trial of the Stimuvax immunotherapy for breast cancer. The study will seek to enroll 900 patients in 30 countries, who are randomly assigned to get Stimuvax or a placebo. Oncothyreon (NASDAQ: ONTY) has shifted most of the responsibility for Stimuvax to Merck KGaA, although it still stands to receive a “double digit” percentage royalty on future sales if this ever becomes a marketed product. Stimuvax is also being tested in a pivotal trial for lung cancer.

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Lots of news from the world of cancer research came out over the weekend at the American Society of Clinical Oncology meeting in Orlando, FL. There was a lot of impressive data coming out of Northwest companies (although most of it is still quite preliminary), so here’s a quick recap to catch up. The conference, which drew 30,000 cancer specialists, continues today and tomorrow.

—OncoGenex Pharmaceuticals. The Bothell, WA-based biotech company was heralded by a Rodman & Renshaw analyst as one of ASCO’s “sleeper hits” heading into the meeting, so a lot of inquiring minds flocked to its presentation. The company reported that its drug, OGX-011, in combination with standard docetaxel chemotherapy, was able to help men with terminal prostate cancer live a median of 6.9 months longer than if they got docetaxel alone.

Framed a little differently, this drug lowered the risk of death during the study by 39 percent. This is known as the hazard ratio, an important statistical measure of a drug’s benefit. For comparison, Seattle-based Dendreon showed its much-heralded prostate cancer drug, sipuleucel-T (Provenge), was able to lower the risk of dying by 22.5 percent when using this statistical measurement.

Of course, the OncoGenex result needs to be taken with a grain of salt because the trial only had 82 patients. OncoGenex will need money and clinical development manpower from a partner to really confirm this result is real in pivotal clinical trials. CEO Scott Cormack has been so busy trying to get those stars to align for the company that he told me before the conference, “I might fall over.” (He was exaggerating a little for dramatic effect, but he did sound a bit tired on the phone.)

—Billionaire Paul Allen doesn’t get much attention for his biotech investing, but one company he helped get started in 2005, Brisbane, CA-based BiPar Sciences, dropped a “bombshell” at ASCO. The company showed that when its drug is combined with chemotherapy, it was able to shrink tumors, slow down their spread, and help people live longer, without adding any new side effects. This was seen in a 116-patient clinical trial of women with an aggressive form of breast cancer known as the “triple negative” variety.

The data was compelling enough to earn a coveted plenary presentation in front of thousands of doctors at ASCO, and prompted Paris-based Sanofi-Aventis to pay $500 million to buy the company last month. That payday was enough to earn Allen a windfall proft of an estimated $100 million, after he invested just $13 million over the past four years.

This result is so impressive that Powel Brown, a cancer prevention researcher at the Baylor College of Medicine told Bloomberg News that BiPar’s drug and another in its class represent “the biggest story in breast cancer, by far, and it’s going to be a huge bombshell.” The result is so positive, he predicted the drug would be FDA approved in a year or two.

—Seattle Genetics offered some more evidence, albeit quite preliminary, that suggests it may have a powerful new drug for Hodgkin’s disease and …Next Page »

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Last Wednesday night, the top dealmaker at Seattle-based Calistoga Pharmaceuticals got a tip that one of his rivals was on the verge of striking a huge deal. Cliff Stocks, the chief business officer, told CEO Carol Gallagher he was hopeful the rumor was true—that some Big Pharma company would pay a fortune for an experimental cancer drug in their class. That would generate lots of buzz for their whole field of biology on the eve of the American Society of Clinical Oncology (ASCO) meeting, an annual extravaganza for cancer drug development.

Thursday morning, Stocks’s wish came true. South San Francisco-based Exelixis announced a partnership with Paris-based Sanofi-Aventis that brought $140 million in upfront cash to the smaller company, and potential milestone payments worth more than $1 billion. For all that loot, Sanofi gets the right to co-develop a drug that blocks one of the hottest targets on cells in cancer biology, the PI3 kinase. The Exelixis drug is still in the earliest stage of clinical trials, the same phase Calistoga is in with its own compound that’s being targeted at different tumor types.

“I was sitting in the office with Carol and said, if Exelixis can close its deal before ASCO, that will make us the darling of the conference,” Stocks says. “It puts a very big spotlight on the PI3 kinase.”

Calistoga already raised its profile by a couple notches earlier this month when it raised $30 million in a second round of venture capital from Frazier Healthcare Ventures, Alta Partners, Three Arch Partners, and Amgen Ventures. The company is facing a lot of serious competitors in its category, including Novartis, Roche, and GlaxoSmithKline in the Big Pharma crowd, and Oncothyreon, Semafore Pharmaceuticals, and Intellikine in the biotech startup space. Calistoga claims to be carving out a niche within the niche, by aiming its drugs at an even more specific type of the PI3 kinase, known as the delta isoform, which it hopes will cause it to have compelling effectiveness for blood cancers, without hitting similar structures on cells that might lead to unwanted side effects. Other drugs that block more variations of PI3 kinase are thought to have greater use against solid tumors, Stocks says.

Some data to support Calistoga’s hypothesis is being presented at the ASCO meeting in Orlando, FL, today, but it’s still very preliminary. The Calistoga drug, CAL-101, showed an ability to partially shrink tumors …Next Page »

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It was a relatively light week for deals in the Northwest, perhaps owing to the holiday weekend. But there was still action in biotech, marketing software, and alternative energy.

—Kennewick, WA-based Infinia raised $14.1 million in debt financing out of a $50 million offering. The company, which is backed by Vulcan Capital, Khosla Ventures, and other investors, develops solar power generation technology that uses free-piston Stirling engines and power systems.

—Luke reported on the story behind Vulcan Capital’s investment in BiPar Sciences, the Brisbane, CA-based cancer biotech firm that was recently sold to Paris-based Sanofi-Aventis for $500 million. Vulcan led the seed financing round for BiPar back in 2005, and pumped $13 million in capital into it through its lifetime. The sale will earn Vulcan more than $100 million in cash, which managing director Steve Hall says has helped put the firm in the top 10 percent of all U.S. venture funds over the past five years. BiPar’s drug, BSI-201, could be a fundamental advance against breast cancer, ovarian cancer, and other tumors.

—Bellevue, WA-based Visible Technologies, a startup that makes software for online brand reputation management and customer service, raised $6 million in debt financing. Visible Technologies was founded in 2003, and is backed by Bellevue-based Ignition Partners and New York-based WPP.

—Seattle-based Survey Analytics, a marketing and customer relations software startup, scored a partnership with the White House to power the Open Government Dialogue website, which seeks to solicit ideas from the public on how the government can be more transparent, participatory, and collaborative. Financial terms of the deal were not given. Survey Analytics, which has been bootstrapped since 2004, has developed a software platform for hosting and managing feedback communities called IdeaScale.

—Luke reported that Seattle-based Uptake Medical, which is developing minimally invasive technology to treat emphysema, raised $3.1 million in a debt financing. Uptake makes a device that seals off access to diseased parts of the lung where air gets trapped. The technique does not leave an implantable device behind. The latest funding adds to the $3 million bridge financing the company raised for its clinical trials in December.

—HealthUnity, a Bellevue, WA-based maker of software for connecting healthcare IT systems, raised $2 million out of a $4 million equity financing, Luke reported. The company was founded in 2004 and is led by CEO Prem Urali, a former group manager in the BizTalk Server division at Microsoft.

—Luke also reported that Oncothyreon, a Seattle-based developer of cancer drugs, received commitments from several investors to buy new shares and warrants for $11.1 million. The deal was underwritten by Boenning & Scattergood. Oncothyreon (NASDAQ: ONTY) has been diversifying its pipeline, and has gotten renewed interest from investors in its cancer immunotherapy program, since Seattle-based Dendreon has had recent success in that field.

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Seattle’s biotech companies must be trying to get a lot done before Memorial Day weekend, because we had reports on deals, layoffs, and big strategic moves.

—Dendreon (NASDAQ: DNDN) has spent years trying to prove that its immune-boosting therapy for prostate cancer really works, and now it has to show it can make enough of it to meet coming demand. The company has just one commercial manufacturing facility, and it is rapidly trying to scale it up over the next 14 months so it can pump out a maximum of $500 million to $1 billion worth of Provenge each year, says CEO Mitchell Gold.

—Archus Orthopedics, the Redmond, WA-based developer of spinal implants that help people remain mobile after back surgery, has laid off most of its employees and significantly scaled back operations to conserve its remaining cash.

—Accelerator, the Seattle-based investment vehicle for biotech startups, bankrolled its 10th company, called Xori. The company raised $2.1 million out of a $4.5 million round, toward a goal of developing technology that will make antibody drugs much more quickly, and with better properties, than existing methods.

—Cancer drugs represent one of the most intense fields of interest in biotechnology, so it shouldn’t be a surprise that a lot of Seattle biotech companies have news coming out at this year’s meeting of the American Society of Clinical Oncology from May 29 to June 2. ASCO posted brief online summaries of a lot of clinical trial data to be presented, and I combed through the most interesting abstracts from companies in the Northwest.

—Bionavitas, a Redmond, WA-based developer of light technology to help algae grow much more efficiently, explained its strategy in this feature story. It sees more promising markets in using algae to make food additives and for toxic cleanup—at least in the early days—than for biofuels.

—I heard about an intriguing new startup called Presage Therapeutics, a spinoff from the Fred Hutchinson …Next Page »

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