Drug development programs got extended at two San Diego life sciences companies, while others had some good news on the fund-raising front. We wrap it all up for you here.

—Fate Therapeutics, a startup working to supply “industrialized” stem cells for the pharmaceutical industry without using embryos, said it raised $30 million in venture capital. That brings the total amount raised by the San Diego-based company to about $50 million since its inception two years ago.

—Cadence Pharmaceuticals (NASDAQ: CADX) said the FDA has delayed its review of the San Diego company’s intravenous pain reliever by three months, to Feb. 12. Cadence provided additional data to the FDA after an advisory panel raised concerns about liver damage from excessive doses of acetaminophen. But Cadence said it remains confident it will win FDA approval of its drug, which contains acetaminophen.

—Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) and its Big Pharma partner, Genzyme (NASDAQ: GENZ), have extended the timeline for their much-anticipated cholesterol-lowering drug by nearly a year. The companies reported encouraging results from a clinical trial, but noted that four out of 34 patients saw their liver enzymes increase to three times normal, a sign of potential liver damage. The companies plan to tinker with the dose of the injectible drug in future trials.

—San Diego-based NextImage Medical, a developer of a Web-based system for scheduling and managing diagnostic imaging services, reporting raising $5 million in a venture round led by Chrysalis Ventures of Louisville, KY.

—San Diego-based Altair Therapeutics, a company developing inhalable drugs to block inflammatory proteins involved in asthma and other respiratory diseases, has closed on the second part of a Series A venture financing, bringing the total amount raises this year to $17 million.

—San Diego-based Cyntellect, which makes work stations used by biotechs for cell analysis, purification, and processing, raised $15.5 million so far in a secondary round that aims to raise a total of $18.6 million, according to a recent regulatory filing.

—GenVault, a Carlsbad, CA-based company that markets dry-storage technologies that allow scientists to store biological samples at room temperature, said it expects to break even by the end of next year. The startup has raised about $32 million so far.

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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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Believe it or not, the troubles besetting Genzyme (NASDAQ: GENZ) were not the only life science stories coming out of the Boston area this week, although they sure grabbed most of the attention. So let’s get them all out of the way first:

—On Friday the 13th, the FDA said bits of steel, rubber, and fiber had been detected in vials of five major enzyme replacement drugs made by Genzyme, all manufactured at the company’s troubled Allston Landing plant in Boston. But the agency said that the problem affected only about 1 percent of Genzyme’s products, and that no serious side effects have been reported. In a statement, Genzyme said a review of its safety database “has not identified any safety concerns to suggest that patients treated with Genzyme products have been exposed to foreign particles.”

—On Monday the 16th, Genzyme got word that the FDA won’t approve its application to market its drug alglucosidase alfa (Lumizyme), a proposed treatment for Pompe disease, until the company fixes deficiencies at the Allston Landing facility, where it wants to mass-produce the drug in large batches. But Genzyme continues to make the drug in smaller batches and sell it under the name Myozyme.

—On Tuesday the 17th, shares in Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) fell 16 percent after Isis and Genzyme released the full details of joint clinical trials of mipomersen, a cholesterol-lowering drug that the two companies see as a potential successor to Pfizer’s blockbuster atorvastatin (Lipitor). The drug lowered “bad” LDL cholesterol levels by 25 percent on average, but in several patients it raised liver enzymes to triple their normal levels, indicating potential liver damage. In new trials, Genzyme and Isis say they’re going to study what side effects, if any, mipomersen causes at different doses.

—On Wednesday the 18th, Genzyme said it had decided to scrap an experimental kidney disease drug, an “advanced phosphate binder,” after a clinical trial of 349 patients showed that it was no better at ridding phosphorus from the blood of dialysis patients than Genzyme’s existing drug sevelamer carbonate (Renvela). Genzyme’s two existing phosphate binders, which generate $850 million per year in sales, go off-patent in 2014, and the company is anxious to find a next-generation treatment.

—In non-Genzyme news, Chelmsford, MA-based Zoll Medical (NASDAQ: ZOLL), which makes cardiac defibrillators and other emergency medical devices, released a CPR training app for the Apple iPhone and iPod Touch that Ryan called the “most advanced” he’s seen. The “PocketCPR” app, which provides visual and audio instructions on proper CPR technique, could help lower the death toll from sudden cardiac arrest, which kills 300,000 Americans each year.

—Alkermes (NASDAQ: ALKS) of Cambridge, MA, said a 250-patient clinical trial showed that its drug naltrexone (Vivitrol), which is already used as a treatment for alcoholism, was more effective than a placebo at treating dependence on opioids such as heroin. The company plans to ask the FDA to approve this new use of the drug next year.

—Waltham, MA-based Polaris Venture Partners contributed to a $30 million Series B venture financing round for San Diego-based stem cell startup Fate Therapeutics. Kirkland, WA-based OVP Venture Partners led the deal, which also involved Arch Venture Partners, Venrock Associates, Astellas Venture Management, and Genzyme Ventures. Fate has collected about $50 million in venture funding all told.

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Just when I thought venture deals, especially for software and tech companies, had headed south for the winter (or longer), the Northwest erupted with a slew of financings in the past week.

—But first, some serious biotech. Kirkland, WA-based OVP Venture Partners led a $30 million Series B round for Fate Therapeutics, a San Diego-based stem cell company with ties to the University of Washington, as Luke reported. Existing investors Arch Venture Partners, Polaris Venture Partners, and Venrock Associates also participated in the funding, as well as three strategic corporate investors—Astellas Venture Management and Genzyme Ventures were named.

—Seattle-based DocuSign, a maker of software to automate and control the process of electronic signatures, received a strategic investment from Second Century Ventures, the VC fund of the National Association of Realtors. The funding amount was undisclosed, but the money will be used to accelerate and extend DocuSign’s efforts with real estate customers.

—Beaverton, OR-based Avnera pulled in an $8 million equity round from undisclosed investors, according to a regulatory filing. The company’s previous investors include Bessemer Venture Partners, Redpoint Ventures, Jafco Ventures, Intel Capital, and DAG Ventures. Avnera was founded in 2004, and designs novel chips for wireless audio applications.

—Seattle stealth startup Doxo raised $5.25 million in equity financing, according to a regulatory filing and media reports. The investors were not disclosed, but David Feinleib of Mohr Davidow Ventures was listed on the SEC form as a director.

—Bellevue, WA-based Enroute Systems, a developer of software that helps companies manage their parcel-shipping logistics, closed a Series A funding round worth $810,000 from Keiretsu Forum, Zino Society, Puget Sound Venture Club, and angel investors. Next up, Enroute is looking …Next Page »

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San Diego serial entrepreneur Michael Robertson is going to have to find something else to do now that Gizmo5, the VoIP (voice-over-Internet-protocol) company he founded in 2003, has become part of a certain search giant to the north. We have that news and more.

—Google confirmed that it’s buying San Diego-based Gizmo5, a six-year-old company that provides Internet-based calling software for mobile phones and computers. The service will become part of the Google Voice number-unification service. Google did not disclose the purchase price, which media reports put at about $30 million. Gizmo5’s 6 million users will still be able to use the service, according to a statement. But Google is suspending new Gizmo5 signups, and existing users can no longer sign up for a call-in number.

—Platformic, a Web-based startup that enables customers to create and manage their own websites, said it is adding social media capabilities. The two-year-old San Diego-based company, which has targeted broadcast companies, says its expanded software-as-a-service product will help a broadcaster’s audience share photos, create their own user profiles, and create personal blogs on the broadcaster’s Platformic-powered website.

—Qualcomm’s No. 2 executive opened a regional mobile technology conference in San Diego by providing an overview of steps the chipmaking giant is taking to help ease the pressure on wireless network bottlenecks as mobile data traffic soars. Qualcomm (NASDAQ: QCOM) Chief Operating Officer Len Lauer told the 3G CDMA Americas Regional Conference that in the year 2014, worldwide mobile data traffic in one month will exceed mobile data traffic for all of 2008.

—Technology innovations that help companies optimize their profitability will likely lead to the next wave of analytics-based software startups, according to Stephen Coggeshall of San Diego-based ID Analytics. Another hot area will be analytics that can help forecast consumer behavior, said Coggeshall, who was participating in a discussion about new opportunities in analytics during the San Diego Software Industry Council’s annual forum on analytics.

—Israel’s Panoramic Power won $250,000 and became the first winner of the top QPrize, the incentive prize competition launched earlier this year by Qualcomm Ventures. Panoramic Power is developing energy-monitoring wireless technology that enables a company or institution to deploy so-called “smart grid” technologies within their existing facilities.

—The San Diego-based Cannon Power Group said is getting $19.4 million in federal renewable energy grants to help fund construction of a giant wind farm in eastern Washington state, about 110 miles east of Portland, OR. The $1 billion Windy Point/Windy Flats project is expected to generate enough electricity for 250,000 homes.

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Several of New England’s life sciences firms had good news to report this week.

—Ryan gave a run-down of the key insights to emerge from our Xconomy Forum on pharma innovation. Sirtris CEO Christoph Westphal, for example, offered insight into one of the biggest biological mysteries around the Xconomy office: how Luke manages to eat so much and stay so thin.

—Cambridge, MA-based Gloucester Pharmaceuticals won FDA approval for romidepsin (Istodax), a treatment for a rare cancer called cutaneous T-cell lymphoma. Gloucester expects to begin marketing the drug in January.

—Noah Beerman took the reins of RXi Pharmaceuticals (NASDAQ: RXII), a developer of RNA interference drugs. Previous president and CEO Tod Woolf will remain on the Worcester, MA-based company’s scientific advisory board.

—Lexington, MA-based Concert Pharmaceuticals started human testing of an anti-HIV drug called CTP-518. Reaching the milestone will trigger a $12 million payment from Concert’s partner, GlaxoSmithKline.

—After announcing earlier this year that it was considering strategic options, including a sale, Cambridge-based Helicos Biosciences (NASDAQ: HLCS) took itself off the block, citing “improving standalone prospects and its current market valuation.”

—Cambridge-based Ironwood Pharmaceuticals inked a $75 million-plus deal with Japan-based Astellas Pharma. The agreement gives Astellas rights to market Ironwood’s lead drug candidate, the constipation treatment linaclotide, in Japan, Indonesia, the Philippines, Korea, Taiwan, and Thailand.

—Aileron Therapeutics, also of Cambridge, published research in the journal Nature indicating that its “stapled peptide” technology can be used to block the production of a protein called Notch that’s implicated in uncontrolled growth of cancer cells. Luke put the news in the context of Aileron’s efforts to develop drugs that hit previously unreachable targets.

—Ryan checked in with Cambridge-based electronic health records provider Dossia. After launching to much fanfare in December 2006, the non-profit is making slow progress in getting its system adopted, but it has recently solidified its leadership team and made other changes it hopes will help.

—Cambridge-based Alnylam Pharmaceuticals (NASDAQ:ALNY) announced the formation of an internal group called Alnylam Biotherapeutics focused on applying the company’s RNAi technology to increase the output of biomanufacturing processes.

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Some San Diego life sciences companies reported a burst of new financing, while embattled Sequenom told investors it’s trying to conserve its available cash. Here’s our rundown of the latest highlights:

—San Diego’s Trius Therapeutics, a venture-backed biotech developing a new antibiotic for treating acute and life-threatening bacterial infections, disclosed plans to raise as much as $86 million in an initial public stock offering. With additional funding, the company will proceed to Phase 3 clinical trials of torezolid, which Trius describes as a second-generation successor to linezolid, the Pfizer antibiotic known as Zyvox.

—Life Technologies (NASDAQ: [[ticker: LIFE]]), the Carlsbad, CA-based provider of biotech instruments and lab supplies, agreed to acquire Woburn, MA-based BioTrove, which has developed a high throughput gene expression and genotyping analysis system.

— SpectraScience, the San Diego medical device maker, has raised more than $4.3 million through a private placement that combines preferred shares and warrants. SpectraScience (OTCBB: [[ticker: SCIE]]) CEO Jim Hitchin told Bruce the offering closes a $5 million round the company began earlier this year.

—PaxVax, a San Diego startup backed by Seattle’s Ignition Capital, has raised $2 million of a planned $6 million investment round. The biotech founded in early 2007 is developing a new type of vaccine that is administered as oral tablets and avoids much of the requirements that conventional vaccines require.

—Sequenom, San Diego’s embattled diagnostics company, said it expects to end the year with $39 million in cash—but that’s not enough to get through 2010 without raising funds or slowing spending. In April, Sequenom (NASDAQ: [[ticker: SQNM]]) disclosed that it had “mishandled data” from a prenatal Down syndrome diagnostic test, indefinitely postponing that product launch.

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This was the week that a little biotech company in Bothell that few of the locals have ever heard of, burst onto the national stage.

—Bothell, WA-based Alder Biopharmaceuticals had its breakout moment this week when it pulled in $85 million in upfront cash, and stands to gain more than $1 billion over time from a partnership with Bristol-Myers Squibb to co-develop a new drug for rheumatoid arthritis. Clinical trial data on this drug hasn’t yet been released publicly, but CEO Randy Schatzman says it’s good enough to give market-leading drugs from Amgen and Abbott Labs a “run for their money.” Seattle Genetics CEO Clay Siegall, an Alder director, says it is now a “force” in regional biotech.

—Over in Seattle’s South Lake Union, another little-known private company called Kineta said it is splitting a little more than half of a federal contract with the University of Washington worth $13 million over the next five years. The goal will be to develop new chemical compounds, called adjuvants, that can boost the effectiveness of a wide variety of vaccines.

—The Institute for Systems Biology is continuing to net a lot of grant money, this week announcing that it has pulled in $8 million from the National Institutes of Health to contribute to The Cancer Genome Atlas. This is a genomic effort to identify potential new targets for cancer drugs.

—The battle between Seattle-based ZymoGenetics (NASDAQ: ZGEN) and Bristol, TN-based King Pharmaceuticals is heating up in federal court in Tennessee. If you’ve missed any of the back-and-forth, or how this ball really got rolling back in August, here’s a quick summary.

—Bellevue, WA-based Light Sciences Oncology, another private company that keeps a low profile, revealed in a regulatory filing that it has lined up another $35 million to support its drug-device combination therapy for cancer. The money is available in the form of a line of credit, and if investors choose to exercise warrants.

—Bothell, WA-based Verathon, the maker of a simple ultrasound tool for diagnosing bladder disorders, was acquired by Sarasota, FL-based Roper Industries (NYSE: ROP) as part of a pair of transactions valued at $356 million. The companies aren’t saying how much of that is going to the Verathon shareholders.

—Seattle-based Dendreon (NASDAQ: DNDN), the king of the moment in Seattle biotech, issued a pretty vanilla quarterly report with the Securities and Exchange Commission. One point worth noting was that it burned $28 million of its cash reserves in the three-month period ending September 30. It ended that quarter with $259.6 million in cash and investments left in the bank as it prepares to manufacture and market sipuleucel-T (Provenge) next year for men with terminal prostate cancer.

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Several of New England’s tech and life sciences firms got juicy deals the past week and a half.

—Boston’s RunMyErrand, an online clearinghouse where busy people can find helpers for odd jobs, raised $1 million in a Series A venture financing round. The cash, from California investors Baseline Ventures and Maples Investments, will help the startup staff up and expand to San Francisco.

—Cambridge, MA-based Cequent Pharmaceuticals raised $3.35 million in the first tranche of its second venture financing round; the round could eventually total $15 million. Cequent, a developer of RNA-interference based drugs, raised $15 million in its 2007 Series A round from Ampersand Ventures, Pappas Ventures, Yasuda, and Novartis Option Fund.

—Pulmatrix raised $30.2 million in a Series B venture round led by Arch Venture Partners and Novartis Bioventures Fund and joined by Polaris Venture Partners and 5AM Ventures. The Lexington, MA-based startup is developing drugs that prevent a variety of microbes, including influenza, from infecting the lungs.

—GTC Biotherapeutics (NASDAQ:GTCB) of Framingham, MA, raised $10 million in a sale of stock to French biotech drug maker LFB Biotechnologies, already a major shareholder

—Waltham, MA-based On-Q-ity, a developer of cancer diagnostic tools, reportedly raised $21 million in a Series A round of venture capital from Mohr Davidow Ventures, Bessemer Venture Partners, Physic Ventures, and Northgate Capital. The startup was formed through the merger of two Mohr Davidow portfolio companies, CELLective Diagnostics and The DNA Repair Company.

—Boston’s Flybridge Capital Partners helped funnel $3.4 million into New York-based open-source database developer 10gen. Returning investor Union Square Ventures also contributed to the Series B round.

—Special effects software startup GenArts of Cambridge, MA, acquired St. Louis, MO-based Wondertouch, whose software generates so-called “particle-based” special effects. Financial terms of the deal were not disclosed. Wade took a fun look at the companies’ technologies.

—We got the inside scoop last week at our Xconomy event on pharmaceutical innovation when Boston-based Enlight Biosciences revealed that it struck a deal with Abbott Laboratories (NYSE:ABT). Abbott agreed to join the consortium of big pharmas that are …Next Page »

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Healthcare deals are going one way, tech deals another. That’s my read from the past week in the Northwest, where we’ve seen some of the biggest biotech deals around, even as a prominent Seattle tech venture firm (and software financings in general) head south.

—Bothell, WA-based Alder Biopharmaceuticals scored one of the biggest biotech partnerships of the year, as Luke reported today. The company has formed a collaboration with Bristol-Myers Squibb (NYSE: BMY) to develop Alder’s experimental rheumatoid arthritis drug, ALD518, and the deal could be worth more than $1 billion. In exchange for granting Bristol a worldwide exclusive license to develop ALD518 for all uses except cancer, Alder will get $85 million upfront, as much as $764 million in development and regulatory milestone payments, sales-related milestone payments that could exceed $200 million, and royalties on product sales.

—I took a look at the venture and debt financings for Washington companies last month (and the previous two months), and concluded that large investments in software startups aren’t coming back anytime soon. The data, courtesy of New York-based ChubbyBrain, shows most of the money is in healthcare and life sciences.

—Kirkland, WA-based Clearwire has secured an additional investment of $1.5 billion from Sprint, Comcast, Time Warner Cable, and Intel, as first reported by the Wall Street Journal. Google, a previous investor, is not participating in the round. The money will support Clearwire’s (NASDAQ: CLWR) deployment of its WiMax broadband network.

—Verathon, a Bothell, WA-based maker of ultrasound technology, has been acquired by Sarasota, FL-based Roper Industries (NYSE: ROP) as part of a pair of transactions worth a combined $356 million, as Luke reported. The price of Verathon’s sale by itself was not announced. The company develops a 3-D diagnostic imaging tool that helps doctors diagnose bladder disorders.

—One of Seattle’s most prominent tech VC firms will not be raising another fund or making new investments. Len Jordan of Frazier Technology Ventures confirmed the news as he announced he’s moving to Madrona Venture Group at the beginning of next year.

—Bellevue, WA-based Light Sciences Oncology has lined up $35 million in follow-up financing to develop its drug-device treatment for cancer, as Luke reported. The investors weren’t disclosed, but the deal gives Light Sciences the right to access a $23.3 million line of credit, and $11.8 million more if investors choose to exercise warrants. The company raised $40 million from undisclosed VCs last year.

—Seattle startup Movaya Wireless has been acquired by Digby, a mobile commerce firm based in Austin, TX, for an undisclosed price. Movaya was founded in 2006 by Phil Yerkes and Stanley Wang, and focuses on making digital goods storefront applications for the iPhone, Android, and mobile Web platforms. The company’s development team in China will serve as the basis for Digby’s operations in Asia.

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It was a busy week for local technology news.

—Two teams from San Diego and a third from Northern California demonstrated their development of advanced chemical sensor prototypes that are tiny enough to be found inside ordinary cell phones. The U.S. Department of Homeland Security is funding the Cell-All program, with a goal of basically creating an anti-terrorism app for cell phones that would enable authorities to crowd-source chemical detection.

—MaxLinear has filed for its initial public stock offering. The Carlsbad, CA-based fabless chipmaker, which specializes in designing semiconductor-based television receivers, intends to raise about $100 million through its IPO. The market may be de-frosting a bit, with 47 IPOs so far in 2009, compared with 45 last year, and 272 in 2007.

—ProQuo, a San Diego-based Web 2.0 company that was founded in 2007, was quietly shut down after taking in a total of $15 million in venture capital from Menlo Park, CA-based Draper Fisher Jurvetson and San Diego-based Mission Ventures. ProQuo was never able to validate its business model; its website offered consumers a way to remove their names from mass-mailing lists for free, and the company planned to sell its optimized lists back to mass marketing companies.

—San Diego’s wireless industry group, CommNexus, celebrated the opening of EvoNexus, its free high-tech incubator, by announcing the selection of three more startup companies: EcoATM, MicroPower Technologies, and TetraVue. CommNexus CEO Rory Moore says EvoNexus is believed to be the first incubator that is completely free for startups—that is, it doesn’t even require an equity stake in participating companies, as most incubuators do.

—Jitterbug, the San Diego wireless provider that puts an emphasis on simplicity, has acquired MobiWatch, a Waltham, MA-based startup developing mobile personal emergency response services. A regulatory filing shows that Jitterbug’s parent, GreatCall, provided 630,000 shares of common stock to MobiWatch and its shareholders in a deal valued at $107,100.

—San Diego-based Networkfleet is using its technology to help companies that operate fleets of vehicles go green by monitoring engine emissions and ensuring that vehicles are operating efficiently. Co-founder Diego Borrego told me the company also expects to be a player as consolidations sweep through the fleet tracking industry.

—EcoDog, a Vista, CA, cleantech startup that has developed a device that helps homeowners sniff out savings in their electric utility bill, was named best of show at GadgetFest, the annual fall competition sponsored by CommNexus, the San Diego wireless industry group. EcoDog founding CEO Ron Pitt won over the crowd when he declared, “My product is the only product up here tonight that saves you more money than it costs.”

—San Diego-based cleantech startup EESG is looking to raise $1.2 million to expand the 10-employee company’s sales staff, purchase inventory, and ramp up public relations and marketing. The company’s founders told me they have raised about half so far, including $300,000 from Longboard Capital Advisors, a green investment firm based in Santa Monica, CA.

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The local life sciences scene was pretty quiet this week, although we heard more than usual from medical device companies.

—Paul Yager, the University of Washington’s chair of bioengineering, offered a detailed status update on a tool called the DxBox his lab has been developing the past four years in collaboration with Redmond, WA-based Micronics, Seattle-based PATH, and Bothell, WA-based ELITech Group, all with the support of the Bill & Melinda Gates Foundation. They are seeking to develop a portable, fast, accurate, and rugged diagnostic tool to help doctors in the developing world, and while there’s been a lot of progress, it’s entered the “put up or shut up” phase, Yager says.

—Seattle-based Dendreon turned in its complete application to the FDA for clearance to start marketing its first drug, sipuleucel-T, (Provenge) in the U.S. This filing came a bit earlier than Dendreon had forecasted, but it’s also a lot later than the company originally hoped when it first asked the FDA for approval, which you can read more about in this Dendreon history piece I did back in April.

—The Institute for Systems Biology said it has commissioned Mountain View, CA-based Complete Genomics to sequence the full genomes of 100 individuals as part of a Huntington’s disease experiment. This experiment is said to be the largest ever to use full human genome sequences.

—We’ve seen a few medical technology companies that are seeking to repair damaged tissues without leaving behind any implantable devices, and Bothell, WA-based QuantumCor is the latest. CEO Vern Dahl described his company’s plan to do this for a form of heart failure known as mitral valve regurgitation.

—Seattle-based Calypso Medical Technologies, the maker of a device to pinpoint radiation therapy for prostate cancer to minimize side effects, formed a collaboration with Siemens Healthcare. The companies will seek to develop the technology for pancreas and lung tumors.

—We also had an insightful guest editorial from Anthony Rodriguez, a Ph.D. bioengineering student at the University of Washington and an aspiring entrepreneur. He contends that it takes a village to raise an entrepreneur, and that while a few organizations have made some effort to cultivate young entrepreneurs at the UW, the business community could be doing much more.

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TEDMED had Martha, Goldie, and other celebrity speakers, but San Diego-based Amylin Pharmaceuticals broke this week’s big news when it signed up a big Japanese partner to develop its line of obesity drugs. It’s all part of your regular dose of San Diego biotech news, and it’s ready now:

—Amylin Pharmaceuticals, the San Diego-based diabetes drug specialist, announced that it has formed a partnership with Japan’s Takeda Pharmaceuticals, which agreed to carry most of the development costs for Amylin’s weight-loss drugs. In return, Takeda gets a worldwide exclusive license to eventually commercialize Amylin’s experimental obesity drugs, including the combination of pramlintide and metreleptin, and davalintide.

—After a five-year hiatus, TEDMED founder Richard Saul Wurman, and president, Marc Hodosh (who also is an Xconomist), brought the conference on medical technology, entertainment and design to San Diego’s Hotel del Coronado. TEDMED announced during the conference, which included presentations by Boston Scientific co-founder (and Xconomist) John Abele, Martha Stewart, and Goldie Hawn, that the conference will return to the same location next October.

—I only had time to attend a fraction of the presentations at TEDMED last week. One of my favorites talks, though, was delivered by Bill Davenhall, who leads the health and human services marketing team at ESRI, the Redlands, CA, giant in geographic information systems. Davenhall talked about the importance of including patients’ “place histories” as part of their medical records and raised an interesting question: Will the electronic health record systems being created today have the capability to add data in new categories—such as “geo-medicine”–that aren’t typically included in today’s patient records?

—New York-based Xenomics filed a lawsuit against San Diego-based Sequenom that alleges Sequenom misrepresented the progress in its development of a prenatal test for Downs syndrome. Xenomix says it would not have licensed its patents to Sequenom had it known the truth.

—Denise profiled San Diego-based Sirigen, an early stage medical diagnostic company that is developing technology that uses light-emitting polymers to detect bits of DNA. Sirigen founder Brent Gaylord developed the technology at UC Santa Barbara, extending the significance of UCSB physicist and Nobel laureate Alan Heeger’s discovery of conductive polymers.

—The FDA told San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) and its partner Eli Lilly the companies can now market exenatide (Byetta) as a frontline, standalone therapy for diabetes. The drug was previously approved for use with other drugs, or as a fallback option when other tretments failed.

—Vertex (NASDAQ: VRTX), the Cambridge, MA, biotech with operations in San Diego, said the latest trial of its telaprevir treatment for hepatitis C was able to attain the clinical definition of a cure in more than 80 percent of patients who got the drug. The finding is part of the mounting evidence Vertex is gathering on its quest to develop the first-of-its-kind protease inhibitor for the chronic liver disease.

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A number of New England’s life sciences companies had good news to report this week.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX) reported results from clinical trials that indicate its experimental hepatitis C drug, telaprevir, could work well for patients who haven’t responded fully to standard treatments, and could be as effective taken twice a day as it is taken three times a day. Luke explains what the news means for Vertex’s efforts to capture a share of the potentially huge market for hepatitis treatments.

—Medical device maker Interlace Medical of Framingham, MA, won FDA clearance to market its minimally invasive device for removing uterine fibroids and polyps.

—Burlington, MA-based CorNova raised $2.5 million of a proposed $6 million in equity financing, according to regulatory filings. CorNova is developing coronary stents with platinum surfaces.

—Anti-inflammatory drug developer Virdante Pharmaceuticals completed a second closing of its Series A financing round, bringing the total collected so far to $30 million. Thomas, McNerney & Partners led the deal, which was joined by Osage Partners, Biogen Idec New Ventures, Clarus Ventures, MedImmune Ventures, and Venrock Associates.

—Bedford, MA-based iRobot (NASDAQ:IRBT) launched a new healthcare unit. Under the direction of technology veteran Tod Loofbourrow, the unit will focus on developing robots to help seniors live independently.

—Pharma giant Novartis declined an option to continue development of a hepatitis C drug from Cambridge-based Idenix Pharmaceuticals (NASDAQ: IDIX). Idenix, whose stock dropped on the news, will seek another partner to back development of the drug, IDX184.

—RNA-interference drug developer Cequent raised $3.35 million in the first tranche of a venture round that could be worth as much as $15 million. The Cambridge-based startup is engineering E. coli bacteria to deliver RNAi molecules designed to combat a certain type of polyp in the colon.

—Pulmatrix raised $30.2 million in a Series B venture round led by Arch Venture Partners and Novartis Bioventures Fund and joined by Polaris Venture Partners and 5AM Ventures. The Lexington, MA-based startup is using technology from MIT and Harvard to prevent flu viruses and other pathogens from invading lung tissue.

—Cancer diagnostics developer On-Q-ity of Waltham, MA, reportedly raised $21 million in a Series A round of venture capital from Mohr Davidow, Bessemer Venture Partners, Physic Ventures and Northgate Capital. The firm was formed through the merger of CELLective Diagnostics and The DNA Repair Company, both Mohr Davidow Ventures portfolio companies.

—Ironwood Pharmaceuticals of Cambridge and its partner, New York-based Forest Laboratories (NYSE: FRX), said that Ironwood’s lead drug candidate, linaclotide, fared well in two pivotal clinical trials. The drug is designed to relieve chronic constipation; Luke has all (and I mean all) the details.

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It was a quiet week for deals in the Northwest, but we dug up some important ones in business software, wireless, and biotech.

—Seattle-based Amazon’s (NASDAQ: AMZN) acquisition of Zappos, the online apparel and shoe seller based in Las Vegas, has closed. The deal, first announced back in July, is valued at $1.2 billion in Amazon stock.

—Bellevue, WA-based Onehub has raised $1.3 million in Series A funding from Ignition Partners and angel investors. The company was founded in 2007 and makes Web-based software for business collaboration and file-sharing.

—We took a close look at small financing deals in the Northwest, worth between $100,000 and $1 million, that have flown under most people’s radar in the past month. According to stats from ChubbyBrain, a New York-based information and data services company tracking the innovation economy, the following companies raised a small amount of equity in September: Acucela, Adometry, BallLogic, InEnTec, Inson Medical Systems, Second Porch, Site 9, SynapticMash, Smilebox, Vantos, and WA 32609.

—Seattle-based Kineta, a biotech firm developing drugs to fight autoimmune diseases, has formed a strategic alliance with MPI Research, based in Michigan, as Luke reported. Financial terms of the deal weren’t given, but Kineta said it will receive support for animal studies that will enable the company to begin clinical trials next year.

—Portland, OR-based RF Arrays raised $6.5 million in equity, options, warrants, and/or other rights to acquire securities, according to a regulatory filing. The investors were not disclosed, but New York-based New Science Ventures has previously backed RF Arrays, which develops wireless communications technology.

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San Diego’s tech sector got some money and glory during a week that was overshadowed by news from two life science conferences: TEDMED and the annual Biocom Investor Conference. Get your tech news now while it’s still hot.

—To stay connected with open-source development for smart phones, San Diego’s Qualcomm created a subsidiary, the Qualcomm Innovation Center, that is focused on making sure the chipmaker’s technology works smoothly with Android, Symbian, and other open-source wireless platforms. Qualcomm (NASDAQ: QCOM) also joined the Symbian Foundation and is supporting the open source systems used by Nokia and others.

—One of the big selling points for algae-based fuels is that algae absorbs a lot of carbon dioxide before it gets harvested and turned into biofuels. Yet San Diego-based Sapphire Energy and other algae biofuel companies say they are having a hard time getting enough carbon dioxide at an affordable price to support their research and development efforts.

—Federal stimulus funds will help cover almost half the cost of a new $60 million wireless communications system that San Diego Gas & Electric is developing as part of its smart grid program. The $28.1 million grant is part of $3.4 billion to be allocated nationwide.

—Carlsbad CA-based Verdezyne, which is applying advanced biotechnology tools to the development of industrial chemicals and biofuels, raised nearly $3 million of a planned $15.2 million round of venture capital.

—JMI Equity, the venture firm based in San Diego and Baltimore, led a $5 million investment in Axeda, the Waltham, MA-based startup that makes a cloud-based system for wireless tracking of company assets. Axeda also raised $4 million in venture debt from MMV Financial of Toronto.

—TechAmerica San Diego, the local chapter of the industry group previously known as the AeA, issued nine awards at its 16th annual high tech awards luncheon. The group named winners in nine categories: MadCap Software (Software); InterKnowlogy (Internet); Verari Systems (Hardware); Quake Global (Communications); SeaBotix Inc. (Defense); Peregrine Semiconductor (Integrated Circuits); OneRecovery (Medical Device) IPS Group (Cleantech); Legend Films (Emerging Growth).

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An unusually high percentage of this week’s New England tech and life sciences deals came from companies based in Boston proper. What’s up with that?

—Spark Capital of Boston led a $7 million Series B investment in Long Island, NY-based Aviary. Backed also by Bezos Expeditions, Aviary makes cloud-based software for graphic design, audio editing, and the like.

—Boston’s American Well, whose Web-based medical consultation system in used by several large health insurance plans, raised $10 million in new equity funding, according to a regulatory filing. Investors in the round were not named.

—Waltham, MA-based Axeda raised $5 million in a Series B funding round led by JMI Equity and $4 million in venture debt from MMV Financial. Axeda provides a cloud-based system for wireless tracking of company assets.

—Raytheon (NYSE:RTN), also of Waltham, completed its buyout of Cambridge, MA-based BBN Technologies. The purchase price, which wasn’t disclosed when the deal was announced, was about $350 million.

—E-commerce firm GSI Commerce (NASDAQ:GSIC) agreed to acquire Boston-based Retail Convergence Incorporated (RCI) for $180 million in cash and stock and as much as $170 million in performance-based payments. RCI owns Rue La La, an invitation-only website selling designer clothing and accessories at a discount, and Smart Bargains, a site selling more affordable clothing, jewelry, and home goods.

—SEC filings indicate that Burlington, MA-based coronary stent maker CorNova raised $2.5 million of a proposed $6 million in equity financing. Investors in the deal were not specified.

—Cambridge, MA-based Virdante Pharmaceuticals completed a second closing of its Series A financing round, bringing the total raised so far to $30 million. Investors have promised to boost that number to $47.75 million if the startup, which is developing new antibody-based drugs to combat autoimmune diseases, meets certain milestones. Ryan has a nice profile of Virdante and its technology.

—Boston’s ScanScout, an online video ad provider, completed its $8.5 million Series B round of venture capital. EDB Investments, which invests on behalf of the government of Singapore, provided the cash.

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San Diego’s life sciences news picked up a bit last week amid fresh signs of the area’s growing prominence in the laboratory tools and diagnostics sectors.

—Carlsbad, CA-based Helixis, a startup maker of genetic analysis technology from the Caltech labs of Nobel Laureate David Baltimore and Axel Scherer, raised $1.8 million from unidentified investors, according to a regulatory filing. The amount is in addition to the $5.5 million the company reported raising in July. Helixis is developing products that attempt to make real-time polymerase chain reaction (RT-PCR) technology more accessible to the average researcher.

—Enigma Diagnostics CEO John McKinley told Bruce the UK-based medical diagnostics startup plans to close its current U.S. office in San Francisco and make a new office in San Diego its U.S. headquarters. McKinley estimated Enigma would have 30 employees in San Diego—“the diagnostics center for the U.S.,” as he put it—by mid-2010. The company has developed a desktop-size instrument based on advances in PCR (polymerase chain reaction) technology, which McKinley says can identify certain pathogens in less than 45 minutes.

—Sequenom, the San Diego-based maker of laboratory tools and diagnostics, disclosed that it agreed to accept a $1 million payment from Ibis Biosciences, a unit of Abbott Laboratories, to settle a patent infringement lawsuit. As part of the deal, Sequenom (NASDAQ: [[ticker: SQNM]]) granted Ibis a non-exclusive license to three mass spectrometry-based patents. Sequenom, meanwhile, remains under investigation by the Justice Department and Securities and Exchange Commission for “mishandling” experimental data in a clinical trial of its prenatal test for Down syndrome.

—Senomyx (NASDAQ: [[ticker: SNMX]]), the San Diego company using biotechnology to develop proprietary flavor enhancers and blockers, said S6973, a compound it has been developing to enhance the intensity of sucrose, was designated as Generally Recognized As Safe (GRAS) under federal regulations that govern food additives. The GRAS designation allows the company to begin commercialization of the sweetness enhancer, which enables foodmakers to reduce sugar in foods and drinks by as much as 50 percent and still provide an equivalent sweet taste, according to Senomyx.

—San Diego-based Ligand Pharmaceuticals (NASDAQ: [[ticker: LGND]]) agreed to pay $3.2 million to acquire ailing Metabasis (NASDAQ: [[ticker: MBRX]]), a developer of treatments for diabetes and high cholesterol. Ligand committed $8 million to finance Metabasis’ drug development programs within the next 42 months.

—The Burnham Institute for Medical Research made two key hires to support its translational research efforts. Paul Laikind, the co-founder of Gensia Pharmaceuticals, Viagene, and Metabasis, became the institute’s senior vice president of business development and chief business officer to help cut deals with biotech and pharma companies. Michael R. Jackson, formerly senior vice president of drug discovery at Johnson & Johnson, is now Burnham’s first-ever vice president for drug discovery and development, charged with translating Burnham discoveries into drug candidates primed for clinical testing.

—San Diego’s Arena Pharmaceuticals (NASDAQ: [[ticker: ARNA]]) is talking up the safety profile of its experimental obesity drug as it prepares to compete against experimental treatments from San Diego-based Orexigen Therapeutics (NASDAQ: OREX) and Mountain View, CA-based Vivus (NASDAQ: VVUS), both of which produced greater weight loss in clinical trials. None of the drugs have yet been approved by the FDA. Arena CEO Jack Leif told Luke that the company’s drug, lorcaserin, improved diabetic and cardiovascular health markers in clinical trial subjects. He also challenged the notion that lorcaserin is a subpar obesity treatment. “This is not a wimpy weight-loss drug,” Leif said.

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We had a little something for everybody on the life sciences beat this week, with news on biopharmaceuticals, devices, and healthcare software.

—Seattle-based Omeros (NASDAQ: OMER) had potential to be a bellwether for the U.S. biotech sector earlier this month, as the first true biopharmaceutical company to go public since February 2008. But its stock has tanked, making it the worst-performing IPO of the year, according to data from Renaissance Capital. Not surprisingly, no other biotech company has stepped up to put its name on the IPO calendar since.

—ZymoGenetics‘ former chief medical officer, Jan Ohrstrom, told me about his latest passion to develop a dry powder drug for excess bleeding that could be conveniently used by paramedics, and might be a superior alternative to liquid formulations like the one made by his former employer. He has recruited a former Zymonite to work for him at ProFibrix, and he’s set up a new office not far away from his old stomping grounds on Seattle’s Eastlake Avenue.

—Microsoft has been leading the way for a couple years now to make medical records go electronic, and put individuals in charge of them, but the HealthVault software is still a long way from gaining mainstream acceptance. My colleague Ryan McBride reported on all the challenges Microsoft is facing following a talk by Peter Neupert, the vice president of Microsoft’s Health Solutions Group, at the Connected Health Symposium last week in Boston.

—The Washington Biotechnology & Biomedical Association’s big annual meeting in March is being revamped with a new name, new look, and a new program, as we heard in this guest editorial from Valerie Carricaburu of UW TechTransfer and biotech consultant Neile Grayson. The event, formerly known as Invest Northwest, is now going to be called Life Science Innovation Northwest, and will seek to entice not just investors, but also corporate and strategic partners with the wherewithal to support innovation in the Northwest. Valerie and Neile are seeking ideas from the community on how to improve the event, so feel free to post a note at the bottom of this story.

—Seattle-based Kineta, the developer of treatments for autoimmune diseases, formed a collaboration with Matawan, MI-based MPI Research, to support animal studies that will enable clinical trials to start in 2010. Terms weren’t disclosed.

—Bothell, WA-based SonoSite (NASDAQ: SONO) said its sales dropped by 13 percent in the quarter ending Sept. 30, and that it recorded an operating loss of $240,000 in the period.

—ZymoGenetics (NASDAQ: ZGEN) said it has started a mid-stage clinical trial of its pegylated interferon lambda drug for hepatitis C, which triggered a $70 million milestone payment from its partner, Bristol-Myers Squibb.

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Europe’s drug regulators were not kind to a couple of Massachusetts biotech firms this week, but other New England life sciences companies had happier news to report.

—European drug regulators turned down Lexington, MA-based Antigenics’ bid for approval to market vitespen (Oncophage), a “cancer vaccine” for patients with kidney cancer. Shares of Antigenics (NASDAQ: AGEN) tumbled on the news.

—Ryan made a visit to the yeasty-smelling labs of Lebanon, NH-based Mascoma, where researchers are aiming to engineer microbes that can more efficiently produce ethanol from cellulose-rich materials such as wood chips, switch grass, and corn stalks. Mascoma is currently ramping up pilot production at a facility in Rome, NY, and hopes to complete one of the first commercial-scale cellulosic ethanol plants—in Kinross, MI—by 2012.

—Nuclea Biotechnologies raised $3.4 million in new equity financing. The Pittsfield, MA-based startup is developing genomic tools for cancer research and diagnosis.

—Ryan made the rounds of the big healthcare IT symposium put on by Partners HealthCare’s Center for Connected Health. The field is currently riding a wave of interest tipped off in part its inclusion in the economic stimulus bill, he explained, and the event attracted a mix of physicians, entrepreneurs, hospital administrators, academics, and technology executives. Ryan gave a great run-down of highlights from the event.

—Natalizumab (Tysabri), the multiple sclerosis drug from Cambridge, MA-based Biogen Idec (NASDAQ: BIIB), has reportedly come under fresh scrutiny from European regulators now that a total of 23 patients on the treatment have been diagnosed with a rare, potentially fatal brain infection called PML. According to Reuters, the European Medicines Agency has initiated a review to discuss any additional measures necessary to ensure the safety of the drug, which is also approved for Crohn’s disease. Shares of Biogen, and its partner Elan (NYSE:ELN) fell on the news.

—Wellesley, MA-based BioAssets Development Corporation inked a $30 million deal granting Frazer, PA-based Cephalon (NASDAQ: CEPH) to acquire the company. BioAssets will be eligible for various additional payments if Cephalon exercises the option and certain regulatory and sales milestones are reached.

—Boston-based American Well, provider of a Web-based system for remote medical consultations, raised $10 million in new equity funding, according to a regulatory filing. Investors in the round were not named.

—Luke gave a sneak peak of next week’s Xconomy Forum, which will explore how Big Pharma is seeking to boost its pace of innovation—and chances of success—in a notoriously risky industry. We’re all really excited about the event, which will include keynoters Deborah Dunsire, the CEO of Millennium: The Takeda Oncology Company, and Christoph Westphal, the CEO of Sirtris, and the senior vice president of GlaxoSmithKline’s Centre of Excellence for External Drug Discovery.

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