San Diego’s Sanford-Burnham Medical Research Institute says today it’s joining the Centers for Therapeutic Innovation (CTI), a global network that New York-based Pfizer established a year ago to foster collaborations between basic research and clinical applications.

The Pfizer network of drug discovery innovation centers includes academic medical centers in San Francisco, Boston, New York, and is expected eventually to extend overseas as well. When UC San Diego Health Sciences joined the network in August, it said its partnership agreement with Pfizer could be worth as much as $50 million from the pharmaceutical giant over the next five years.

The statement from Sanford-Burnham says nothing about funding, although an institute spokeswoman says its financial agreement with Pfizer is comparable to UCSD’s. The medical research institute says it will likely collaborate with UCSD when a research project reaches the clinical stage, and joint research projects would presumably draw from the same pool of funding at Pfizer.

The Sanford-Burnham also noted it is one of only two participating medical research centers in the CTI network that are not academic medical centers. (The other, Harvard Medical School, is not considered an academic medical center because it does not have its own research hospital with clinical trials and access to patient samples.)

Sanford-Burnham has expanded significantly in recent years. The National Institutes of Health awarded Sanford-Burnham a $97.9 million grant in 2008 to establish a high-throughput screening center. It was renamed as the Conrad Prebys Center for Chemical Genomics in 2009 when San Diego philanthropist Conrad Prebys agreed to donate $10 million to the institute. Philanthropist T. Denny Sanford prompted a similar name change for the institute itself when he pledged $50 million and the research center became the Sanford-Burnham Medical Research Institute.

The institute says working with Pfizer’s Centers for Therapeutic Innovation will provide scientists at Sanford-Burnham with access to additional resources, including select Pfizer compound libraries, proprietary screening methods, and antibody development technologies.

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SG Biofuels, an Encinitas, CA-based startup developing biofuels says it has formed an alliance with Bharat Renewable Energy to produce hybrid varieties of Jatropha that can be grown in India and used to produce biodiesel. SG Biofuels says it is optimizing crop species by using environmentally friendly biotechnology to develop elite hybrids of crops with desired traits—not to be confused with genetically modified organisms (GMOs).  SG Biofuels and Bharat Renewable Energy, a joint venture of India’s second-largest petroleum company, will work to develop the most commercially viable hybrid varieties and plan to plant more than 86,000 acres of Jatropha.

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San Diego algae biofuels developer Sapphire Energy said today it has signed a multi-year agreement with the Linde Group of Munich, Germany, to co-develop a low-cost system for supplying carbon dioxide to commercial-scale, open-pond, algae-to-fuel cultivation systems. Linde, the leading commercial supplier of carbon dioxide in the United States, agreed to deliver carbon dioxide to Sapphire’s commercial demonstration facility near Columbus, NM, and to work with Sapphire to reduce the costs associated with re-purposing manmade carbon dioxide for commercial-scale open pond algae cultivation.

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San Diego-based Nukona, a startup developing security management software for mobile devices, has formed a partnership with Integer Wireless, a Newport Beach, CA, engineering firm that provides HIPAA-compliant wireless networks for hospitals, physician groups, and other healthcare providers. Under a partnership announced this week at the Wireless-Life Sciences Alliance’s annual Convergence Summit in San Diego, Integer Wireless will include Nukona’s mobile device applications management platform in its healthcare-related offerings for voice, data, and video communications.

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Jeff Bluestone has one of those jobs in academia where you almost expect the guy to wear a flak jacket to work.

As executive vice chancellor and provost, part of the gig is to make sure UCSF’s 2,400 very smart, very strong-willed faculty remain happy, and keep doing world-class work in research and teaching. He also has to make sure ethics rules are being followed. Then there’s the task of trying to prove the institution isn’t just full of ivory tower daydreamers, and delivers on the promise of biomedical research, so that folks in Washington D.C., and the corner offices of Big Pharma, will continue to help pay the bills, especially when budgets are tight.

Bluestone, 57, took on this responsibility about a year ago, joining the new leadership team around Chancellor Susan Desmond-Hellmann, the former president of product development at Genentech. Before taking the job, Bluestone was best known in academia as a world-class diabetes researcher, and as a leader of the well-known Immune Tolerance Network. But Bluestone is also well known in the business world, having served as a scientific advisor to numerous biotech companies over the years, like ViaCyte, MedImmune, Pfizer, Biogen, and XDx. Now through one of the top jobs at UCSF, he has applied his experience in both academia and industry to help craft new institutional partnerships with Pfizer, Sanofi-Aventis, and Bayer.

I have plenty of things I want to ask Bluestone, as he’s one of the featured speakers at Xconomy San Francisco’s big event on the 20-year outlook for Bay Area life sciences, coming up next Wednesday. But before that, I wanted to dive into some issues specific to UCSF that won’t exactly fit into the context of that program. Here are excerpts from our conversation earlier this week, edited for length and clarity as always.

Xconomy: How long have you been at UCSF?

Jeff Bluestone: I’ve been here 10 years. I came from the University of Chicago, which is a great institution with a great tradition of research and clinical care. What’s different here, obviously, is being in this environment. It’s the West Coast, the Bay Area, and it’s full of entrepreneurs. We’re starting companies every week. We’re thinking about how to take our discoveries into drug development. We’re working on novel technologies. It feels and functions very differently out here.

X: Have you noticed much of a cultural change at UCSF now that Sue Desmond-Hellmann has been in there for a little over a year and a half? The impression I get, right or wrong, is that for years UCSF had a reputation of not being friendly to industry, as a difficult place for industry to work with. Do you think something has changed?

JB: I’d say two things. The perception is a misperception. If you think about it, UCSF over the last several decades has been an incredible partner with industry in the Bay Area, from the early Boyer patents that helped start Genentech. We’ve started 50-60 companies over the past 30 years and that’s not counting the 40 or so companies we’ve started in the last couple of years in the incubator. Faculty have been involved with industry, they’ve started companies. But like all public institutions, there has always been a balance of the public good, and making sure to protect the interests of the state, while at the same time allowing investigators to be as entrepreneurial as possible. I think UCSF has struck a good balance.

Sue certainly came to the institution with an understanding … Next Page »

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Kayak and Microsoft’s Bing Travel, once competitors in online travel meta-search, are now strategic partners. The companies announced today that in the coming weeks, Kayak will provide flight search results in the U.S. for Bing Travel. Financial terms were not given. Connecticut-based Kayak and Microsoft’s Bing were already allied against Google’s acquisition of Cambridge, MA-based ITA Software. Kayak filed for an IPO in November, sparking lots of discussion about its future strategy. You can read more early commentary on the Kayak-Bing partnership at All Things Digital and Tnooz.

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Few people in biotech have the guts to stir the pot the way Kevin Kinsella did in an interview with Xconomy’s Bruce Bigelow earlier this month.

Kinsella, a venture capitalist with a 30-year track record of biotech investing, delivered a blistering analysis of what he sees as the pharmaceutical industry’s bad-faith negotiating habits, predatory behavior, and short-term, brass knuckle business tactics when dealing with smaller biotech firms. Big Pharma, basically, risks killing the golden goose of biotech innovation it needs to survive, he contends.

Big Pharma, of course, is branded as the bad guy every day of the week. It gets attacked for gouging Grandmas on fixed incomes with excessive drug prices. It takes heat for paying “key opinion leader” physicians who then influence peers to prescribe expensive brand-name drugs. It gets ripped for donating to Congressmen who then protect the industry’s profits through legislation like the new healthcare reform law, or the Medicare drug benefit.

But Kinsella’s charge is different: This comes from an insider within the biomedical/financial complex—someone who would normally be considered an ally of Big Pharma. Biotech and Big Pharma, after all, are supposed to have a symbiotic relationship. Big Pharma has money, manufacturing, and marketing horsepower, but needs a steady supply of innovative new drugs to keep the machine moving forward. Biotech has inventive people with ideas to create new drugs, and the entrepreneurial spirit to navigate the risky early days of R&D, but it often lacks the money and manpower to take a new drug all the way to the marketplace. At some point, the Big Pharma operation strikes a deal to scoop up the little biotech and its drugs to replenish the pipeline, rewarding the shareholders and employees of the biotech company.

That’s the way it’s supposed to work, anyway, but not in the dysfunctional situation Kinsella describes.

Big Pharma companies of today, which are still raking in profits by the billions, sense they have the upper hand in the wake of the Lehman Brothers/Merrill Lynch/Fannie/Freddie-driven financial crisis of 2008. Economists might say the recession is over, but the financial crisis still has a huge impact on early-stage biotech companies today.

Here’s why: Many venture capital firms are slowly, quietly dying off. By and large, they haven’t been able to produce lucrative returns, via IPOs or acquisitions, in the past few years. That means they don’t have the leverage to raise new funds from the pensions, endowments, and other institutions that only consider venture capital as one of many asset classes—a way to get a little better return than, say, a T-bill. Since VCs are struggling to justify their existence, many of the biotech companies that rely on venture capital are also slowly, quietly, running out of the cash they need to sustain this enterprise. Many biotech companies—especially the ones with minimal evidence to suggest their drug works in people—have no choice but to genuflect at the feet of Big Pharma.

So Big Pharma—which has been consolidating through mega-mergers into what amounts to an oligopoly—has sized up a situation it can exploit, Kinsella says. It has been offering up stingy terms to biotech companies that provide practically zero return to the people who shouldered all the risk from the biotech company’s early days. This kind of hardball negotiating has potential to push the whole biotech industry to the brink of extinction, Kinsella argues. After a while, it becomes like commercial overfishing, he says.

The story has been generating chatter all over the web for more than a week. Derek Lowe, the author of the terrific blog “In the Pipeline,” generated a lot of commentary with his own post on Kinsella’s charges. Last I checked, The Atlantic‘s take on this had 154 comments.

Kinsella ran the risk of burning some bridges in pharmaland, or otherwise ticking off lots of people with this kind of commentary. He tells me he was warned … Next Page »

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The birth and death of partnerships was the subject of much of this week’s news in New England’s life sciences sector.

—Rhythmia Medical raised $5 million in an equity offering that could end up being worth $7 million, according to a regulatory filing, bringing the Burlington, MA-based startup’s total funding to $17 million. Rhythmia is developing a catheter-based device that creates a 3D map of the heart in order to pinpoint the tissues responsible for irregular heartbeats.

—Cambridge, MA-based DecImmune Therapeutics raised $1 million in an equity-based financing round led by Astellas Venture Management and joined by return investors Amgen and HealthCare Ventures. DecImmune, a Harvard Medical School spinoff out to develop drugs that reduce inflammation and tissue damage, also won a $2.2 million Small Business Innovation Research grant from the National Institutes of Health.

—Diagnostics maker PointCare Technologies of Marlborough, MA, raised $1.8 million of a planned $3.5 million equity round of funding, according to an SEC filing. PointCare’s products are designed to help patients with HIV/AIDS in developing countries.

—Ryan checked in with John Knopf, CEO and co-founder of Cambridge, MA-based Acceleron Pharma, a developer of drugs that treat disease by boosting or inhibiting the growth of particular tissues. With a newly inked deal with Ireland’s Shire in its pocket, along with other pharma partnerships, “Our hope is that we won’t have to go back to our venture backers,” Knopf said.

—Superstar cancer researcher Tyler Jacks, the director of MIT’s David H. Koch Institute for Integrative Cancer Research, signed up to … Next Page »

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At the Xconomy Smart Energy Forum in San Diego just a couple of months ago, Qualcomm’s Manuel Jaime emphasized that 100-percent electric vehicles (EVs) like the Nissan Leaf will need to be integrated with EV charging stations—and the charging stations have to be integrated with a local power grid. Once they’re integrated, Jaime explained, EV owners will know whether a specific EV charging station will be available when they need it—and electric utilities can begin to manage the “clustering effect” of energy demand that could occur when a bunch of EVs are recharging in the same neighborhood.

Against that background, San Diego-based Qualcomm (NASDAQ: QCOM) and Ecotality (NASDAQ: ECTY), which moved its headquarters last month from Phoenix, AZ, to San Francisco’s Embarcadero Center, announced an agreement today that will add cellular connectivity to Ecotality’s EV charging stations.

With cellular connectivity, the EV charging stations can begin to share the kind of information that Jaime outlined in June. “Cellular networks will play a critical role in connecting the charging stations with ECOtality’s control systems,” Ecotality CEO Jonathan Read says in a statement issued by the two companies. Using a commercial cellular network will help Ecotality and local utilities manage all kinds of data about EVs and the charging stations, providing what Read describes as “real-time monitoring, command, and control.”

The deal between Qualcomm and Ecotality is part of a broader effort to build out EV charging infrastructure. It also puts Qualcomm in the pole position among the technology giants vying to get their IT, chips, and software inside the charging stations and related power grid infrastructure that utilities will need as EVs become more commonplace on U.S. roads. Ecotality is leading a federally sponsored pilot program that is intended to demonstrate how the rollout of EV technology can be accomplished without disrupting the local power grid.

In 2009, the U.S. Department of Energy awarded a grant for almost $100 million to Ecotality, which plans to deploy almost 15,000 EV charging stations in 16 cities (in six states), including San Diego, Seattle, and Portland, OR. The program is intended as a real-world study of … Next Page »

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Crinetics Pharmaceuticals, an early stage San Diego biotech developing specialized biosensors for drug discovery applications, says it has signed a collaboration agreement with the Ferring Research Institute, the peptide research center established in San Diego by Ferring Pharmaceuticals.

Last month, when Crinetics got a small business research grant of nearly $238,000, the startup said its technology is focused on developing biosensors that utilize a family of receptor molecules on cell walls called G protein-coupled receptors (GPCRs). The biotech says it’s own work is focused on studying endocrine GPCRs that can be used in assays for drug molecules, allowing researchers to rule candidate drugs in or out at an earlier stage and thus potentially speeding up pharmaceutical R&D.

In its statement yesterday, Crinetics says it will apply components of its GPCR Dynamics assay platform to a Ferring proprietary drug discovery target. Financial terms of the agreement were not disclosed. Stephen Betz, a Crinetics scientist and spokesman, said no further details would be released about Ferring’s drug target or the agreement itself.

“Our strategy is to initially fund through grants and contracts, with the hope of attracting venture funding in this new year,” Betz writes in an email. “We have the first SBIR grant…and have other applications outstanding. The Ferring deal is by no means exclusive (though certainly the content of their project is) and we are also in discussions with other companies and so hope to have other ‘Ferring-type’ deals in the not-too-distant future. We think we can help a lot of people.”

Based in Saint-Prex, Switzerland, Ferring Pharmaceuticals specializes in developing drugs in the areas of urology, endocrinology, gastroenterology, gynecology, and fertility.

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Somewhere between the turkey prep and the post-pie catatonia, folks at New England’s life sciences companies managed to make some news.

—Idera Pharmaceuticals (NASDAQ:IDRA), a developer of DNA- and RNA-based drugs, announced that Swiss drug giant Novartis will end its four-year-old collaboration with the Cambridge, MA-based firm in February. Idera still has active collaborations with Germany-based drug-maker Merck KGaA and Whitehouse Station, NJ-based Merck & Co. (NYSE:MRK), though.

—Alnylam Pharmaceuticals CEO John Maraganore chatted with Luke about his rather unconventional philosophy on how to make decisions in biotech. Two key steps, according to Maraganore: ditch the spreadsheets, trust the science.

—Cambridge-based Forma Therapeutics nabbed $25.5 million in a Series B venture round led by new backer Lilly Ventures, and joined by the Novartis Option Fund and Bio One Capital of Singapore. Forma CEO Steven Tregay told Luke about the company’s plans to invest in its own drug pipeline, as well as continuing to serve the many pharma partners interested in its drug-discovery engine, which aims in part to find drugs that hit previously inaccessible targets.

—Genzyme (NASDAQ:GENZ) resumed shipments of its best-selling drug for Gaucher’s disease, imiglucerase (Cerezyme), which has been in short supply since Genzyme halted the manufacture of it and other drugs made in the company’s Allston plant this summer to clean up a viral contamination. Meanwhile, a potential competitor to the Genzyme drug took a step closer to market when its developer, Israel-based Protalix Biotherapeutics (NYSE:PLX), struck a development and marketing deal with drug giant Pfizer.

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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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There was a steady serenade of news from New England’s life sciences companies this past week, with both the startups and the public firms chiming in.

—Ryan profiled Boston BioCom, a Pfizer-backed startup aiming to commercialize life science discoveries from Russia. Based in, of course, Boston, the firm is also developing technology from the Massachusetts General Hospital lab of its chief scientific officer, Jeffrey Gelfand.

—Woburn, MA-based Flexion Therapeutics raised $33 million in a Series A financing led by Versant Ventures. 5AM Ventures and Sofinnova Partners joined in backing the company, which is out to reduce the time and expense required to take drugs from the earliest stages of development into initial clinical trials.

—Charles River Laboratories (NYSE: CRL) reportedly cut 115 positions at its Quebec-based subsidiary CTBR Bio-Research. Headquartered in Wilmington, MA, Charles River cut roughly 3 percent of its global workforce back in February.

—Jens Eckstein, a general partner in TVM Capital’s life sciences practice, went to Tokyo and came back with a message for the Boston life sciences community: “We should cherish what we have and work hard to keep things intact and healthy.”

—Lexington, MA-based Cubist Pharmaceuticals (NASDAQ: CBST) teamed up with Cambridge, MA-based Hydra Biosciences to develop new pain medications. Cubist will pay Hydra $5 million upfront, and provide $5 million in R&D funding annually for two years.

—Augmenix of Waltham, MA, raised $6.1 million in a Series B financing round to support the development of its technology for reducing tissue damage during radiation treatment. Ascension Health Ventures led the round; Versant Ventures, Pinnacle Ventures, Catalyst Health Ventures, and several private investors participated as well.

—Drug developer Synageva BioPharma, also of Waltham, raised $12 million, completing a $45 million round of financing. New Leaf Venture Partners, a new investor, and return investors contributed to the round.

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It was a busy week in the land of New England life sciences. Let’s dive in.

—Luke did a massive analysis of the financial health of all the public biotech companies we follow the Boston area and the news… Well, it wasn’t good.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ:VRTX) brought in $155 million in cash by selling $120 million in debt and $35 million for the rights to potential milestone payments. Both deals were related to the potential European commercialization of telaprevir, Vertex’s experimental drug for hepatitis C.

—Adimab, a Lebanon, NH-based biotech startup developing a new platform for discovering antibody drugs, raised $8.2 million in a Series D round of venture financing. Google Ventures led the financing and Polaris Venture Partners, SV Life Sciences OrbiMed Advisors, and Borealis Ventures participated as well.

—Merrimack Pharmaceuticals of Cambridge forged a co-development and co-marketing deal with French pharmaceutical firm Sanofi-Aventis. The partnership, focused on Merrimack’s antibody cancer drug MM-121, will bring the Cambridge firm $60 million upfront and as much as $470 million more in milestone payments, not to mention double-digit percentage royalties, should the drug reach the market.

—Luke chatted with Peter Hecht, CEO of Cambridge -based Ironwood Pharmaceuticals, which recently recruited former Genentech CFO David Ebersman to its board. Does the move signal that Ironwood—whose lead, potential blockbuster, drug is in late-stage clinical trials—is preparing to go public? Hecht wouldn’t say so, but Luke explains why Ironwood might fare well on Wall Street.

—The FDA followed an earlier advisory panel recommendation that clofarabine (Clolar), a leukemia drug from Genzyme (NASDAQ: GENZ), not be approved for use in a broader population of patients. The agency said that Cambridge-based Genzyme should conduct another trial of the drug in patients over age 60; it’s currently approved just for children with leukemia.

—Ryan spent the day at the MassBio Investors Forum in Boston, checking in with folks from Cambridge-based RNAi-drug developer Alnylam Pharmaceuticals (NASDAQ:ALNY), (which referenced a potential spin-off company perhaps in the works); Waltham, MA-based EyeGate Pharma (which has rounded up $12 million of a planned $20 million to $25 million financing); Cequent Pharmaceuticals, another Cambridge-based RNAi-drug developer (which is moving its first drug into clinical trials); and Pathogenica (a brand-new diagnostics firm spun out of George Church’s lab at Harvard Medical School). He also gleaned some insights (and arguments) about the future of biotechnology from Harvard Business School professor Gary Pisano and life sciences investment firm CEO Steven Burrill.

—Epizyme, a Cambridge startups out to turn the science of epigenetics into new drugs that work by turning genes on and off, raised $32 million in a Series B venture round led by Bay City Capital. Amgen Ventures, Astellas Venture Partners, MPM Capital, and Kleiner Perkins Caufield & Byers participated as well.

—Boston-based antibiotic developer Paratek Pharmaceuticals struck an exclusive development and commercialization deal with Swiss drug giant Novartis. The deal, which could be worth as much as $485 million in initial milestone payments, focuses on Paratek’s PTK 0796, which is in late-stage clinical development for treating complicated skin and skin structure infections as well as certain cases of pneumonia.

—Immuneering, which is developing computer models to predict patients’ responses to cancer drugs, became the first life sciences startup to join Polaris Venture Partners’ new Dog Patch Labs startup incubator in Cambridge. The move will take the company out of CEO Ben Zeskind’s apartment in Boston’s Back Bay.

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This week we had the usual mix of news on partnerships, clinical trials, and the like, as well as some fascinating in-depth discussions with key players in the life sciences arena.

—Antibiotic developer Rib-X Pharmaceuticals announced that the oral form its experimental antibiotic radezolid passed a mid-stage clinical trial as a treatment for a common form of pneumonia. The New Haven, CT, firm is looking to partner with a pharmaceutical company to help move the drug toward FDA approval.

—Genzyme (NASDAQ:GENZ) of Cambridge, MA, won approval from European regulators to market plerixafor (Mozobil) for patients with lymphoma and multiple myeloma who need stem cell transplants. The drug helps boost the number of stem cells that can be collected from the blood for such transplant procedures.

—Altus Pharmaceuticals (NASDAQ:ALTU) of Waltham, MA, said it will need to raise more capital before the end of next month in order to continue its operations. In March, the firm reduced its staff and abandoned development of a cystic fibrosis treatment in order to focus on ALTU-238, a treatment for patients with growth hormone deficiency.

—Cambridge-based Alnylam Pharmaceuticals (NASDAQ:ALNY) joined forces with Vancouver’s Tekmira Pharmaceuticals (TSX:TKM) to come up with new drug-delivery particles to get RNA-interference drugs where they need to go in the body. Alnylam will fund the research and gets exclusive rights to the resultant discoveries.

—Anti-viral drug maker Idenix Pharmaceuticals (NASDAQ:IDIX) priced a secondary public offering of 7.25 million shares at $3.14 each. The Cambridge-based firm expected to raise $21.2 million from the offer.

—Irish drug company Elan filed suit against its Cambridge-based partner, Biogen Idec (NASDAQ:BIIB), over Biogen’s objections to a deal with affiliates of health Johnson & Johnson (NYSE:JNJ) that Elan announced last month. That deal focuses on … Next Page »

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New England tech and life sciences firms forged several interesting new partnerships this week.

—Apperian, a Boston-based startup developing enterprise-oriented iPhone applications, raised $1 million in a Series A venture round led by CommonAngels of Lexington, MA.

—Cambridge, MA-based Akamai (NASDAQ: AKAM) teamed with Seattle’s Delve Networks to provide a new online platform for publishing videos and distributing them to any digital media player. The new service will compete against that offered by Cambridge-based Brightcove.

—Cardiorobotics of Newport, RI, and Pittsburgh, PA, raised $11.6 million in a Series A round from Eagle Ventures, the Slater Technology Fund, the Pittsburgh Life Sciences Greenhouse, and others. Eric wrote a nice profile of the startup’s efforts to develop a “snake robot” that would make heart surgeries less invasive.

—Advanced Electron Beams of Worcester, MA, closed a Series C round of financing worth $14.2 million. Flagship Ventures led the deal, which was joined by return investors Agman Partners, Atlas Venture, GE, General Catalyst Partners, and RockPort Capital Partners.

—Cancer drug developer Ariad Pharmaceuticals (NASDAQ: ARIA) of Cambridge netted $30.9 million in an offering of 19 million new shares of stock-–$3 million worth of which were purchased by CEO Harvey Berger.

—Boston-based data-storage firm Iron Mountain (NYSE:IRM) announced a planned notes offering worth $450 million.

—IT-focused venture firm Longworth Venture Partners of Waltham, MA, reportedly raised $122 million of a targeted $180 million for its third fund.

—Cambridge-based drug developer Alnylam Pharmaceuticals (NASDAQ:ALNY) inked a deal with Vancouver-based Tekmira Pharmaceuticals (TSX:TKM) to develop new particles to deliver RNA-interference drugs. Financial terms of the agreement were not disclosed.

—Idenix Pharmaceuticals (NASDAQ:IDIX), also of Cambridge, priced a secondary public offering of 7.25 million shares at $3.14 each. Idenix develops treatments for Hepatitis C.

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New England’s life sciences companies gave us a number of cool new technologies and interesting deals to talk about this week.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ) finished cleaning up its Allston, MA-based plant after a viral contamination which caused 6-to-8 week supply shortages of two of its best-selling drugs.

–-Archemix, also of Cambridge, forged an alliance with Boulder, CO-based miRagen Therapeutics to develop drugs that combine the Massachusetts firm’s “aptamer” technology with the Colorado company’s microRNA technology. Specific financial terms of the arrangement weren’t disclosed.

—Waltham, MA-based medical device company Augmenix revealed in an SEC filing that it had collected $4.7 million out of an equity round potentially worth $7.5 million. Augmenix is developing a synthetic material to protect healthy tissue during radiation treatments for prostate cancer.

—Joule Biotechnologies, a heretofore stealthy startup in Cambridge stepped into the sunlight to show off its technology, which aims to produce fuels and chemicals using engineered microbes capable of photosynthesis—no plant material or algae required. Founded in 2007 by partners at Flagship Ventures, Joule believes its technology is capable of producing more than 20,000 gallons of ethanol or hydrocarbons per acre on an annual basis, and yielding transportation fuels at prices that rival those of petroleum-based fuels.

—Waltham-based Avila Therapeutics raised $30 million in a Series B financing round led by the Novartis Option Fund and joined by return investors Abingworth, Advent Venture Partners, Atlas Venture, and Polaris Venture Partners. Avila and Novartis Option Fund also reached an agreement worth as much as $200 million in upfront and future milestone payments to co-develop Avila’s drugs, which are designed to bind more tightly to their targets that traditional drugs.

—Clinical trials management software maker Phase Forward (NASDAQ: PFWD), also of Waltham, shelled out $11 million to acquire Indianapolis, IN-based Maaguzi. The Indiana firm runs an online service for collecting data from patients.

—Cerulean Pharma of Cambridge raised $10 million in a Series B financing round from return investors Polaris Venture Partners, Venrock Associates, Lux Capital, and Bessemer Venture Partners. The startup is developing nanoparticle-based treatments and plants to use some of the new funding to push it’s lead drug candidate, a cancer drug, through clinical trials.

—Shares of Cambridge-based Ariad Pharmaceuticals (NASDAQ: ARIA) surged after the company released promising preliminary data from a mid-stage trial of its lead drug candidate, ridaforolimus, as a treatment for breast cancer. More complete data on the drug should be available later this year.

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Three big pharmaceutical firms partnered with two New England life sciences companies this past week, and one ended a partnership.

—Ryan learned that some 60 of the 240 people who were employed by Lexington, MA-based Indevus Pharmaceuticals when it was acquired for $370 million by Endo Pharmaceuticals in March will be laid off. Chadds Ford, PA-based Endo (NASDAQ:ENDP) will also move research programs out of the Indevus facility in Lexington to Endo’s headquarters in Pennsylvania.

—Boston’s Partners HealthCare System revealed that it’s assembling a startup to commercialize a health self-monitoring system developed by Partners’ Center for Connected Health. The nascent company, which has yet to find a CEO or formally launch, already has two paying customers: storage giant EMC (NYSE:EMC) and Partners HealthCare itself.

—Exact Sciences (NASDAQ: EXAS)—a maker of a DNA-based screening test for colorectal cancer–-raised $8.2 million in a private placement of stock. The Marlborough, MA-based firm also licensed technology from the Mayo Clinic related to sample processing and data analysis for such tests.

—Drug giant GlaxoSmithKline pulled out of a co-development deal with Lexington, MA-based Synta Pharmaceuticals (NASDAQ: SNTA) after the subject of that collaboration, Synta’s elesclomol, failed in a pivotal clinical trial for patients with melanoma.

—Drug behemoth Novartis became the latest pharmaceutical company to back Boston-based Enlight Biosciences, which is developing technologies to bolster drug discovery and development. Enlight now has six such partners in total; each gains accesses to the technologies the startup develops on a pre-competitive basis.

—Drug colossuses Merck and Roche became the first research collaborators of Lebanon, NH-based Adimab, whose yeast-based antibody-drug discovery platform is designed to generate drug candidates in weeks rather than months. Adimab will use the proprietary platform to identify antibodies against multiple targets for Merck and against one target for Roche; both deals provide Adimab with upfront payments and licensing fees, as well as potential additional fees for pre-clinical commercial milestones.

—Two-time Boston-area startup founder Jeff Carbeck has signed up to work on a stealthy startup project with Flagship Ventures, Ryan reports. Carbeck, a former Princeton professor, is maintaining active roles at both Watertown, MA-based medical devices firm Arsenal Medical and Cambridge, MA-based nanotech firm Nano-Terra.

—Interlace Medical of Framingham, MA, raised $20.5 million in a Series C funding round led by Baird Venture Partners and HLM Venture Partners and joined by Hambrecht & Quist Capital Management, Aperture Venture Partners, New Leaf Venture Partners, and Spray Venture Partners. The startup will use the funds to begin commercializing its “MyoSure” system for removing uterine fibroids and polyps.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ) halted production at one of its major drug manufacturing plants after discovering viral contamination in one of the six bioreactors at the Allston, MA, site. The problem, which is expected by be resolved by the end of July, sent Genzyme’s stock price tumbling and is expected to cause shortages of the company’s two best sellers, Cerezyme and Fabrazyme.

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San Diego Gas & Electric says it is one of eight utilities in the United States, India, and Canada that will enable customers to access their daily energy use online by using Google’s PowerMeter gadget. When connected to a utility-installed smart meter, the PowerMeter displays personal electricity consumption data on home computers. SDG&E began installing smart meters last year, and plans to roll out the PowerMeter service in a partnership with Google later this year. SDG&E is a regulated public utility owned by San Diego’s Sempra Energy (NYSE: SRE).

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This past week produced a cornucopia of life sciences news, including new partnerships, personnel and real estate changes, venture deals, and some intriguing science.

—A team led by UMass Medical School researcher Michael Czech, co-founder of Worcester, MA-based RXi Pharmaceuticals (NASDAQ: RXII), reported in the journal Nature that it has come up with an oral pill form of an RNA-interference based drug, which passed an early test in mice. RXi has an exclusive license to the technology, which could conceivably help solve one of the biggest challenges in RNAi—getting the gene-silencing molecules where they need to go in the body.

—Luke pulled together some of the most interesting lessons that emerged in last week’s Xconomy Forum: Tomorrow’s Biotech—Innovators and Innovations. Definitely worth a read if you missed the event (or if you were there an want to reminisce).

—Cambridge, MA-based Acceleron Pharma unveiled plans to expand its workforce from 114 to 160 by the end of 2009, and to lease another 19,700 square feet of lab and office space in Cambridge, bringing its total footprint in the city to 95,000 square feet.

—Ironwood Pharmaceuticals of Cambridge, MA, inked a deal giving European development and commercial rights to Barcelona, Spain-based Laboratorios Almirall for linaclotide, Ironwood’s experimental drug for irritable bowel syndrome with constipation. The Cambridge firm will collect $40 million in up-front payments, another $15 million in payments for reaching near-term milestones, and $40 million in payments before the drug is commercialized—as well as a percentage royalty on sales if linaclotide can become a marketed product.

—Waltham, MA-based Inverness Medical Innovations (NYSE:IMA), a provider of medical diagnostics and health management … Next Page »

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