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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Stem cells and RNAi were the subject of a couple of interesting alliances announced this week. More on those, and the rest of the week’s New England life sciences news, below.

—Alkermes (NASDAQ: ALKS), a maker of drugs for central nervous system disorders, addiction, and diabetes, signed a lease to move its headquarters from Cambridge, MA, to Waltham, MA. The move, which should be complete in early 2010, is supposed to save the company $8 million a year starting in fiscal 2011.

—Ryan gave an intriguing look inside Lebanon, NH-based GlycoFi nearly three years after its acquisition for $400 million by drug behemoth Merck. Where such transactions often result in the smaller company’s dismantling and absorption into the larger firm, GlycoFi and its yeast-based technology are now the focal point of Merck’s strategy for taking on the market for generic versions of biotech drugs.

—Stemgent of Cambridge, MA, and Fate Therapeutics of San Diego launched the joint “Catalyst” program to offer new developments in stem (iPS) cell technology to large pharmaceutical companies, big biotech firms, and academic labs for a fee. For Stemgent, the program is an extension of its strategy of selling stem cell technologies from leading academic labs to the research market.

—Luke talked to Al Sandrock, senior vice president of neurology R&D at Cambridge, MA-based Biogen Idec (NASDAQ:BIIB), ahead of the annual meeting of the American Academy of Neurology. Biogen planned to highlight its multiple sclerosis products and pipeline at the meeting; yesterday, for instance, it presented a small study indicating that natalizumab (Tysabri) might help the body actually repair damage done by MS to nerves’ myelin coating.

—Cambridge, MA-based Vertex (NASDAQ: VRTX) reported more positive data on its experimental hepatitis C drug, telaprevir, at a scientific meeting in Denmark. If the results hold up in ongoing pivotal trials and Vertex wins …Next Page »

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It’s only been a few days since last I rounded up the deals news from New England’s tech and life sciences firms, but there are still a few transactions worth mentioning.

—Millennium, the Cambridge, MA-based subsidiary of Japan’s Takeda Pharmaceutical Company, paid $4 million up front to Seattle Genetics (NASDAQ: SGEN) for a worldwide license to the Bothell, WA-based firm’s antibody-based cancer drug technology. Millennium will also pay for development of the product candidate and royalties on any eventual sales.

—Watertown, MA-based A123Systems inked a deal to supply Chrysler with advanced lithium ion batteries for its new line of electric vehicles, the first of which is expected to hit the road next year. A123 will build a plant in Michigan to manufacture the batteries.

—Epix Pharmaceuticals (NASDAQ:EPIX) commenced an exchange offer for $100 million in debt in a bid to avoid bankruptcy. The Lexington, MA-based firm also sold certain market rights to its cardiovascular imaging agent, gadofosveset trisodium, to Lantheus Medical Imaging of North Billerica, MA, for $28 million.

—Bedford, NH-based Segway teamed with General Motors to develop a new electric-powered, two-wheeled, two-seater vehicle. The firms have already begun testing prototypes of the vehicle, called Project P.U.M.A. (for Personal Urban Mobility & Accessibility), which can go up to 35 miles per hour.

—Enterprise sales software maker Basho Technologies, of Cambridge, MA, raised $2 million in an initial close of its Series B round. Harbor Island Equity Partners of Wilmington, NC, led the deal, which was joined by Wilmington Investor Network, an angel group.

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It was a fairly quiet week for Northwest deals, with activity in biotech, software, and mobile. Let’s see if the sunny weather brings more action.

—Seattle Genetics (NASDAQ: SGEN), a Bothell, WA-based developer of cancer drugs, provided a worldwide license to use its technology to Millennium: The Takeda Oncology Company in exchange for $4 million upfront, as Luke reported. The technology combines antibodies that seek out tumors with toxins to make them more potent. Millennium will pay to develop the drug candidate, as well as a mid-single-digit percentage royalty on sales if it turns the technology into a product.

—Luke reported on the ongoing partnership between biotech startup VLST and Danish pharmaceutical giant Novo Nordisk in the South Lake Union neighborhood of Seattle. The original deal, announced in December, brought in $12 million to VLST in exchange for Novo gaining the rights to develop drugs against cell targets VLST has discovered for autoimmune and inflammatory diseases.

—Seattle-based Swype, which makes text-input software for mobile devices, raised $1.3 million in funding from angel investors and company management. Swype’s technology lets people enter text by tracing a path on a touch-screen keyboard using a stylus or their fingertip.

—Bellevue, WA-based Onehub, a maker of collaborative software for business users, closed about $600,000 in funding as part of an ongoing $1 million fundraising round. The investors and other terms were not disclosed. Onehub, founded in 2007, has developed a Web-based application that helps companies share information and manage projects.

—MDRNA (NASDAQ: MRNA), a Bothell, WA-based developer of drugs that use RNA interference technology, sold its assets related to a nasal spray drug for osteoporosis to Par Pharmaceutical, as Luke reported. MDRNA receives an undisclosed cash payment upfront, as well as a double-digit percentage royalty on sales of the product. Par will assume the manufacturing and operating costs related to the drug.

—Luke reported that Cambridge, MA-based Genzyme (NASDAQ: GENZ, the world’s largest maker of drugs for rare genetic diseases, is moving into cancer and multiple sclerosis by acquiring three drugs from German drugmaker Bayer AG—including one, Leukine, that gives Genzyme its first foothold in Seattle. Leukine, which is made in Seattle and Bothell, WA, boosts production of white blood cells for chemotherapy patients. Genzyme is not paying upfront fees, but expects to take over manufacturing of Leukine at a new factory in Snohomish County next year.

—Seattle cloud computing startup Skytap’s $7 million funding round from last month was worth a closer look. I spoke with CEO Scott Roza and director of product management Ian Knox about the financing, which came from the company’s existing Seattle-area investors Ignition Partners, Madrona Venture Group, and WRF Capital. Roza and Knox also touched on Skytap’s strategy as it prepares to take on big players in the cloud like Amazon, Google, and EMC.

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The executive suites of several New England’s biotech and medical device companies saw new faces this week.

—Cyberkinetics Neurotechnology Systems (OTC:CYKN), a Foxborough, MA-based developer of devices to treat and aid patients with spinal injuries, revealed to the Boston Globe that it is shutting down. Earlier this year Cyberkinetics sold the rights to its Andara Oscillating Field Stimulator to Waltham, MA-based NeuroMetrix for $350,000.

—The board of diagnostics maker Exact Sciences (NASDAQ:EXAS) replaced the Marlborough, MA-based firm’s CEO and CFO with veterans of another diagnostics firm. Kevin Conroy, Exact’s new chief executive, and Maneesh Arora, its new CFO, previously held those roles at Madison, WI-based Third Wave Technologies, which was acquired last year by Bedford, MA-based Hologic (NASDAQ:HOLX) for $582 million.

—Boston-based MedAptus raised $6 million to support the expansion of its medical-billing-software business. Previous investor Boston Millennia Partners led the deal.

—Former Wyeth executive George Vlasuk was named president and head of Sirtris, a Cambridge, MA, unit of British drug behemoth GlaxoSmithKline (NYSE:GSK). Vlasuk will head Sirtris’ efforts to develop treatments for Type 2 diabetes and other diseases of aging.

—Natick, MA-based Boston Scientific (NYSE: BSX) settled a lawsuit filed against it by Bruce Saffran, a doctor who alleged that two of Boston Scientific’s stent products infringed on patents he owns. As a result of the settlement, the Natick device maker will record a pre-tax charge to earnings of $50 million this quarter.

—Claros Diagnostics reportedly raised $4 million in a second round of financing. Previous investors in Woburn, MA-based Claros, which is developing point-of-care diagnostic tests for prostate cancer and other ailments, include Oxford Bioscience Partners, Bioventures Investors, Accelerated Technologies Partners, and Commons Capital.

—Two Cambridge, MA-based biotechs, Aveo Pharmaceuticals and Biogen Idec (NASDAQ:BIIB), both based in Cambridge, MA, inked a development deal around Aveo’s effort to discover antibody drugs targeting ErbB3, a cellular receptor found in abundance on several types of cancer cells. Financial terms of the agreement were not disclosed.

—Robert “Duffy” DuFresne was appointed as CEO of Ischemix, a developer of drugs for preventing tissue damage after heart attacks and other cardiac events. The Maynard, MA-based firm expects to begin mid-stage trials of its lead drug by the middle of this year.

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This week’s life sciences news was dominated by New England’s public companies—starting with three developments from Dyax.

—Last Wednesday, an FDA advisory committee voted by a margin of just 6-5 to recommend approval of ecallantide from Cambridge, MA-based Dyax (NASDAQ:DYAX). The drug, a treatment for the rare blood disease hereditary angioedema, is the lead drug candidate in Dyax’s pipeline.

–The next day, Dyax and its Cambridge neighbor Biogen Idec (NASDAQ:BIIB) announced that they’ve expanded a previous deal under which Dyax has discovered antibody drugs for Biogen. The new agreement, under which Biogen is entitled to 10 additional product licenses, includes a $5 million up-front payment to Dyax, research funding, up to $85 million in milestone fees, and royalties for each drug that Biogen brings to market through the partnership.

—And the day after that, Dyax announced it had inked an exclusive license deal with French drug firm Fovea Pharmaceuticals to develop a version of ecallantide for eye diseases.

—Worcester, MA-based RNAi-drug developer RXi Pharmaceuticals (NASDAQ:RXII) agreed to sell up to $25 million of its common stock to YA Global Investments over the next two years, in increments worth up to $500,000.

—Vertex Pharmaceuticals (NASDAQ: VRTX) of Cambridge, MA, announced a changing of the guard: founder, president, and CEO Josh Boger will retire on May 23, to be replaced by Vertex director Matthew Emmens, who will become president, CEO, and chairman of the board. Boger expressed his confidence in Emmens’ ability “to take the reins and guide Vertex as we bring our innovations to patients.”

—Cambridge, MA-based Idenix Pharmaceuticals (NASDAQ: IDIX) forged a deal granting pharma giant GlaxoSmithKline worldwide rights to its HIV drug IDX899. GSK will pay …Next Page »

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Everything else around here is frozen solid this week (hello, minus two degrees real-feel!), but the tech and life sciences deals are flowing.

—Two Massachusetts firms—Alnylam Pharmaceuticals (NASDAQ: ALNY) of Cambridge and Cubist Pharmaceuticals (NASDAQ: CBST) of Lexington—inked a marketing deal focused on Alnylam’s RNAi-based treatment for respiratory syncytial virus, or RSV. Under the terms of the deal, Cubist will pay Alnylam $20 million upfront, with an additional $82.5 million in future milestone-based payments on the table as well.

—Newton, MA-bases student-loan-search toolmaker SimpleTuition reportedly closed a $6 million Series C funding round from Atlas Venture, Flybridge Capital Partners, and North Hill Ventures, among others.

—Software maker StreamBase Systems of Lexington, MA, reportedly raised $6.24 million in a Series D funding round from return investors Accel Partners, Bessemer Venture Partners, Highland Capital Partners, and In-Q-Tel.

—Cancer drug developer Kolltan Pharmaceuticals of New Haven, CT—a spinoff of Yale University Medical School—closed a Series A round worth an impressive $35 million.

—Another cancer drug company, Cambridge, MA-based Forma Therapeutics, inked a license and option agreement with Novartis potentially worth more than $200 million.

—Woburn, MA-based Kiva Systems gained an important new customer—Gap Inc. Direct, which handles online orders for clothing chains Gap, Banana Republic, Old Navy, and Piperlime—for its system of robotic warehouse workers.

—Software maker WebLayers of Cambridge, MA, announced it had raised $3 million in an equity financing from Ascent Venture Partners, Cedar Fund, and Veritas Venture Partners.

—Boston-based Ze-gen raised $20 million in a Series B round of financing led by …Next Page »

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Lots of news from the bigger players (think Genzyme and Biogen Idec) in the Boston-area life sciences arena last week, plus a peep here and there from the startups.

—Alnylam Pharmaceuticals (NASDAQ: ALNY), a developer of RNAi-based drugs in Cambridge, MA, extended its collaboration with pharma giant Novartis (NYSE: NVS) through October 2009; the deal is worth up to $700 million for Alnylam.

—Allied Minds, a Boston-based investment firm that backs very young companies spun out of academic institutions, helped found a University of Colorado spinoff called Precision Biopsy; the startup is developing “optical” biopsy needles for prostate cancer diagnosis.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ) inked a deal worth up to $437 million in upfront and milestone payments to co-develop and co-market a drug from South Plainfield, NJ-based PTC Therapeutics. The drug is already being tested as a treatment for Duchenne Muscular Dystrophy, and could theoretically be useful against a host of other genetic diseases.

—And speaking of Genzyme, Luke profiled the company’s efforts to capture a big piece of the market for multiple sclerosis drugs—a market that fellow Cambridge firm Biogen Idec (NASDAQ: BIIB) currently leads.

—Speaking of Biogen’s multiple sclerosis drugs, the company and its partner, Ireland’s Elan, reported that their MS drug Tysabri is being taken by more than 31,800 patients worldwide—and and that they haven’t detected any new cases of PML among the drug’s users. Tysabri was temporarily pulled from the U.S. market several years ago after a few patients on the drug came down with the rare brain infection.

—Speaking of Biogen one more time, a company spokesperson reassured us that if Swiss pharma giant Roche succeeds in its unsolicited bid to acquire South San Francisco-based Genentech (NYSE: DNA) it will not rock the boat for Rituxan, a lymphoma drugs that Biogen currently co-markets in the U.S. with Genentech; Roche, which already markets the drug overseas, will simply become Biogen’s new partner.

—Having abandoned plans to go public back in January, Waltham, MA-based molecular diagnostics firm BG Medicine raised $40 million in a Series D financing. New investors Legg Mason Capital Management, GE Asset Management, and SMALLCAP World Fund joined existing investors Flagship Ventures, Gilde Healthcare Partners, Humana, and Stelios Papadopoulos in the deal.

—Luke had an interesting talk with Tod Woolf, the CEO of Worcester, MA-based RXi Pharmaceuticals (NASDAQ: RXII), which is seeking to turn RNAi science from the likes of Nobel Prize winner Craig Mello and others into treatments for a host of diseases. Luke looked at the unusual path RXi took to the NASDAQ exchange and the firm’s plans for funding its research while the market is down.

—Luke also had an interesting talk with the CEO of Lexington, MA-based Epix Pharmaceuticals (NASDAQ: EPIX). Michael Kauffman gave a preview of data that Epix plans to present at a big Alzheimer’s disease conference in a few days showing that its experimental treatment for the ailment is promising—though not quite as promising as a number-crunching error last year originally led observers to believe.

—Medical needle maker Needletech Products of Attleboro, MA, said it will be acquired for $47.8 million by Buford, GA-based medical device maker Theragenics (NYSE: TGX).

—Cambridge, MA-based Peptimmune completed a second close of its Series D financing worth $8.9 million and plans to use the money to further development of its treatment for multiple sclerosis. The round was led by New Enterprise Associates, MPM Capital, Hunt Ventures, Boston Medical Investors, and Silicon Valley Bank Capital.

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New England’s public life sciences firms were feeling particularly newsworthy this last week, it seems. But plenty of private firms are represented in this first item:

—Wade uncovered yet another thriving New England tech cluster: The thirty-odd “Health 2.0″ firms using the Web to deliver various kinds of healthcare services. The next day he profiled one such company, Newton, MA’s InnovationRx, that uses e-mail, text messages, and phone calls to help patients remember to take their medicine.

—At an annual meeting, shareholders rejected billionaire investor Carl Icahn’s bid to put his people on the board of Cambridge, MA-based Biogen Idec (NASDAQ: BIIB).

—Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ: ALNY) inked a deal worth up to $93 million, plus royalties, with Japan’s Kyowa Hakko Kogyo to commercialize an RNAi-based treatment for respiratory syncytial virus in Japan and other major Asian markets.

—ImmunoGen (NASDAQ: IMGN) of Waltham, MA, raised about $25 million in a sale of 7.8 million shares of stock to Ziff Asset Management.

—GTC Biotherapeutics of Framingham, MA, forged a partnership worth as much as $257 million with Deerfield, IL’s Ovation Pharmaceuticals. The firms will work together to try to bring GTC’s ATryn—an anti-clotting and anti-inflammatory drug produced in the milk of genetically engineered goats–to market in the United States.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ) and Isis Pharmaceuticals (NASDAQ: ISIS) of Carlsbad, CA, finalized the terms of their partnership to develop Isis’s cholesterol-lowering drug, mipomersen. The new terms shift $50 million more of the development costs to Isis.

—RXi Pharmaceuticals (NASDAQ: RXII), a Worcester, MA-based firm seeking to commercialize RNAi-based medicines, raised about $8.7 million in a private placement of stock.

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Alnylam Pharmaceuticals (NASDAQ: ALNY) announced it has forged an alliance with Japan’s Kyowa Hakko Kogyo to commercialize the Cambridge, MA-based firm’s RNAi-based treatment for respiratory syncytial virus in Japan and other major Asian markets. The deal calls for Kyowa Hakko to pay Alnylam $15 million upfront, with as much as $78 million in development and sales milestone payments, plus royalties, on the table.

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The face of online health care is changing in Massachusetts—and probably for the better. Today one of the state’s leading health insurance companies, Blue Cross Blue Shield of Massachusetts (BCBSMA), announced that it has signed an agreement to integrate with the Google Health platform. It is the first health insurance company to do so.

Google Health, a free service that patients can use to organize their health information online, launched in the U.S. last month with a list of provider partners that includes the Beth Israel Deaconess Medical Center (as we reported here), Cleveland Clinic, Walgreens, and CVS/CareMark.

The integration is supposed to be finished sometime this fall, at which time Google Health will be offered to BCBSMA members. The service will allow members to store and manage their medical records and health info (including insurance claims) in one secure location, download their prescription history from other connected providers such as pharmacies and doctors’ offices, and search for a doctor or hospital online.

You wouldn’t necessarily expect a huge insurance company to be quick on its feet when it comes to adopting technology, but BCBSMA has previously funded the Massachusetts eHealth Collaborative and is a founding member of the Massachusetts eRx Collaborative. The Google partnership should give members “easier and more portable access to their health care information,” said Steven Fox, BCBSMA’s vice president of provider network management, in a statement.

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Japan’s Takeda took another bite out of Boston-area biotech this week, while Ernst & Young’s numbers showed just how juicy that apple is. Here’s more on that, and the rest of the week’s life sciences news.

—Not long after its $8.8 billion acquisition of Millennium Pharmaceuticals, Japanese drug giant Takeda Pharmaceutical Company forged an agreement with one of the firm’s Cambridge, MA, neighbors, Alnylam Pharmaceuticals (NASDAQ: ALNY). The deal is potentially worth more than $1 billion over five years.

—Ernst & Young revealed, presumably to nobody’s surprise, that 2007 rocked for New England biotech. Greg summed up the sunny stats.

—In a letter to shareholders, activist investor Carl Icahn once more made the case for his slate of nominees to the Biogen Idec (NASDAQ: BIIB) board, and said if his representatives are elected they’ll do more than agitate for a quick sale of the Cambridge, MA-based biotech.

—Boston Scientific (NYSE: BSX) was hit with a $250 million jury verdict in a patent dispute with Medtronic. The Natick, MA, firm said it would look for the verdict to be set aside.

—Differential Proteomics, a diagnostics startup based in Beverly, MA, took the $10,000 first prize in the 2008 North of Boston Business Plan Competition.

—Atlas Venture of Waltham, MA, placed a bet on the emerging field of mircoRNA by co-leading an $8 million Series A investment in Boulder, CO-based Miragen Therapeutics, which plans to use the approach to develop treatments for heart failure and muscle disease.

—The assets and operations of Meriden, CT-based flu vaccine maker Protein Sciences were bought by Emergent BioSolutions, of Rockville, MD, in a deal worth up to $78 million.

—HyperMed, a medical imaging firm in Burlington, MA, raised $4 million from Greenwich, CT’s GBP Capital.

—NxStage Medical (NASDAQ: NXTM) of Lawrence, MA, a dialysis products maker, unveiled its plan to raise $43 million via a private placement of common stock and warrants.

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