—It wasn’t exactly news when the board at San Diego-based Illumina (NASDAQ: ILMN) said it had rejected the $5.7 billion hostile takeover offer from Swiss drug maker Roche. Now Wall Street’s arbitragers are placing their bets on whether Roche can prevail. The most intriguing news about the deal, however, came from The Wall Street Journal, which revealed potential conflicts of interests with Illumina’s key adviser, Goldman Sachs.

—A new molecular diagnostics startup stepped into the light in San Diego. Applied Proteomics named Peter Klemm as CEO, and disclosed it raised $22.5 million in venture capital last summer from Vulcan Capital and Domain Associates. Applied Proteomics also said it moved to San Diego last June from the Los Angeles area, and double its staffing over the next year.

—San Diego-based Tocagen and Siemens Healthcare Diagnostics disclosed a partnership that will begin with Siemens’ support of clinical trials Tocagen has planned for its viral gene therapy treatments for primary brain cancer. Siemens said it will help provide companion diagnostics that are intended to help doctors decide the best course of treatments for patients, based on their unique genetic characteristics.

—San Diego’s OncoSec Medical, which was created out of a reverse merger less than a year ago, is beginning mid-stage trials of a treatment that combines electroporation and immunotherapy in patients with three types of skin cancer. Electroporation is a technology that causes cancer cells to take up higher concentrations of anti-cancer drugs by administering pulses of electricity directly to the cancer cells. OncoSec is trying it on patients with metastatic melanoma, Merkel cell carcinoma, and cutaneous T-cell lymphoma.

—Brooks Life Science Systems, a Poway, CA-based division of Brooks Automation, (NASDAQ: BRKS), said it had established a development and commercialization partnership with The Scripps Research Institute (TSRI). Brooks plans to manufacture and commercialize a microplate imaging system under an exclusive licensing agreement with the biomedical research institute.

—San Diego-based Prometheus Laboratories Inc., a specialty pharmaceutical and diagnostic company, said it signed a research and collaboration agreement that provides its proprietary cancer diagnostic technology to an unnamed global pharmaceutical. Financial terms were not disclosed. Prometheus said its technology can detect the activation of specific cancer pathways with high levels of sensitivity and specificity.

—San Diego-based Synthetic Genomics and Ipswich, MA-based New England Biolabs (NEB) said they signed a non-exclusive licensing agreement allowing NEB to commercialize the “Gibson Assembly Master Mix,” a one-step, isothermal approach to enable the rapid assembly of multiple DNA fragments. The companies said Daniel Gibson and colleagues at the J. Craig Venter Institute (JCVI) developed the technology as part of a program sponsored by SGI. Financial terms were not disclosed.

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Plans for IPOs and venture funding dominated the New England deals news this week.

—A new seed fund, backed by venture firm New Enterprise Associates and hosted by Harvard, came out of the woodwork last week. The Experiment Fund will invest up to $250,000 in seed funding in selected startups, with a focus on technologies that come out of Cambridge, MA. The news broke just a few days ahead of Facebook—the one that got away—revealing its plans to go public.

—Radius Health, a Cambridge-based startup working on treatments for osteoporosis, filed paperwork indicating its plans to raise as much as $86 million in an initial public offering.

—A PricewaterhouseCoopers and National Venture Capital Association report shows a mixed picture for life sciences investing in 2011, my colleague Arlene reported. Biotech companies raised $4.7 billion, showing a 22 percent increase over 2010, but the deal volume for the sector dropped 9 percent to 446 transactions. Medical devices companies also showed an increase in funding dollars but a drop in number of deals.

—Cambridge-based Brightcove set the price range of its initial public offering at $10 to $12 per share, according to an amended filing with the SEC. The video hosting startup plans to sell 5 million shares, and give underwriters the option to purchase another 750,000 shares. Brightcove first filed paperwork last August indicating it intended to raise $50 million in an IPO.

—Synchroneuron of Waltham, MA, nabbed $6 million in Series A funding from Morningside Technology Ventures. The startup is developing treatments for movement disorders such as tardive dyskinesia.

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We’re starting to see fresh signs of life among the Internet software startups in San Diego. Check out this news.

—During a visit last week, TechStars CEO David Cohen talked with the leaders of San Diego’s grassroots Web startup community about the factors that help to create and sustain entrepreneurial communities. One crucial issue confronting San Diego is a crying need for savvy and experienced Internet entrepreneurs who are willing to “pay it forward” by mentoring a new generation of startups.

—A dozen seed-stage companies moved into the new EvoNexus incubator in downtown San Diego. EvoNexus, which was founded by the CommNexus non-profit industry group, will continue to operate its original incubator in University City, where eight startups are taking root. In both locations, EvoNexus provides office space, utilities, and other services free of charge and with no strings attached.

—Sigma Partners led a $10 million round in venture funding for San Diego-based MOGL, a Web startup that has developed a comprehensive customer loyalty program for restaurants and bars, to fuel its expansion into San Francisco and New York. San Diego’s Avalon Ventures and Austin, TX-based Austin Ventures joined in the round.

—San Diego’s MicroPower Technologies named two new board members after raising $6.5 million in Series C funding in a deal that was led by Motorola Solutions Venture Capital and joined by an undisclosed private fund. MicroPower Technologies, which uses wireless networking technologies to create low-cost surveillance capabilities, named PacketVideo CEO Jim Brailean and former DivX CEO Kevin Hell to its board. Hell, who is now chairman of San Diego’s EvoNexus incubator, will join as MicroPower chairman.

—San Diego’s StockTwits said it has established a partnership with Toronto’s Q4 Web Systems, which provides … Next Page »

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—San Diego’s Amylin Pharmaceuticals says Bydureon, its new once-a-week drug for treating Type 2 diabetes can hit the market as early as next month, after the FDA cleared Bydureon. The FDA rejected the Amylin’s drug twice before. An estimated 26 million people in the United States, or roughly 8 percent of the population, have type 2 diabetes.

—San Diego’s life sciences sector has expanded since 2009, with employment increasing by more than 5,550 jobs, or 15 percent, over the past two years, according to a new economic report from Biocom, the local industry group. The comprehensive study counted more than 1,700 life sciences companies with a total of 41,937 employees throughout San Diego County in 2011, and says those numbers are expected to grow over the next two years.

—The FDA gave its approval to Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX), which has substantial operations in San Diego, for a new drug called Ivacaftor (Kalydeco), developed to treat a rare form of cystic fibrosis. The twice-a-day pill targets about 4 percent of the 30,000 patients in the U.S. with cystic fibrosis.

—Johnson & Johnson’s reorganized R&D operation in San Diego, now known as Janssen Healthcare Innovation, is trying an experiment in innovation by creating an incentive prize challenge. Janssen is offering a total of $250,000 for technology that helps improve care for patients who have just been discharged from a hospital.

—The folks who produce the quarterly MoneyTree report on venture capital funding just released a deeper dive into the details of life sciences investments. The survey shows that VC funding for life sciences increased 21 percent nationwide in 2011, with a total of $7.5 billion going into 785 deals. San Diego ranked third among metropolitan regions in terms of capital invested in the fourth quarter. The top five are Bay Area ($498 million), Boston ($384 million), San Diego Metro ($193 million), NY Metro ($98 million), and Orange County ($97 million

—Optimer Pharmaceuticals (NASDAQ: OPTR) CEO Pedro Lichtinger outlined his plans for expanding the market for the company’s first product, the antibiotic fidaxomicin (Dificid), as a preventative therapy for hospital patients at risk for a nasty intestinal infection called C. difficile. San Diego-based Optimer is planning a clinical trial to prove the drug can help prevent severe diarrhea in patients undergoing bone-marrow transplants.

—A tweet from Bob More of Frazier Healthcare Ventures prompted Luke to delve into the importance of character among life sciences leaders in his BioBeat column. “Politics pretty similar to backing CEO’s,” More said. “Newt may be smart and a good debate guy. But Newt=Smug. Never back smug,”

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This week’s deal news covered a breadth of sectors: biotech, medical devices, mobile applications, software, and robotics. Not to mention a major venture capital fund raise.

—Waltham, MA-based drugmaker Avila Therapeutics was bought by New Jersey-based Celgene (NASDAQ: CELG) for $350 million, with as much as another $575 million available in milestones. Avila is a maker of “covalent” drugs that are designed to shut down the activity of disease-causing proteins for a prolonged period of time.

—Verastem, a young Cambridge, MA-based biotech working on drugs targeting cancer stem cells, completed its initial public offering, led by UBS and Leerink Swann. The IPO (5.5 million shares sold at $10 apiece) represented a strong showing among investors, as Verastem originally indicated it planned to sell 4.5 million shares priced between $9 and $11 each. The underwriters have a 30-day option to buy another 825,000 shares.

—Burlington, MA-based ConforMIS, a maker of knee implant systems, raised $89 million in a Series E funding from private equity investors and government investment funds abroad. The company said it will put the money toward sales, manufacturing, and expansion of its technology.

—Co3 Systems, a maker of data loss management software, received new funding from Fairhaven Capital. The Cambridge, MA-based startup said it will put the money (whose sum was undisclosed) toward sales, marketing, and engineering.

—Malborough, MA-based medical device startup Navilyst Medical will be acquired by Albany, NY-based AngioDynamics (NASDAQ: ANGO) in a transaction valued at $372 million, based on the company’s $14.20 per share closing stock price Monday. Navilyst, which focuses on … Next Page »

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—Peter Clarke of EE Times reported that San Diego’s Qualcomm (NASDAQ: QCOM) has acquired Andover, MA-based Pixtronix, a startup founded in 2005 to develop Microelectromechanical systems (MEMS) display technology. Qualcomm, which confirmed the deal with EE Times but provided no details or press release about the deal, reportedly spent between $175 million and $200 million for Pixtronix. The Massachusetts company founded by Nesbitt Hagood raised more than $53 million in venture funding, athough the Pixtronix technology has not yet been introduced to the market. Qualcomm has spent years working to refine its own MEMS-based display technology—known as Mirasol.

—More than 200 entrepreneurs turned out to hear TechStars founder and CEO David Cohen talk about the startup accelerator program he helped to launch in Boulder, CO, in 2007. Cohen told the rapt audience during a San Diego Tech Founders meetup that the Internet software community in Boulder “is just totally on fire” compared to five years ago. This was the night after Cohen met with local tech leaders to discuss the steps that helped boost the entrepreneurial ecosystem in the Colorado college town. Xconomy San Diego arranged the dinner discussion, and I plan to have more about our conversation later this week.

—Meteorologist Stephen Bennett and investor John Plavan founded San Diego’s EarthRisk Technologies in mid-2010 with the idea of creating predictive analytics technology that could extend the range of weather long-term forecasts from two weeks to 30 or 40 days. They are now providing their Web-based technology to commodities and energy-trading firms on a subscription-basis. Bennett told me the core business at EarthRisk Technologies is focusing on extreme weather events—heat waves, frigid cold snaps, and storms because extreme events are the ones with the highest impact.

—Mark Heesen of the National Venture Capital Association gave a good-news, bad-news presentation to the San Diego Venture Group last week. Among the interesting bright spots: Corporate venture capital is growing and San Diego-based Qualcomm now ranks as the nation’s second-largest corporate venture outfit. The bad news? U.S. VC firms invested $28 billion in startups last year, but only … Next Page »

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It was a busy news week in the New England life sciences scene, with acquisitions, clinical data, and partnership deals.

—Thanks to a new co-promotion deal, Genzyme will begin marketing a diagnostic test for thyroid cancer developed by South San Francisco-based Veracyte. Genzyme, the Cambridge, MA-based unit of Sanofi (NYSE: SNY) makes a common drug for treating the disease.

—Cambridge-based Infinity Pharmaceuticals (NASDAQ: INFI) presented data from a 16-patient study indicating saridegib, its experimental once-daily pill, could potentially shrink tumors and help people live longer when combined with chemotherapy.

—Millennium, also of Cambridge, nabbed FDA clearance to begin selling a version of the multiple myeloma drug bortezomib (Velcade) that can be injected just under the skin, as well as intravenously. It’s significant because the under-the-skin drug seems to be more tolerable, reducing the drug’s side effect of nerve damage in the fingers and toes.

—Xconomy national biotech editor Luke Timmerman wrote about how Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) and its South San Francisco-based partner Alios Biopharma are positioning themselves to defend their share of the hot growing market for hepatitis C treatments.

—And my colleague Arlene wrote about the family-run business that is Woburn, MA-based Courtagen Life Sciences. Three brothers fill the roles of CEO, president, and chief scientific officer, while their dad chairs the board. Read about more about how it all came together.

—Bedford, MA-based Avila Therapeutics, a maker of so-called covalent drugs for treating cancer, was bought by New Jersey-based Celgene (NASDAQ: CELG) for $350 million upfront. Potentially $575 million more could come to Avila through milestones. The startup’s venture investors included Polaris Venture Partners, Atlas Venture, Abingworth Management, and Advent Venture Partners. Check out investors’ and friends’ reactions to the deal across the Web here.

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The unsolicited $5.7 billion offer that Roche made for Illumina will no doubt dominate San Diego’s biotech news for weeks to come. We have it and more.

—Switzerland’s Roche offered $5.7 billion, or $44.50 a share, for San Diego-based Illumina (NASDAQ: ILMN in a hostile bid disclosed yesterday. Roche’s bid to stake a claim in genetic diagnostics by acquiring the market-leading maker of DNA sequencing instruments would be the Swiss pharma giant’s biggest deal since its $46.8 billion buyout of Genentech almost two years ago. Roche is the world’s biggest maker of cancer drugs, which suggests its quest for Illumina represents a significant move to base cancer treatments on each patient’s genome.

—Venture capital investors sank $4.73 billion into 446 biotechs nationwide in 2011, according to the MoneyTree report from the National Venture Capital Association, PwC, and Thomson Reuters. But as Luke pointed out in his BioBeat column, there is an alarming drop in support for early stage life sciences startups. Only 153 biotech and medical device startups got their first round of financing in 2011, the lowest amount of seed investment activity in 15 years.

—At an Xconomy dinner discussion, former Amira Pharmaceuticals CEO Bob Baltera said insufficient access to capital is the biggest driver for decision-makers on both sides of biotech-pharma partnerships. So what are some other key factors? We asked some of San Diego’s life sciences leaders to explore the question in an “on the record” dinner discussion late last year.

—San Diego’s Sequenom (NASDAQ: SQNM) completed its secondary public offering, raising roughly $62 million in gross proceeds (before underwriting costs) in the sale of 14.95 million shares, including additional allotments granted to underwriters. Sequenom said it plans to use the net proceeds for … Next Page »

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An acquisition and startup financings made up the New England deals news this week.

—Waltham, MA-based marketing software firm Constant Contact acquired the Boston startup CardStar, the developer of a mobile app for customer loyalty and rewards programs. The deal, whose terms were undisclosed, enables Constant Contact (NASDAQ: CTCT) to expand its marketing offerings for small businesses.

—My colleague Greg rounded up the top 10 venture deals in the Boston area from the fourth quarter of 2011. Rapid7, Warp Drive Bio, and Agios Pharmaceuticals were at the top.

—Hewlett-Packard has spent more than $10 million to set up a new office near the Alewife train station in Cambridge, MA. The office serves as the new headquarters for Vertica, the big data company HP acquired last winter (previously based in Billerica). The new facility will also serve as a center for technology development and local outreach.

—Bluefin Labs, a Cambridge-based startup focused on understanding social media conversation surrounding TV, nabbed $12 million in Series B financing. The deal was led by Time Warner Investments, and included new investor SoftBank Capital and return backers Redpoint Ventures and Lerer Ventures. Bluefins says it will put the money toward sales and client services, as well as its social analytics technology and further R&D.

—Mevion Medical Systems, a radiation therapy company based in Littleton, MA, announced it had pulled in $45 million in funding from ProQuest Investments and existing investors Caxton Heath Life Sciences, Venrock, and CHL Medical Partners. The money will go toward development of its proton beam radiation therapy system, which is designed to be smaller and less expensive than existing X-ray radiation therapy devices.

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—Venture capitalists invested $269 million in 23 deals in the San Diego area during the last three months of 2011, according to the MoneyTree Report from the National Venture Capital Association, PwC, and Thomson Reuters. That was almost a 20 percent gain in dollars, but a 28 percent slide in deal count from MoneyTree data for the fourth quarter of 2010. For the full year of 2011, the MoneyTree VC survey said $829 million was invested in 104 deals in San Diego, a 5 percent decline in dollars and a 17 percent slide in deals from the $871.7 million sunk into 126 San Diego deals in 2010.

—What should students study now to be prepared for the workplace 10 years from now? We asked that question of 22 Xconomists, including San Diego Xconomists Ramesh Rao, Duane Roth, Drew Senyei, Larry Bock, and Robert Noble. We’ve compiled all 22 answers in an Xconomy special report on education, which you can find here.

—San Diego Gas & Electric hosted a grand opening of its new Energy Innovation Center, which is designed to serve as an energy innovation showcase and education facility, and to meet the U.S. Green Building Council’s requirements for a platinum LEED (Leadership in Energy & Environmental Design) certificate. The center includes a full commercial “food service demonstration kitchen” where San Diego chefs can test their recipes on energy efficient appliances and restaurant owners can learn about the advantages of new and more energy efficient equipment. Utility officials said Commercial kitchens are particularly energy intensive.

—San Diego-based Tealium raised $1.1 million in Series A financing from private investors, and plans to use the funding to expand development of the tag management technology the company created to help enterprise customers manage their online marketing. Tealium said the investors include Limelight Networks CEO Jeff Lunsford, former Visual Sciences CEO Jim MacIntyre, Collective CEO Joe Apprendi, EyeWonder CEO John Vincent, and eValue Group CEO Thomas Falk.

—After previewing their plans last year, the X Prize Foundation and San Diego-based Qualcomm Foundation officially unveiled the Qualcomm “Tricorder” X Prize, a competition offering $10 million to the team that can develop new wireless diagnostics technology. The winning entry must be able to accurately diagnose a set of 15 diseases across 30 consumers in three days, capturing real time, critical health metrics such as blood pressure, respiratory rate, and temperature, and providing information in a consumer-friendly way.

—Qualcomm’s leadership has been talking for several years about the anticipated competition between its ARM-based semiconductors and the CPUs developed for desktop computing in the expanding market for smart devices. Now some of those skirmishes are beginning. Illinois-based Motorola Mobility (NYSE: MMI)  said recently it would use Intel’s (NASDAQ: INTC) latest low-power x86 Atom processor in a number of future Motorola products, marking Intel’s opening move into the smartphone market. A Motorola spokeswoman told me by email, “We will continue to use multiple chip set vendors.” Qualcomm (NASDAQ: QCOM) already has hundreds of mobile devices using its Snapdragon processor, and has been working with manufacturers on hundreds more.

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Here’s our weekly roundup of San Diego’s life sciences news.

—Jeff Shuren, director of the FDA’s Center for Devices and Radiological Health (CDRH), briefed reporters in San Diego on his efforts to make the regulatory review of new medical devices more predictable, transparent, and efficient. Shuren is undertaking reforms at a time when eight out of 10 biomedical CEOs say they “agree or strongly agree” that the FDA regulatory approval process has slowed the growth of their organizations.

—More than 500 people turned out Monday evening for the open house that Johnson & Johnson’s (NYSE: JNJ) new Janssen Labs startup center. The first four startups to be inducted are Diomics (diagnostics, integrated DNA analysis); Neurolixis (drugs for schizophrenia, Parkinson’s and other CNS disorders); Tem Systems (comprehensive blood test for anti-coagulants); and Yolia Health (optometry device company).

—San Diego-based Auspex Pharmaceuticals, which is developing deuterium-based drugs, has raised $3 million of a $6 million round of debt and convertible promissory notes, according to a regulatory filing. Previous investors include CMEA Ventures, Costa Verde Capital, and Thomas McNerney & Partners. Auspex uses deuterium to replace metabolically sensitive hydrogen atoms in compounds to create new versions of existing drugs.

—BrainCells, a San Diego developer of neurological drugs, raised $2 million toward an $8 million round of debt, rights and securities, according to a regulatory filing. BrainCells previously raised $77 million from Alexandria Real Estate Equities, Bay City Capital, MedImmune Ventures, Mitsubishi UFJ Capital, Mizuho Capital, NeuroVentures, New Enterprise Associates, Oxford Bioscience Partners, Pappas Ventures and Technology Partners, according to VentureWire. The company says it is developing novel therapies for treating central nervous system (CNS) diseases, based on the principal of blocking select metabotropic glutamate receptors (mGluR).

—To have the skills needed in 2022, San Diego Xconomists Robert Noble and Larry Bock recommend that students should “learn how to learn.” Drew Senyei says students should study anything they are passionate about; Duane Roth would like to see a new major that encompasses engineering, biology, chemistry, physics, law, business, humanities and communications; and Ramesh Rao would emphasize studying new techniques for sensing data, as well as data analysis. They all offered their views for an Xconomy special report on education, and what students should be studying today to be prepared for 10 years from now. Their comments are available online here.

—In a talk with Sanofi CEO Chris Viehbacher, Luke explained the company’s strategy since it acquired Cambridge, MA-based Genzyme, and cut back on its internal research and development.

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Web startups, venture firms, life sciences companies, and a biofuels developer rounded out the deals news this week.

—Cambridge, MA-based Flagship Ventures announced it had closed a $270 million fund, surpassing the $250 million it had originally targeted for its fourth fund.

—Extreme Reach, a Needham, MA-based startup developing cloud storage technology for delivering video ads to TV and Web publishers, said it closed a $9 million credit line from TD Bank. The startup also acquired commercial talent rights management and payment firm Spotlight Business Affairs, in a deal that enables Extreme Reach’s ad distribution system to be in compliance with existing talent and rights agreements.

—Massachusetts regained the number two spot for venture funding and deals in the fourth quarter of 2011, with $959 million invested in 93 transactions, according to a report from the data firm CB Insights. Nationally, venture dollars and deals had their strongest showing in a decade, at $30.6 billion invested in 3,051 deals.

—Cambridge-based Constellation Pharmaceuticals inked a drug development deal with Roche’s Genentech unit that’s worth $95 million in an upfront payment and three years of research support. It’s also eligible for milestone payments and royalties on the products that could potentially result from the deal.

—Bedford, MA-based Joule Unlimited announced it had pulled in $70 million in financing from the aforementioned Flagship Ventures and other new and existing investors whose identities it did not reveal. The money will go to a New Mexico facility that Joule hopes will demonstrate its ability to scale its technology for producing fuels from sunlight and carbon dioxide.

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Development deals, clinical advances, startup funding, and new hires made up the New England life sciences news this week.

—Chelsea, MA-based Civitas Therapeutics, a spinout from the Waltham, MA, biotech Alkermes (NASDAQ: ALKS), said that its inhaled form of the Parkinson’s disease drug L-dopa performed well in a Phase 1 clinical trial. The study aimed to test the drug’s safety and whether the drug’s delivery to the lungs gets it into the bloodstream in levels that produce a therapeutic outcome.

—Serial biotech entrepreneurs Bob Langer (of MIT) and Omid Farokhzad (of Harvard Medical School) have founded their newest company, Blend Therapeutics, alongside MIT professor Stephen Lippard. Blend is reportedly backed by Flagship Ventures, New Enterprise Associates, and NanoDimension.

—Cambridge-based genomics analysis startup Knome named former NormOxys CEO Martin Tolar its new chief executive and landed a new contract from Johns Hopkins University.

—Watertown, MA-based Forma Therapeutics announced a cancer drug discovery partnership with Johnson & Johnson’s (NYSE: JNJ) Janssen Biotech, worth up to $700 million over time. That’s less than a week after Forma’s $65 million partnership with Boehringer Ingelheim was announced.

—Warp Drive Bio came out of the woodwork this week with $125 million in funding, and hopes to examine the genetic makeup of plants, animals, and other organisms to find hot new drugs. Cambridge-based Warp is backed by Boston firm Third Rock Ventures, Greylock Partners, and French pharmaceutical giant Sanofi, and has an elite roster of founders, including Harvard genomics expert George Church.

—Cambridge-based Flagship Ventures surpassed its initial $250 million expectation for its fourth fund, announcing the fund closed at $270 million. It will focus on investments in the life sciences and cleantech sectors.

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There was a whole lot of life sciences news over the past week. Here’s my roundup.

—Carlsbad-based Life Technologies (NASDAQ: LIFE) said it’s taking orders for a benchtop genome sequencer that can to decode an individual’s DNA within 24 hours and at a cost of roughly $1,000. The company priced its new Ion Proton Sequencer at $100,000 to $150,000, which also represents a dramatic reduction compared with the cost of existing DNA sequencers, and might even entice some practicing physicians to buy into the idea of personalized medicine. A cross-town rival, San Diego-based Illumina, also introduced an improved version of its gene-sequencing machine capable of same-day service, although Forbes’ Matthew Herper says Illumina’s HiSeq 2500 is priced at $740,000.

—A $1 million gift to the Tech Coast Angels from the family of slain TCA member and life sciences investor John G. Watson has enabled the angel group to establish a nonprofit foundation to support entrepreneurism in the San Diego region. A financial adviser, who awaits sentencing following his conviction two months ago, murdered Watson in his La Jolla town home. Watson’s sister, Gillian Ison, told the TCA, “John loved investing, innovation, and the entrepreneurial spirit that he discovered when he arrived in San Diego. We believe that a foundation supporting entrepreneurism is the best way to honor his memory and his life.”

—San Diego’s AnaptysBio said it has established strategic alliances with Novartis and an undisclosed pharmaceutical company. The company plans to use its proprietary technology to discover and develop new therapeutic antibodies with multiple cancer-related therapeutic targets. AnaptysBio said the two deals provide global rights to develop and commercialize a limited number of antibodies against each cancer target that AnaptysBio generates.

—In his BioBeat column, Luke previewed the five myths likely to make the rounds at this week’s JP Morgan Healthcare Conference in San Francisco. You could say that Luke inoculated readers from excessive optimism by writing, “Hope and hype are a couple essential ingredients in this business, and every year both are on display at this conference. Sometimes the wishful thinking can congeal into conventional wisdom.” Is that good, or what?

— Wylie Vale, a Salk Institute scientist, renowned expert on brain hormones, and founder of San Diego’s Neurocrine Biosciences (NASDAQ: NBIX), died on Jan. 3 while vacationing in … Next Page »

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Boston area software and life sciences startups are starting off the new year right with a slew of financing, acquisitions, and partnerships news.

—Marlborough, MA-based Physicians Interactive Holdings received a $17 million pledge from Merck Global Health Innovation Fund to develop Web and mobile apps for connecting physicians and life sciences companies.

—Repeat biotech entrepreneurs Bob Langer and Omid Farokhzad founded a new startup, called Blend Therapeutics, along with Stephen Lippard. Blend is backed by $2.8 million from Flagship Ventures, New Enterprise Associates, and NanoDimension, according a FierceBiotech report.

—Last Friday saw a number of financings, some for quirkily named startups: $4 million more for Cambridge-based GrabCAD and $4.5 million for Cambridge-based Krush, $6 million for Boston- and Nashville-based Moontoast, $8.3 million for Linkwell Health, and $4 million for Novogy.

—Safari Books Online, a joint venture between O’Reilly Media and Pearson Education, acquired Threepress, a Boston area company focused on digital publishing tools. The price tag of the deal wasn’t disclosed.

—Woburn, MA-based LogMeIn (NASDAQ: LOGM), which makes remote access and customer support software, paid $16.5 million to acquire Kansas-based Bold Software, a developer of technology for live-chat systems and click-to-call customer service.

—A cluster of area digital marketing startups inked deals: Newton, MA-based Neolane raised $27 million, Boston-based … Next Page »

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—San Diego’s Active Network (NYSE ACTV), which provides online event registration and related services, acquired Philadelphia-based StarCite for about $51 million in stock and cash. StarCite, which provides Web-based event management services for companies around the world, has about 300 employees. The Active Network said StarCite will become part of its newly launched “Business Solutions” division, which will serve the events industry.

—San Diego-based Accelrys (NASDAQ: ACCL), which provides scientific enterprise research and development software and services, said it’s paying $35 million to acquire VelQuest, a Boston-area developer of systems that support good manufacturing practices for FDA-regulated industries. Accelrys said the VelQuest acquisition would expand its product line to include software used in pharmaceutical quality assurance and quality control.

—San Diego’s Entropic Communications (NASDAQ: ENTR), which specializes in Multimedia over Coax (MoCA) technology used in home entertainment systems, said it wants to purchase certain assets of Trident Microsystems’ set-top box and system-on-a-chip business. Entropic submitted its $55 million offer as part of a Chapter 11 bankruptcy reorganization that Sunnyvale, CA-based Trident filed last Wednesday. The bankruptcy court in Delaware must approve the Entropic offer, which could happen by the end of March if no other bidders step forward.

—Qualcomm Chairman and CEO Paul Jacobs is set to deliver the opening keynote address tomorrow morning at the annual Consumer Electronics Show in Las Vegas. Jacobs is expected to talk about Qualcomm’s vision for mobile computing as smart phones and tablets increasingly become a mainstay tool for consumer media and entertainment. The three-day show also will serve as a global stage for Sony Electronics, the San Diego-based arm of Sony’s U.S. business. San Diego’s Razer, Entropic Communications, Leap Wireless, Independa, Skin-It, and Marchon 3D, also are displaying products at the show.

—I profiled San Diego-based Verimatrix, a venture-backed company that develops encryption software and related security technologies for pay-TV networks. Verimatrix CEO Tom Munro told me the company has been successful in creating piracy protection software for Internet-Protocol Television (IPTV), and today more than half of the company’s business is in so-called unmanaged networks, such as Netflix, which provides streaming video “Over the Top” (OTT) of a cable- or satellite-based broadband Internet platform.

—The 2011 executive compensation survey showed a 3.7 percent increase nationwide in tech sector CEO pay over 2010. The annual CompStudy survey produced by executive search firm J. Robert Scott and law firm WilmerHale in collaboration with Noam Wasserman, associate professor of business administration at Harvard Business School. The study found that non-founder technology CEOs brought in average base salaries of $242,000 in 2011, up from $233,000 in 2010.

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We’re back in the swing of things after the holidays, which means this is your first weekly rewind of the new year. Read on, especially if you were too busy catching up on e-mails and meetings to pay attention to the Seattle-area headlines the first time around:

—Former Microsoft software chief Ray Ozzie resurfaced this week with a proto-company looking for talented young techies (um, get in line). The only thing said for sure about the new company, called Cocomo, is that it’s in the mobile and social communications realm—the job ad says the startup is building “a new communications product for this new world” and “compelling tools for social interaction.”

—Mobile consultant and analyst Chetan Sharma released the latest version of his year-ahead predictions survey of mobile industry insiders. The 150 or so respondents are looking for big things from Microsoft and Amazon, rating those two companies’ mobile strategies in the top three biggest storylines of the year to come. Sharma says Microsoft’s main phone-hardware partner, Nokia, is on the clock for a must-win year in terms of new devices, while Redmond can afford to play a longer game. Amazon, of course, is still riding the (apparent) sales success of its new media tablet, the Kindle Fire—and has everyone waiting for the next move.

—Reaching back a little more than a week, I checked in during the post-Christmas lull with a list of 12 big questions for Seattle’s tech scene in 2012. It’s a good roundup of the stuff that we think might define the broader industry in these parts in the months ahead, from the moves and missteps by big boys down to the ongoing efforts to fertilize a stronger startup ecosystem and supply good technical talent. Let me know if I booted any of those—and send me tips for how to answer everything!

—The growing team at Startup Weekend had a bit of a setback to end 2011 as it pulled the plug on the ambitious Startup Foundation project. As I first reported last summer, the foundation was seen as a sister organization that could provide a permanent hub and resource center for early stage entrepreneurs and wannabes in cities around the country. It was co-founded by former Startup Weekend marketing chief Jennifer Cabala. But the concept couldn’t find enough money to keep running beyond the pilot project phase, and has ended in the eight original cities (including Seattle). Startup Weekend CEO Marc Nager says the organization plans to fold some of the foundation work back into the larger nonprofit’s mission.

—Seattle interactive learning company Headsprout was featured in Wade Roush‘s latest digital life column, making an appearance at the family holiday retreat via a young tablet user. After watching his 4-year-old nephew in action with one lesson, Wade wrote, “Headsprout claims that kindergartners who complete its 80-lesson course end up with reading comprehension levels typical of 2nd graders, and I can believe it.”

—Guest columnist Bill Lemon of the Northwest Energy Angels checked in with a survey of the regional cleantech investing landscape in 2012. Two big strengths he sees for the Northwest: Boeing’s support of alternative aircraft fuels, and a strong military presence that brings a commitment to energy projects, particularly initiatives that can improve efficiency.

—There were a handful of small-company deals announced, including mobile developer Ubermind‘s sale to Deloitte, new investment cash for  the content licensing company iCopyright, and a polished-off initial fundraising round for Seattle TechStars 2011 graduate Vizify.

—Finally, more shuffling at RealNetworks (NASDAQ: RNWK) as CFO Michael Eggers announced his resignation, effective April 15. Some other longtime Real hands have left in recent months, following the company’s restructuring and transition to a new CEO, former Adobe VP Thomas Nielsen, who was hired in early November.

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As the time draws near for the annual J.P. Morgan Global Healthcare Conference in San Francisco, it seems as if there has been a surge in deals for local life sciences companies. Here’s our rundown:

—Biogen Idec (NASDAQ: BIIB) agreed to pay Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) $29 million, with the potential for more payments down the road as part of a new drug development partnership. Biogen and Isis agreed to collaborate to advance an experimental drug that Isis has identified for treating spinal muscular atrophy, a rare genetic disease that causes severe muscle atrophy and weakness in newborns. The deal could eventually be worth as much as $299 million for Isis.

—Denmark’s Novo Ventures led a $30 million Series B financing for San Diego-based Elevation Pharmaceuticals to fund development of an aerosol therapy Elevation has been developing for patients living with chronic obstructive pulmonary disease (COPD). Heath Lukatch, a San Francisco-based partner of Novo Ventures told me the funding should be enough to carry development of Elevation Pharmaceutical’s aerosolized bronchodilator drug to the threshold of final-stage trials.

—San Diego-based Santarus (NASDAQ: SNTS) asked the FDA to approve its new drug application for budesonide (Uceris), an oral tablet it has been developing with Italy’s Cosmo Technologies for treating mild cases of ulcerative colitis. If the FDA accepts the new drug application for review, Santarus says it has agreed to make a $4 million milestone payment to Cosmo. Ulcerative colitis is a form of inflammatory bowel disease that causes painful inflammation and ulcers inside the colon.

—Proacta, a San Diego-based cancer-drug developer has raised $500,000 toward a $3 million round of financing, according to VentureWire. The biotech was founded at least six years ago to advance a new group of anti-cancer molecules that are active in hypoxic tissue, which were identified by researchers at New Zealand’s University of Auckland and Stanford University. The company says it has raised $43 million through two private financings, and its investors include Alta Partners, Clarus Ventures, Delphi Ventures, Endeavour Capital (New Zealand), GBS Venture Partners (Australia), Genentech, No 8 Ventures (New Zealand) and Roche.

—San Diego-based Afraxis, which is developing drugs to treat Fragile X syndrome and autism, secured $300,000 toward a $2 million round of debt, rights and securities, according to a recent regulatory filing. The startup is pursuing a … Next Page »

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Clinical trial results and drug collaborators made up the New England life sciences news this week.

—New Jersey-based drugmaker Merck announced backing a few Boston-area companies in the past few weeks. Its Global Health Innovation Fund led a $10 million financing for Cambridge, MA-based Daktari Diagnostics, a developer of technology for testing small quantities of blood and other fluids that it hopes can monitor HIV patients in the developing world. And Merck pledged $17 million to Marlborough, MA-based Physicians Interactive Holdings. The company will put the money towards developing its online and mobile tools to connect doctors and pharmaceutical companies.

—An experimental drug from Cambridge-based Alnylam Pharmaceuticals (NASDAQ: ALNY) helped lower so-called bad cholesterol by an average of 39 percent at the highest dose studied in a small clinical trial.

—Aveo Pharmaceuticals (NASDAQ: AVEO) of Cambridge said it met it goals in a clinical trial called TIVO-1 of its experimental drug for treating kidney cancer. In the study of 517 patients, Aveo’s tivozanib was able to keep tumors from spreading a median of 11.9 months, compared with 9.1 months for another drug in its class from Bayer and Onyx Pharmaceuticals. It was a narrow victory, though, as the trial’s goal was to show the Aveo drug kept tumors from spreading about an extra three months.

—Weston, MA-based Biogen Idec (NASDAQ: BIIB) said it will pay Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) up to $299 million for collaborating on a treatment for a spinal muscular atrophy, a rare disorder found in newborns.

—Inspiration Biopharmaceuticals moved into its new digs in Kendall Square, after more than seven years of operating as a virtual biotech company that’s pursuing hemophilia treatments. It was founded by hedge fund manager John Taylor and Scott Martin, a Texas energy veteran whose son has hemophilia.

—The founders of Sermo, a Cambridge-based provider of an online community for doctors, are moving on to a new spinoff called par8o, the online publication Pharmalot reported. CEO Daniel Palestrant and chief medical officer Adam Sharp say on the par8o website that the new company will be focused on more efficiently connecting doctors and patients.

—Watertown, MA-based Forma Therapeutics inked a deal with Germany-based Boehringer Ingelheim that provides $65 million in upfront cash and four years of R&D support for discovering cancer drugs. Forma, which now has seven partnerships with heavy hitters, could also get potentially $750 million more from Boehringer Ingelheim as the cancer drugs move through development.

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Been on vacation? Get back up to speed with our end-of-the-holidays roundup of San Diego tech news.

—Almost half of the top 50 venture-backed startups had at least one founder who was an immigrant, according to a study from the National Foundation for American Policy. Such findings led author Stuart Anderson, who also is executive director of the Virginia-based foundation, to conclude, “America gains a great deal when we’re open to talent, wherever that talent was born.”

—The FCC approved Qualcomm’s sale of some spectrum rights to AT&T for nearly $1.93 billion. Qualcomm (NASDAQ: QCOM) had spent $683 million acquiring the lower 700-megahertz band and UHF Channels 55 and 56 for its FLO-TV network for transmitting television programming to mobile devices. As we recently reported, Toronto’s QuickPlay Media acquired the network operation center that Qualcomm built in San Diego for its FLO-TV operations. Qualcomm said the FCC approved the spectrum sale after AT&T abandoned its proposed $39 billion acquisition of T-Mobile. AT&T plans to use the additional spectrum to improve its network capacity as it rolls out its 4G wireless network.

—In a separate announcement, Qualcomm disclosed that founding CEO Irwin Jacobs plans to retire from the company board at its annual meeting on March 6. The 78-year-old Jacobs will officially become Qualcomm’s founding chairman and CEO emeritus.

—Razer, the Carlsbad, CA-based maker of computer and video gaming peripherals, said it is raising $50 million in a Series A venture round led by the IDG-Accel China Capital Fund, a global investment fund established by IDG and Accel Partners. The 12-year-old startup’s funding previously came from … Next Page »

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