Here in Boston, we like to tout our universities, our faculty, our students. The academic community is one of the crowning strengths of the New England economy, not to mention a major driver of its global impact. But what have universities done for the local startup and business innovation community lately?

I’m not going to give a full answer here—it’s one of the broader themes I’m exploring around town—but I’ll give you a piece of the puzzle.

Harvard University’s Office of Technology Development has what it calls an “Accelerator Fund” that has been chugging along for four years now, and it has achieved some notable results. As of last month, the $10 million fund has given out $5.2 million in grants, which have supported more than 30 projects over five annual cycles. It’s still early to add up the returns on this investment, but already it has led to more than $10 million in partnership money for the university, and several startups that have received outside venture funding. (The Harvard office declined to give specifics on licensing revenues to date.)

What’s more, the model apparently has proven successful enough that the team is about to begin raising a much bigger fund, in the $20 million to $30 million range. And unlike in the past, when Harvard developed a laggardly reputation when it came to commercializing its research, universities around the country are starting to look at the school as a possible role model for technology transfer and startup development practices.

The Accelerator Fund, which Xconomy wrote about in early 2008, was created to help Harvard scientists commercialize their inventions by forming industry partnerships, licensing technology, and starting new companies, primarily in life sciences and biomedical fields. As technology development head and senior associate provost Isaac Kohlberg puts it, “The pipelines of Harvard were empty.” The school “suffered from a branding issue with stakeholders about the role of technology development,” he says.

Kohlberg and his team, which includes Curtis Keith, chief scientific officer of the Accelerator Fund, were brought in to overhaul Harvard’s tech transfer and development offices. Kohlberg joined … Next Page »

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Boston-based Foundation Medicine has only been around for about two years, but it’s already making friends in big places. Today the company—which is developing advanced cancer diagnostics—announced a collaboration with Celgene (NASDAQ: CELG), based in Summit, NJ. Celgene plans to use Foundation Medicine’s genomics testing technology in trials of cancer drugs, in the hopes of identifying patients who are most likely to respond well to the medicines. The deal comes just four months after Foundation Medicine announced a collaboration with Novartis (NYSE: NVS) to optimize a genome panel for use in cancer research.

The financial details of the Celgene and Novartis deals were not announced, but the big-name backing is vital to Foundation, says Michael Pellini, a diagnostics-industry veteran who joined the startup as CEO on May 12. “These are two fantastic partners to have at this stage, because they bring tremendous insight into cancer biology and drug development,” Pellini says. “They will help us refine our tests.”

Foundation Medicine is built around the increasingly popular idea that cancer treatments should be tailored to individual patients. Foundation’s technology, which it’s currently marketing to pharmaceutical companies, uses high-throughput DNA sequencing to analyze tumors for alterations in more than 200 cancer-related genes. Pellini expects that number to reach 300 “in the coming months.”

Even before the Celgene and Novartis deals, Foundation Medicine’s pedigree had helped it win over … Next Page »

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It was New England’s public life sciences companies that made the most news in the sector this week.

—Ryan chatted with Mark Corrigan, CEO of Zalicus (NASDAQ: ZLCS), about the Cambridge, MA-based company’s efforts to rebuild its image among investors after a long period of upheaval. Originally known as CombinatoRx, the firm has seen the failure in 2008 of its lead drug candidate, a series of layoffs, the departure of founding CEO Alexis Borisy, a merger with Vancouver BC-based Neuromed Pharmaceuticals, the approval of its first drug, and, last week, the name change. So what does the new name mean, Ryan asked Corrigan? “Zalicus doesn’t mean anything per se,” Corrigan said, “so it gives us an opportunity to essentially create the brand with our efforts.”

—Boston Scientific (NYSE: BSX) doubled down on its bet on Sunnyvale, CA-based Asthmatx, in which the Natick, MA-based medical device giant had previously invested, by agreeing to acquire the startup for $193.5 million. The agreement also includes potential payments, based on sales of Asthmatx’s catheter-based device for treating asthma, that could bring the total value of the deal to $443.5 million.

—Cambridge-based Ironwood Pharmaceuticals (NASDAQ: IRWD) sold its Lexington, MA-based bio-manufacturing subsidiary Microbia to Royal DSM, the Dutch chemicals giant, for an undisclosed sum. Ironwood, which went public in January 2010, recorded $1 million in losses from the Microbia business on its 2009 balance sheet.

—Worcester, MA-based RXi Pharmaceuticals (NASDAQ: RXII) teamed up with Waltham, MA-based EyeGate Pharma to develop RNAi-based treatments for retinal disorders. Financial details of the deal were not disclosed.

—Biogen Idec (NASDAQ: BIIB), the Weston, MA-based maker of multiple sclerosis drugs, was beaten in the race to gain FDA approval for the first oral MS treatment by Swiss drug giant Novartis. Novartis’s once-daily pill fingolimod (Gilenya) crossed the finish line ahead of Biogen’s BG-12, which is in late-stage development.

—Ryan took a fascinating look at Henri Termeer, CEO of biotech giant Genzyme (NASDAQ: GENZ), at a time when observers wonder if the executive’s days at the helm of the embattled firm are numbered. Should French drug giant Sanofi-Aventis (NYSE: SNY) succeed in its efforts to acquire Cambridge-based Genzyme Termeer would likely leave, but sources close to the CEO believe he’s not nearly ready to do so, and would rather see the firm through its current challenges with manufacturing trouble and investor discontent. Termeer, they indicated, did not build Genzyme to sell, but rather to thrive as a stand-alone company.

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Mark Corrigan, the chief executive of the biotech Zalicus (NASDAQ:ZLCS), has been shuttling back and fourth from Boston to New York this week as part of the Cambridge, MA-based firm’s effort to gain greater visibility on Wall Street. In fact, last Friday he was due to ring the closing bell at the NASDAQ stock market in Times Square.

Founded in 2000, the company, known for most of its history as CombinatoRx, has burned through more than $230 million to develop its drugs. It was one of the high-flyers in the local biotech scene until its lead treatment for arthritis faltered in a mid-stage clinical trial two years ago. Now the company, with a new name and a new FDA-approved drug, is out to reinvent its image in the investment community.

Last week the company changed its name from CombinatoRx to Zalicus (and no, the firm didn’t name itself after Zalicus, the armored character from the video game World of Warcraft). While name changes aren’t typically news, this company’s renaming deserves special attention because it relates to the December 2009 merger of CombinatoRx and Vancouver BC-based Neuromed Pharmaceuticals. By acquiring Neuromed, the new company obtained a long-lasting opioid pain reliever (Exalgo) that has been available on the U.S. market since April. It’s the first marketed product for Zalicus, and it changes the complexion of the company quite a bit.

Before the merger with Neuromed, Zalicus’s business was built entirely on its system that seeks synergistic combinations of compounds to form new treatments for diseases. That technology has helped the firm gain its research and development deals with the Swiss drug maker Novartis (NYSE:NVS) and Thousand Oaks, CA-based biotech giant Amgen (NASDAQ:AMGN). Neuromed, like the name used to suggest, developed neurological drugs like the long-lasting opioid pain reliever. The product (Exalgo) is marketed by health products giant Covidien (NYSE:COV). Zalicus has also chosen to maintain a research operation in Vancouver that is focused on discovering drugs that block proteins called calcium channels to treat pain.

Still, the company’s lead clinical candidate is an arthritis treatment called Synavive. It’s a combination of a cardiovascular drug and a corticosteroid that resulted from the firm’s original combinatorial drug-screening technology.

The name change gives the company an excuse to tell its story to investors and regain faith among stock buyers on Wall Street. Investors bolted from the firm’s stock after it reported in October 2008 that … Next Page »

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All eyes continued to be on Genzyme this week, but other New England life sciences companies had interesting developments to report as well.

—Good Start Genetics, a three-year-old Boston startup built in part around technology from the Harvard lab of George Church, completed an $18 million Series A round of funding from OrbiMed Advisors, Safeguard Scientifics (NYSE:SFE), and SV Life Sciences. Good Start aims to use gene sequencing technology to help prospective parents assess their risk of conceiving a child with genetic defects.

—Ryan had a chat with Rob Friel, chairman and chief executive of PerkinElmer (NYSE: PKI), about how the Waltham, MA-based maker of lab tools is planning to grow its businesses in the diagnostics, biotech/pharma, and environmental health markets. Some of that growth will be organic, Friel said, and some will come through acquisitions, like PerkinElmer’s recent purchase of Bedford, MA-based VisEn Medical.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ) announced it will cut 1,000 jobs over the next 15 months and sell its Genzyme Genetics unit to Burlington, NC-based Laboratory Corporation of America (NYSE:LH) for $925 million in cash. Both moves are part of an effort on Genzyme’s part to boost shareholder value at a time when it’s facing increasing investor scrutiny and an unsolicited acquisition offer from French drug maker Sanofi-Aventis.

—Third Rock Ventures announced it has raised $426 million for its second fund. The healthcare-focused venture firm, which launched in 2007 in Boston and recently expanded to San Francisco, also announced several personnel changes, including promoting CombinatoRx founder Alexis Borisy from entrepreneur-in-residence to partner.

—Ironwood Pharmaceuticals (NASDAQ:IRWD) of Cambridge reported that linaclotide, its lead product candidate, had passed muster in a clinical trial as a treatment for irritable bowel syndrome with constipation. The trial is the third of four planned before Ironwood and its partners can file for approval of the drug; results from the final study are expected by year’s end.

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Third Rock Ventures, a healthcare-focused venture firm with offices in Boston and San Francisco, says today it has raised $426 million for its second fund. The fund represents a vote of support for the firm’s model of investing in and starting life sciences ventures that have the potential to transform healthcare.

The Boston-based firm, which launched in 2007 with a $378 million first fund, says that it has also made some personnel moves, in part to facilitate its recent expansion in the Bay Area. Charles Homcy, the former CEO of South San Francisco-based Portola Pharmaceuticals, has been named a venture partner at Third Rock and will head the firm’s West Coast office. Alexis Borisy, the former chief executive of Cambridge, MA-based Zalicus (formerly CombinatoRx), has been promoted from entrepreneur-in-residence to partner. Also, Nick Leschly has left the partnership at Third Rock to become CEO of its Cambridge-based portfolio company, Bluebird Bio (former Genetix Pharmaceuticals).

Meantime, Third Rock has recently added Chris Varma, previously of Flagship Ventures, and David Armistead, the former chief scientist of CGI Pharmaceuticals, as entrepreneurs-in-residence. With the recent West Coast expansion, Third Rock partner Craig Muir and principal Jake Bauer are moving from the Boston office to the San Francisco outpost, according to the firm.

Third Rock—which includes founding partners such as Mark Levin and Kevin Starr who previously served as senior executives at Millennium Pharmaceuticals—has been one of the few venture outfits in the Boston area to aggressively launch and invest in life sciences startups during the past years, a period of financial turmoil for many of their counterparts in the venture industry. Since 2007, the firm has launched or invested in more than 15 life sciences companies, such as Cambridge-based cancer drug developer Agios Pharmaceuticals and Zafgen, a developer of obesity treatments in Cambridge, as well as Bay Area firms Ablexis, an antibody drug specialist, and Afferent Pharmaceuticals, which is focused on new treatments for chronic pain.

“These companies were formed around disruptive areas of science and medicine and many were developed as part of Third Rock’s unique company discovery process,” Starr said in a statement. “We look forward to continuing to partner with entrepreneurs, researchers and company founders to pursue bold ideas and groundbreaking science that promise to dramatically improve the lives of patients.”

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—Needham, MA-based Celldex Therapeutics announced that Pfizer (NYSE: PFE) had terminated a agreement in which it licensed Celldex’s experimental cancer vaccine rindopepimut, because it no longer views the drug as a strategic priority. Celldex (NASDAQ: CLDX) will regain full rights to develop and commercialize the drug, effective November 1.

—Ryan checked in with Oliver Fetzer, chief executive of Cambridge, MA-based Cerulean Pharma, about his company’s progress in developing nanoparticle drugs designed to kill tumors. Cerulean’s lead drug candidate, CRLX101, was well-tolerated in an initial human trial.

—The FDA put clinical trials of two of Idenix Pharmaceuticals’ hepatitis C drugs on hold, causing the Cambridge-based biotech company’s stock to plummet almost 50 percent to $3.11 per share on Wednesday afternoon. Idenix was testing two of its drugs in healthy volunteers, and the FDA put the red light on the trials when the company found elevated liver toxicity in three of the patients who took both drugs.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX), on the other hand, had good news about its own hepatitis C drug candidate, telaprevir. A combination of telaprevir and standard hepatitis drugs was able to cure two-thirds of patients who had failed to respond to a prior round of the standard drugs alone, in a trial involving more than 660 volunteers. Based on that study and two others, Vertex plans to file an application for FDA approval of the drug by year’s end.

—Boston-based Rhythm Pharmaceuticals, a developer of peptide-based drugs for metabolic ailments, closed a $40 million Series A financing round which included new investor Third Rock Ventures. The startup, which licensed its two lead drug candidates from the French biotech Ipsen, announced it had raised the first $21 million of the round from MPM Capital and New Enterprise Associates back in March.

—Gene sequencing instrument maker Helicos Biosciences (NASDAQ: HLCS) of Cambridge, MA, filed a patent infringement lawsuit against Menlo Park, CA-based Pacific Biosciences. Helicos claims that the California firm’s technology violates its patents on a technology known as single molecule sequencing, which extend to as far as 2028.

—Anchor Therapeutics, also of Cambridge, MA, forged a partnership with the Ortho-McNeil-Janssen Pharmaceuticals division of Johnson & Johnson (NYSE: JNJ) that could be worth up to $480 million. The deal involves several drug targets in the fields of cancer and metabolic disease, and centers around Anchor’s “pepducin” drug technology, which the startup says offers a new way to hit a lucrative class of drug targets called G protein coupled receptors.

—U.K.-based Shire (NASDAQ: SHGPY) agreed to pay Cambridge, MA-based Acceleron Pharma as much as $498 million to co-develop and co-market drugs for Duchenne Muscular Dystrophy and other muscle disorders. Acceleron, which will get a $45 million upfront cash payment, has shown in animal studies that its lead drug candidate can increase muscle mass and improve strength in animals.

—Following a merger last year with Vancouver-based Neuromed Pharmaceuticals, Cambridge, MA-based drug developer CombinatoRx announced it has changed its name to Zalicus. The company, which won its first drug approval earlier this year for the pain treatment hydromorphone HCL (Exalgo), now trades on the Nasdaq under the symbol ZLCS.

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Cambridge, MA-based drug developer CombinatoRx announced today that it has changed its name to Zalicus to better reflect its assets and focus, following its merger last year with Vancouver-based Neuromed Pharmaceuticals. The company garnered its first drug approval earlier this year for the pain treatment hydromorphone HCL (Exalgo), which is being marketed by healthcare products company Covidien (NYSE: COV). “Our new name reflects the Company’s transformation into a biopharmaceutical company with product revenues, two powerful and differentiated drug discovery platforms, a pipeline of product candidates and proven drug development expertise focused on the treatment of pain and inflammation,” announced Mark Corrigan, president and CEO of Zalicus (NASDAQ: ZLCS), which started trading under its new stock symbol today.

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Acquisitions, partnership agreements, and early round financing for some stealthy operations made it a busy deals news week for us.

—Third Rock Ventures, a Boston firm focused on investments in life sciences companies, plans to raise $400 million for its second fund, according to an SEC filing. The firm closed its first fund, with $378 million, in 2007.

—Waltham, MA-based scientific instrument maker PerkinElmer revealed it agreed to acquire Spokane, WA-based Signature Genomic Laboratories for about $90 million in cash.

—Foundation Medicine, a company that’s focused on fighting cancer by testing for genetic traits in a tumor and matching them with treatments, reported that it pulled in part of a $25 million Series A funding round. The startup is incubated out of Boston’s Third Rock Ventures, which also led the financing. In February, Ryan was the first to report that former CombinatoRx (NASDAQ: CRXX) CEO Alexis Borisy was leading Foundation.

—Catabasis Pharmaceuticals, a Cambridge-based startup run by Sirtris Pharmaceuticals veterans, revealed in a regulatory filing that it pulled in $7.7 million of a planned $39.7 million financing. The stealthy operation is developing treatments for inflammatory and metabolic diseases by leveraging the protective effects of omega-3 fatty acids.

—Cambridge’s Agios Pharmaceuticals nabbed $130 million from Summit, NJ-based Celgene (NASDAQ: CELG), in exchange for an exclusive option to license and develop Agios’ experimental cancer drugs, for a certain span of time. The deal essentially makes the Cambridge company Celgene’s cancer metabolism drug unit without outright acquiring it.

—The Daily Grommet, a Lexington, MA-based e-commerce company that promotes consumer products with online videos, has raised $3.4 million in Series A funding. The financing included … Next Page »

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Looks like last week’s flurry of information technology news is long gone. Headlines of partnerships, board appointments, and venture funding in biotech companies made it a busy life sciences news week for us.

—MedVentive, a Waltham, MA-based provider of software for tracking medical data, raised a $10 million series C round. MedVentive got part of the boost from included Clarian Health Ventures, the investing unit of one of its key customers.

—Ryan tracked the growing fervor, on the part of both investors and biotech companies, in developing drugs for rare diseases, as opposed to the traditional focus on big patient populations like those with heart disease, arthritis, or cancer. Alnara Pharmaceuticals, a Cambridge, MA, drug developer backed by Third Rock Ventures, is among the companies taking a cue from Genzyme (NASDAQ: GENZ), whose three best-selling drugs each target diseases affecting fewer than 10,000 patients. Bigger pharma companies are also taken on developments in rare disease treatments as a way to offset potential losses from generic knockoffs of their big-selling mass-marketed drugs.

—Cambridge-based Mersana Therapeutics, a maker of drugs designed to last longer in the bloodstream, announced its first big partnership deal, with Israel’s Teva Pharmaceutical Industries, which could be worth as much as $334 million over time.

—Alkermes (NASDAQ: ALKS) filed an application with the FDA to start marketing a long-lasting version of its naltrexone drug (Vivitrol) to help treat people addicted to opioid-based narcotics. The once-monthly injection from Waltham-based Alkermes is already FDA-approved for treating alcohol dependence.

—Two area biotech companies announced they had brought on new CEOs. Bedford, MA-based MicroCHIPS, a maker of wireless medical implants, hired Ajit Gill, who previously helped lead startup Nektar Therapeutics to an IPO. And Marlborough, MA-based Xcellerex, which is developing methods for more efficiently manufacturing biomolecules, tapped Thermo Fisher Scientific veteran Guy Broadbent to lead the company.

—Third Rock Ventures plans to raise $400 million for a second fund, according to a filing with the SEC. The Boston-based firm targeted life sciences companies with its maiden $378 million fund, which closed in 2007. Luke profiled Third Rock’s strategy around financing disruptive biotech ideas, back in September 2008.

—PerkinElmer (NYSE: PKI), a Waltham-based maker of scientific instruments, will acquire Spokane, WA-based Signature Genomic Laboratories for about $90 million, it revealed in a regulatory document.

—Foundation Medicine pulled in the first tranche of a planned $25 million Series A round, which will go toward … Next Page »

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The trick to beating cancer could be a single test that shows all known genetic traits in each person’s tumor, and that also matches those results to the best treatments. Boston-based Foundation Medicine reports today that it has raised the first part of a planned $25 million round of Series A venture funding to make comprehensive genomic analyses of tumors a standard tool in the fight against cancer.

A crack team of cancer, genetics, and industry veterans from the Boston area has assembled around the startup. Boston-based Third Rock Ventures, founded by former executives of the cancer drugmaker Millennium Pharmaceuticals, has incubated the company and led the first-round financing. Alexis Borisy, an entrepreneur-in-residence at Third Rock and the former CEO of Cambridge-based CombinatoRx (NASDAQ:CRXX), is the startup’s founding chief executive (something we were the first to report back in February). And Eric Lander, a pioneer of genomics research and an advisor to President Barack Obama on science and technology policy, is headlining the group of scientists and physicians who are advising the startup.

Foundation Medicine, which was formed in 2009, has come into being as high-speed DNA sequencing and a slew of academic studies help to uncover new genetic mutations that, say, protect tumors from certain therapies, or help cancer cells grow out of control. Drug companies are developing cancer drugs for patients who have specific genes that make them likely to respond well to the treatments, building on Roche-Genentech’s success in marketing the breast cancer drug trastuzumab (Herceptin) for women with the HER2 gene. Also, a growing number of startups are focusing on providing new genetic tests that help guide physicians in treating cancer patients.

Foundation Medicine is taking its own approach to personalizing cancer treatments. While many previous firms have focused on developing tests to detect specific genes linked to likely outcomes of cancer treatments, Foundation Medicine is planning to use high-throughput DNA sequencing technologies to expose the plethora of genes and genetic variants in cancer genomes, according to Borisy. Borisy and Third Rock are betting that the future of cancer treatment will involve a single analysis of cancer DNA in guiding treatments, rather than multiple tests that screen for individual genes or groups of genes.

Today DNA sequencing is done primarily in research settings, with extremely limited clinical use. Borisy, however, says that it’s time to put this technology to work for people with cancer. “If many patients would benefit from this deep understanding, then there needs to be a way to take this from being a research tool to something that would be useful and meaningful and work in the routine practice of clinical oncology,” he says. “That has been the driving motivation and inspiration behind Foundation, and it’s quite clear that this is the way the world is going.”

The company’s exact strategy is evolving, according to Borisy, yet some details are clear. The firm plans to set up a central lab in the … Next Page »

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Stories of drugmakers, deals, health IT companies, and even some nonprofits made it a busy life sciences news week for us.

—Waltham’s Avila Therapeutics is on a quest to outdo well-known Boston drugmaker Vertex Pharmaceuticals when it comes to treating hepatitis C, Luke wrote last week. The company’s drugs rely on forming covalent bonds to shut down targets on virus-infected cells, preventing the virus from mutating and escaping, which could give it an edge on the Vertex drug that has varying degrees of effectiveness on different mutations of hepatitis C, Avila’s CEO said.

—Dossia, a Cambridge, MA-based nonprofit electronic health records provider, rolled out its system to another two of its founding companies. Computer chip maker Intel and mail system provider Pitney Bowes will offer some of their workers the Dossia system, which is sustained by subscription fees and is designed to lower overall healthcare costs for corporate clients.

—Speaking of electronic health records, Athenahealth is looking for some opinions on the matter and announced a partnership with Cambridge’s doctors-only social networking site Sermo to get just that. Financial terms of the partnership between Sermo and Watertown, MA-based Athena (NASDAQ:ATHN), a maker of Internet healthcare software, weren’t revealed.

— Millipore shook things up this week when it announced plans to accept a bid from Germany’s Merck KGaA, which offered to buy the company for $107 a share, or $7.2 billion. Thermo Fisher had previously made an unsolicited $6 billion bid for the Billerica, MA-based life sciences equipment supplier, according to media reports.

—Stealthy Guilford, CT and San Francisco-based startup Ion Torrent Systems opened up a bit to discuss its digital DNA readout technology, leaving plenty of genomic science bloggers buzzing. And the machine from Ion Torrent, which is advised by a Harvard genomics pioneer and supported by a Seattle partner, costs … Next Page »

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CombinatoRx has garnered its first drug approval. It’s a milestone for the Cambridge, MA-based drug developer, even if the path the company took to reach this point isn’t the one its founders had mapped out when they launched the company in 2000.

The FDA has approved the pain drug hydromorphone HCL (Exalgo), which is an extended-release tablet taken once a day for people with moderate to severe aches and pains, the company (NASDAQ:CRXX) reports today. The firm took on U.S. development of the drug through its December merger with Vancouver-based Neuromed Pharmaceuticals. In other words, the pain tablet is not a product of CombinatoRx’s own drug-discovery system, which uses computers to find novel treatments based on synergistic combinations of other drugs.

The approval has earned CombinatoRx—which still has a Vancouver office—a $40 million milestone payment from the healthcare products giant Covidien (NYSE:COV). Covidien, which has its corporate offices in Mansfield, MA, acquired U.S. rights to the pain treatment from Neuromed last year and is handling all marketing of the drug through its Mallinckrodt unit. CombinatoRx will get royalties on drug sales from Covidien, which plans to begin selling the product in the first half of this year.

CombinatoRx’s work on this pain drug is largely over, since Covidien is now responsible for all marketing and post-approval studies of the drug. Also, the ALZA unit of Johnson & Johnson (NYSE:JNJ), which licensed U.S. rights to the drug to Neuromed in 2007, is in charge of manufacturing supplies of the product that will be sold by Covidien in the U.S. CombinatoRx’s next closest drug to the market is its combination therapy for arthritis, which is in mid-stage clinical development.

The approval has given CombinatoRx’s stock a shot in the arm. According to Google Finance, the stock was up 45 cents, or 40.5 percent, to $1.56 per share in pre-market trading this morning.

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This week we’ve got another crop of great interviews with the founders and executives of some of New England’s most fascinating life sciences companies.

—Zafgen CEO Tom Hughes filled Luke in on his Cambridge, MA-based startup’s plans to begin human tests of its anti-obesity drug, which the company hopes will be the first drug to produce weight loss dramatic enough to compete with stomach stapling and other bariatric surgery. Hughes also shared some surprising news from animal studies that the Third Rock Ventures- and Atlas Ventures-backed company has completed over the last year: its original idea about how its drug works has turned out to be completely wrong.

—Solace Pharmaceuticals CEO Eliot Forster confirmed to Ryan that the startup, founded in 2006 to develop pain treatments, has shuttered its Cambridge operations. The move came in late November, after Solace’s lead drug candidate failed in a mid-stage clinical trial. Backed by PureTech Ventures, Polaris Venture Partners, and InterWest Partners, Solace will continue to operate out of its remaining office in Canterbury, UK.

—Veteran biotech dealmaker Adelene Perkins talked to Luke about her journey to the corner office of Cambridge-based Infinity Pharmaceuticals (NASDAQ: INFI). Perkins, who became Infinity’s CEO on January 1, also shared her plans to build up the commercial side of the company, which has yet to bring a drug to market, and to transform it into a fully integrated organization.

—Ryan chatted with PatientsLikeMe co-founder and president Ben Heywood, whose social networking site for people with diseases such as multiple sclerosis and epilepsy has grown from about 25,000 users in December 2008 to more than 55,000 early this month. The Cambridge-based startup, which sells anonymous data culled from the members of its 10 patient communities to pharmaceutical and research companies, has also staffed up from 20 to 30 employees.

—Cambridge, MA-based Genzyme (NASDAQ:GENZ) and Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ:ISIS) reported results from a Phase III clinical trial indicating that their experimental cholesterol-lowering drug, mipomersen, significantly lowers the cholesterol of patients with a rare condition called heterozygous familial hypercholesterolemia. The drug was also associated with increases in liver enzymes called transaminases, which can indicate liver damage, however—this issue, seen in previous trials, has caused some nervousness about mipomersen among investors.

—Boston Scientific (NYSE:BSX) announced plans to cut 1,000 to 1,300 jobs, or 8 percent to 10 percent of its total work force, as part of a company-wide restructuring effort. The Natick, MA, medical devices giant is aiming to reduce its 2009 gross expenses by $200 million to $250 million during the next two years.

—CombinatoRx (NASDAQ:CRXX) co-founder and former CEO Alexis Borisy talked to Ryan about his new gig as an entrepreneur in residence at Boston’s Third Rock Ventures—and about the super-stealthy new life sciences firm he’s helming, Foundation Medicine. Borisy joined Third Rock in October, a few months after leaving his post at CombinatoRx as part of its merger with NeuroMed Pharmaceuticals.

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Alexis Borisy is back in company-building mode. The former CEO of the drug developer CombinatoRx tells Xconomy that he has joined Third Rock Ventures in Boston as an entrepreneur in residence—and he’s already at the helm of a secretive new life sciences firm called Foundation Medicine.

Borisy gave few details on the startup, other than saying that the firm is focused on personalized medicine. He was more forthcoming, though, about his new role at Third Rock, whose team he quietly joined in early October, about four months after officially stepping down from his post as chief executive of Cambridge, MA-based CombinatoRx (NASDAQ:CRXX).

Borisy’s departure from CombinatoRx, a developer of combination drugs that he co-founded in 2000, was revealed in July when the company announced its merger with NeuroMed Pharmaceuticals. Borisy is officially a scientific advisor to CombinatoRx, but he says that he isn’t spending much time working with the company.

He and Third Rock partner Mark Levin have been discussing new entrepreneurial opportunities in biotech for the past year. Third Rock, which was launched in 2007 with a $378 million initial fund, is appealing to Borisy because the firm is focused on backing life sciences startups with the potential to fundamentally improve how certain diseases are treated, he says, and the firm’s members often take active roles at the companies in which it invests.

“When we founded Third Rock, we realized great companies take more than just great science; they require passionate people who share our commitment to making a difference for patients,” Third Rock partner Kevin Starr said, in an e-mail. “Alexis is one of those rare people that has the tools to take a disruptive idea and transform it into an exciting vision for a company that will have a significant impact. He has made a big difference in the firm already and we are all very excited to work with him on our next generation of companies.”

As an entrepreneur in residence, Borisy has an office at Third Rock’s Newbury Street headquarters and spends time with other members of the firm assessing and pursuing opportunities to start or invest in companies. And he places particular emphasis on pitching in as an executive of young portfolio companies, he says.

Borisy’s interests have recently focused on the field of … Next Page »

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Cambridge, MA-based CombinatoRx (NASDAQ: CRXX) said today it has named Mark Corrigan as its new CEO, following the merger with NeuroMed Pharmaceuticals. Corrigan, 52, is the former executive vice president of R&D at Sepracor and a director of CombinatoRx. He will be paid an annual base salary of $450,000, may get a bonus worth half his base salary, and could get restricted stock units worth as much as 3 percent of the company’s market capitalization if CombinatoRx’s lead pain drug wins FDA approval by October 1, according to a regulatory filing. Robert Forrester, the former chief operating officer, is leaving the company, while NeuroMed’s former CEO, Christopher Gallen, will stay as executive vice president of R&D.

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New England has a deep pond with many of the very biggest fish in the global life sciences industry, but it also has its share of minnows, and they are getting eaten alive in the downturn.

That finding leaped out at me after I scoured through financial data on 85 publicly traded life sciences companies in greater Boston, Seattle, and San Diego as part of our regular Biotech Survival Index feature. The final numbers aren’t pretty for Boston. Just 15 of the 46 public life sciences companies we follow in Massachusetts had more cash on their balance sheet at the end of June 2009 than they did on New Year’s Day, based on a review of the most recent round of quarterly financial filings with the Securities and Exchange Commission. (Companies were included if they were listed on the NASDAQ or NYSE, and had market capitalization of at least $100 million).

Even though jobs have been cut, drug candidates have been shelved, and some last-ditch partnerships have been struck, all that frenzied activity didn’t really add up to a strengthened financial future for a majority of the region’s money-losing companies. The cash crunch has prompted a couple of Massachusetts companies to fold this year (Altus Pharmaceuticals and Epix Pharmaceuticals), a couple more to sell out for a pittance (Targanta Therapeutics and NitroMed), and one company that actually improved its financial position to move to Wisconsin (Exact Sciences).

While those companies were vanishing, there was some good news to be found in the filings. Some of Boston’s anchor tenants took advantage of their financial strength to beef up their cash balances, pay down debt, or otherwise tidy up financial matters. Essentially, the rich (Biogen Idec, Genzyme, Thermo Fisher Scientific, and Millipore, to name a few) got richer.

But what really shocked me the most was how poorly Boston’s life sciences companies have coped with the downturn compared with peers in the two other cities where Xconomy follows life sciences—Seattle and San Diego. Granted, neither of those cities has anywhere near the number of profitable life sciences companies that Boston does (18). And many of the little biotechs in those cities were backed into a corner in the first half of 2009, and either had to do or die—and things don’t appear quite that dire yet at many companies in Boston. But a majority of companies in Seattle (7 of 12) actually strengthened their balance sheets during the first half of the year. The same pattern emerged in San Diego, where 15 of the 27 companies built up their cash reserves in the same period.

If you combine those two hubs into a West Coast cluster that has a sample size similar to Boston’s (39 companies versus 46), the Bay State doesn’t look so resilient in comparison. About 56 percent of companies on the West Coast (22 of 39) strengthened their financial position in the first half of the year, while just 33 percent of the companies in Boston (15 of 46) did that well.

Read on for a complete rundown of the financial position for all 46 Massachusetts companies, listed in alphabetical order. To purchase a much expanded version of this report, in PDF format, click the “Add to Cart” button below. The expanded version, available for $95,* includes an assessment of each company’s financial position at the end of June compared to six months earlier, the projected length of time it can survive on its existing cash reserves, and an analysis of the strategic moves it has made to stay afloat in the current environment. Click here to see a sample entry. *Price is subject to change without notice.

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

Abiomed (NASDAQ: ABMD)
Cash on hand: $54.5 million
Related Xconomy coverage:
“Abiomed Wins FDA Approval of Heart Pump”

Alkermes (NASDAQ: ALKS)
Cash on hand: $380.4 million
Related Xconomy coverage:
“Alkermes Knocks on Door of Biotech Big Leagues, Aims to Make Drugs of its Own”
“Alkermes, Swinging for the Fence, Touts New Anti-Addiction Drug”
“Alkermes’ Ambitious Builder, Richard Pops, Grabs Reins to Re-Ignite Growth Phase”

Alnylam Pharmaceuticals (NASDAQ: ALNY)
Cash on hand: $473.8 million
Related Xconomy coverage:
“Alnylam Takes Time to Mull Over RSV Game Plan”
“Alnylam, With Tekmira and New Northwest Firm Alcana, Look to Push Borders of RNAi Delivery”
“Alnylam Pushes First RNAi Drug That Circulates Through Body Into Human Test”
“Alnylam’s In the Money, Expects $500 Million in Bank At Year End”
“Alnylam Looks to Spinoffs to Unleash RNAi Technologies for Stem Cells, Vaccines“ … Next Page »

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If you’re fortunate enough to be gainfully employed, you may have joined the droves of other Boston-area innovators who have headed for the Cape, the White Mountains, or another summertime retreat in recent months. Or perhaps you’ve been busy looking for your next career challenge. Either way, with Labor Day fast approaching, we thought it’d be useful to tie together labor trends and some of the larger layoffs that have occurred at technology and life sciences firms in New England since Memorial Day.

First, it’s been encouraging to see that our Boston Tech Layoff Tracker has not been as busy this summer as it was over the previous spring, winter, and fall seasons. Perhaps this is another sign that the worst of this economic recession is behind us. Since June 1, we’ve recorded that Massachusetts-based life sciences and tech firms announced a total of 718 jobs would be cut in their organizations. Now, that doesn’t include the small startups we follow that have been cutting jobs without officially announcing the layoffs: For example, we reported this month that Chelmsford, MA-based online music startup OurStage downsized its ranks from 38 to 17 workers last fall after some investment dollars failed to come through. But this summer’s layoff total to date marks a significant falloff from the 971 layoffs we recorded at Massachusetts life sciences and tech firms in the spring months of April and May.

It’s been a tough year for innovation companies here and everywhere, but layoffs seem to have peaked in the first quarter of this year. State figures show that the impact of layoffs among tech and life sciences workers in the Bay State is consistent with the impact on workers in the rest of the economy. (Of course, the state says that jobs in industries such as construction and financial services have been hit the hardest by layoffs in the commonwealth.) According to the most recent employment figures from the state’s Executive Office of Labor and Workforce Development, the number of professional, scientific, and technical jobs in the commonwealth fell from about 258,200 in June 2008 to 249,700 this June, a 3.29 percent decline. (Admittedly, these figures are just an indication and the job category the state uses does not reflect all the jobs in tech and life sciences firms.) The state labor agency reported that year-over-year employment levels for all non-farming jobs in June were down about 3.2 percent, meaning that the layoff trend has far from spared local innovation-based firms.

Here is our recap of the summer’s largest tech and life sciences layoffs in the Boston area:

—Just last week, Sonus Networks (NASDAQ: SONS), a Westford, MA, company helping cable, wireless, and telephone companies with the transition to Internet-based communications, announced a fourth round of layoffs as part of its ongoing “rightsizing” effort, this time affecting 93 people. Sonus let go 50 workers in December, 40 in January, and 60 in March, for a total of 243.

—Analog Devices (NYSE:ADI), the Norwood, MA-based maker of micro-electro-mechanical system (MEMS) chips for multiple industries, told the Boston Globe earlier this month that the company plans to cut … Next Page »

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Boston- and Cambridge-based tech and life sciences firms cut the usual assortment of deals this week, but their brethren further out in New England were unusually active as well.

—Marathon Technologies raised a $7 million round of equity financing from undisclosed investors. The Littleton, MA-based firm makes disaster-recovery software for virtual and physical servers.

—Norwalk, CT-based Akademos, an online seller of used college textbooks and course materials, raised $2.5 million in equity funding from Kohlberg Ventures of Portola Valley, CA.

—Online video game maker Turbine, of Westwood, MA, reportedly collected $6.57 million of a planned $50 million Series D round of financing from existing investors. If completed, the new round would bring Turbine’s total venture funding to $145 million.

—EMC (NYSE: EMC) virtualization subsidiary VMware (NYSE: VMW) agreed to acquire San Mateo, CA-based SpringSource for $420 million in cash and stock. The deal marks VMware’s largest acquisition to date.

—Boston and U.K.-based crowdsourcing software firm Imaginatik (AIM:IMTK) raised $2.6 million from unnamed new and previous investors.

—MyWebGrocer, a Colchester, VT-based provider of … Next Page »

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Cambridge, MA-based drug developer CombinatoRx (NASDAQ:CRXX) has licensed a compound from Clinical Data (NASDAQ:CLDA), of Newton, MA, to develop a combination treatment for multiple myeloma and other B-cell cancers, according to a press release. Clinical Data is eligible for up to $252 million in milestone fees from CombinatoRx and royalty payments on potential drug sales.

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