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

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

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

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

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

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

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

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

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

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

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For some former employees of Indevus Pharmaceuticals, it’s not such great news that the Lexington, MA, drug developer was acquired by Endo Pharmaceuticals. Chadds Ford, PA-based Endo (NASDAQ:ENDP), which completed its $370 million buyout of Indevus in March, is in the process of laying off a quarter of Indevus employees and moving research programs out of the Indevus facility in Lexington, Endo confirms.

Endo will lay off roughly 60 of the 240 workers who were employed by Indevus when the acquisition closed this spring, according to an e-mail from Endo spokesman Kevin Wiggins. The cuts are mostly targeting employees in finance, corporate affairs, and other areas that overlap with the responsibilities of Endo’s staff in place before the buyout. However, Endo has kept all the sales and manufacturing employees from Indevus as well as some of the commercial and research positions, Wiggins indicated. He did not specify how many of the layoffs will affect employees based in Massachusetts or how many workers have already been let go.

Endo is also in the process of moving all the research and development programs from Indevus’s operation in Lexington to labs at Endo’s headquarters in Pennsylvania, according to Wiggins. He declined to be specific about whether the Lexington facility would be shuttered completely, but such a closure would seem likely given the exiting of research projects and workers from the operation.

The layoffs are not a huge surprise. Endo told investors back in January that it planned squeeze out cost savings of $40 million after the acquisition, though it was not specific about how it would trim expenses. Endo, which specializes in providing pain relievers, also wanted to expand its product portfolio to include treatments for the endocrinology and urology markets.

Though its purchase of Indevus, Endo has acquired testosterone undecanoate (Nebido), an experimental testosterone-replacement therapy. Indevus also brought to Endo an approved and marketed drug, histrelin (Supprelin LA), for premature puberty. Its other product, octreotide implant, a treatment for excessive production of growth hormone, is in late-stage clinical development.

As part of the buyout deal, Endo agreed to pay Indevus shareholders up to $267 million or $3 per share if the products Endo acquired from the firm achieve certain development and sales milestones.

The Boston Tech Layoff Tracker has been updated to include the layoffs of former Indevus employees.

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When I last crunched the numbers on the financial health of the Boston area’s public life sciences companies, back in November, I noted that 15 of them had more than $100 million stockpiled. These firms, I reasoned, were likely in a decent position to weather the economic storm. Now with quarterly financial reporting through December now in the books for most of the firms in the sector, I came to a surprising conclusion. There are now even more companies, 19, in that position of relative financial strength. Infinity Pharmaceuticals, Momenta Pharmaceuticals, Hologic, and Bruker are all newcomers to the $100 million club as of December 31.

Then again, in my review of the new numbers I also spotted 16 companies that likely had less than $50 million in the bank at year’s end (I say “likely” because three haven’t reported their numbers). That sign of thin reserves suggests those companies will face tough choices ahead.

Here’s the full rundown, in alphabetical order, of the 44 Boston-area life sciences companies for which I tracked down end-of-year financial figures.

—Abiomed (NASDAQ: ABMD). The Danvers, MA-based medical device company had $63.8 million in cash and investments at the end of December, and a $7.7 million net loss in the quarter. That’s more cash than it had socked away at the end of September—$50.6 million.

—Acusphere (OTCBB: ACUS). This biotech company has cut about two-thirds of its workforce, or 40 jobs, and consolidated all its facilities in a manufacturing plant in Tewksbury, MA. It has avoided making a formal financial report to the SEC, although it says the cuts will help it stretch its cash into the third quarter of 2009, which it hopes will buy enough time to come up with “financing alternatives.” The stock is down to 3 cents. Acusphere is a newcomer to the list, which I overlooked last time.

—Alkermes (NASDAQ: ALKS). This Cambridge, MA-based company has maneuvered itself into position of financial strength, with $423 million in cash and investments at the end of the year, and with a $112.3 million profit in the quarter. As I mentioned last month, Alkermes has potential for revenue growth this year if Eli Lilly and Amylin Pharmaceuticals win FDA approval for once-weekly exenatide for diabetes, which is based partly on a technology license from the Massachusetts firm.

—Alnylam Pharmaceuticals (NASDAQ: ALNY). This Cambridge, MA-based biotech company doesn’t have to worry about cash, with $512.7 million at the end of 2008, and a relatively skinny net loss in the quarter of $9.4 million. It expects to burn through no more than $77 million of its cash this year, ending 2009 with more than $435 million. Indeed, rather than fretting over finances, CEO John Maraganore is thinking about how to prioritize opportunities, as he told me last month.

—Altus Pharmaceuticals (NASDAQ: ALTU). Alarm bells must be going off at Waltham, MA-based Altus. This company used almost $90 million of its cash reserves in 2008, and closed the year with $48.6 million left in the bank. Even after cutting 107 jobs, or three-fourths of its workforce, Altus still expects to spend $50 million to $60 million for operations this year. It says it has enough cash to run “into the fourth quarter” and that it will try to raise more capital in the next three to six months. … Next Page »

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

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

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

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

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

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

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

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Indevus Pharmaceuticals (NASDAQ:IDEV) says that a clinical study of its anti-HIV microbicide sponsored by the National Institutes of Health showed the treatment was safe but did not show statistically significant benefits. The 3,100-patient study showed that the drug—a vaginal gel applied before intercourse—lowered the risk of infection by 30 percent, shy of the study’s goal of lowering risk by at least 33 percent. The Lexington, MA-based firm expects to reveal results of a larger, 10,000-patient clinical trial of the microbicide by the end of this year.

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New England tech and life sciences firms have cut many a deal since last we rounded up. Here are some of the most interesting ones.

—Cambridge, MA-based Semprus Biosciences, a spinoff from the famed Langer Lab at MIT, closed an $8 million Series A round of venture capital co-led by 5AM Venture and Pangaea Ventures. Semprus is working on long-lasting polymer surfaces to help combat the microbes that like to grow on medical devices.

—Y Combinator startup Posterous, a developer of tools for “dead simple blogging” raised $750,000 from Zimbra CEO Satish Dharmaraj, former Netscape CTO Eric Hahnof, Guy Kawasaki, Mitch Kapor, and other high-profile investors.

—Archemix of Cambridge, MA, inked a deal with pharma giant GlaxoSmithKline worth $27.5 million upfront and potentially another $200 million in milestone payments for each of the seven of Archemix’s “aptamer” drugs covered by the agreement. The deal will not affect a planned reverse merger with Lexington, MA-based NitroMed (NASDAQ: NTMD), according to Archemix’s CFO.

—EMC (NYSE: EMC) acquired some of the assets and personnel of Seattle’s SourceLabs. The Hopkinton, MA-based firm plans to integrate the new assets and staff into its cloud computing business.

—Lexington, MA-based Indevus Pharmaceuticals (NASDAQ: IDEV), which is developing several drugs for hormonal disorders, said it will be acquired by Endo Pharmaceuticals (NASDAQ: ENDP) for $370 million, with another $267 million on the table if regulatory and sales goals are met.

—Forma Therapeutics, a Cambridge, MA-based startup co-founded by scientists at the Broad Institute of Harvard and MIT, raised $25 million from the Novartis Option Fund, Bio*One Capital, and others. Forma aims to turn new knowledge about the genetic underpinnings of cancer into new treatments for the disease.

—Needham, MA-based ClickSquared, a provider of a software-as-a-service system for direct marketing, raised an $11 million Series B round led by JMI Equity, ABS Venture, and Flybridge Capital Partners. The round brings ClickSquared’s total raised to $46 million.

—RatePoint, ClickSquared’s Needham neighbor, also completed a Series B round, this one worth $10 million. Castile Ventures led the deal, and .406 Ventures and Prism VentureWorks joined in backing the developer of online surveys and widgets.

—Satori raised $22 million in venture capital from InterWest Partners, Prospect Venture Partners, New Enterprise Associates, and others. The Cambridge, MA-based startup, founded by Boston-based PureTech Ventures, which also joined the funding round, is aiming to develop small-molecule drugs that can be safely taken on a chronic basis to block the production of toxic proteins that cause Alzheimer’s disease–hopefully halting it in its early stages.

—Waltham’s Polaris Venture Partners participated in a $7.5 million Series C round for JibJab, the online parody maker that has recently begun making e-cards. Overbrook Entertainment and Sony Pictures Entertainment led the deal.

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We’ve got some M&A activity, some board-room drama, and some cool new companies and drug-development strategies–the year’s off to an interesting start for New England’s life sciences firms.

—Forma Therapeutics, flush with $25 million from the likes of the Novartis Option Fund and Singapore’s Bio*One Capital, emerged from stealth mode to unveil its strategy for discovering new ways to battle cancer. Ryan gave an early look inside the startup, which was co-founded by a group that included three stars from the Broad Institute of Harvard and MIT—Todd Golub, Stuart Schreiber, and Michael Foley—and which already has operations in Cambridge, MA (where it’s headquartered); Branford, CT; Beijing; and Singapore.

—The Massachusetts Ethics Commission fined Massachusetts Biotechnology Council president Bob Coughlin $10,000 for taking part as a state official in meetings about policies relevant to the biotech industry while he was “secretly” a candidate for the MBC leadership post.

—Luke got an overview of Cambridge, MA-based Biogen Idec’s (NASDAQ: BIIB) efforts to develop a new type of treatment for Parkinson’s disease. Results from a mid-stage trial of the drug, currently known as BIIB-014, are due out next week at the JP Morgan Healthcare Conference in San Francisco.

—Ryan reminisced about some of last year’s most interesting life sciences deals. Between GlaxoSmithKline’s $720 million buyout of Sirtris Pharmaceuticals, ProteoStasis Therapeutics’ $45 million launch, and the like, perhaps it wasn’t such a bad year after all.

—Cheshire, CT-based Alexion Pharmaceuticals (NASDAQ:ALXN) agreed to license a patent related to humanizing antibodies for $25 million from PDL BioPharma (NASDAQ:PDLI) as part of a settlement of a legal dispute between the two companies.

—Indevus Pharmaceuticals (NASDAQ: IDEV) of Lexington, MA, agreed to be acquired by Endo Pharmaceuticals (NASDAQ: ENDP) for $370 million, or $4.50 a share. Indevus shareholders could get another $267 million if certain regulatory and sales goals are met.

—David Barlow, the former CEO and chairman of Molecular Insight Pharmaceuticals (NASDAQ:MIPI), resigned from the Cambridge, MA-based company’s board of directors citing “significant and sustained disagreements…regarding business philosophy, strategy and practice” with the rest of the board.

–Natick, MA-based Boston Scientific (NYSE:BSX) acquired drug-eluting stent developer Labcoat of Galway, Ireland. Financial terms of the deal weren’t disclosed.

—Synta Pharmaceuticals forged a drug-development alliance with Swiss drug giant Roche that could eventually yield up to $1 billion in payments for Lexington, MA-based Synta. The agreement, which focuses on treatments for inflammatory diseases, calls for Roche to pay Synta $25 million in upfront license fees.

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Indevus Pharmaceuticals has reached the end of its road. The Lexington, MA-based biotech company (NASDAQ: IDEV) said today it has agreed to be acquired by Endo Pharmaceuticals for $370 million, or $4.50 a share in cash.

The acquisition, approved by the boards of both companies, also has a sweetener clause which could kick in another $267 million, or $3 a share, to Indevus shareholders in the future if Endo (NASDAQ: ENDP) can reach certain regulatory and sales goals, the companies said today in a statement. Even without the sweetener, the offer represents a 45 percent premium for Indevus shareholders over today’s closing stock price of $3.10.

Indevus is coming off a rocky 2008. The company lost two-thirds of its stock value on June 4 after it was slapped down by an FDA request for a new clinical trial before it would approve testosterone undecanoate (Nebido), a long-lasting testosterone replacement therapy for men who lack the hormone, suffering from so-called “male menopause.” The company said it was “very surprised and disappointed,” by the FDA’s decision. But Endo, a specialty pharmaceutical company in Chadds Ford, PA, sees an opportunity to expand its portfolio, and boost its profits in 2009. The company plans to focus on urology and endocrinology.

“This merger reflects our desire to expand our business beyond pain management into complementary medical areas where we can be innovative and competitive,” said David Holveck, Endo’s CEO, in a statement.

Endo said it expects to wring out $40 million in cost savings through the deal, although it didn’t say exactly how it would do that.

Besides the testosterone replacement drug, Indevus sells histrelin (Supprelin LA) to treat precocious puberty. It has another drug in the final stage of clinical trials, octreotide implant, for acromegaly, a disease of excessive production of growth hormone.

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Boston is the biggest center of life sciences in the Xconomy network, and by our analysis, the Bay State’s biotech sector is also the best equipped to survive the economic crisis.

I reached this conclusion by combing through public company filings of more than 70 life sciences companies in Boston, Seattle, and San Diego. For all those companies, I asked the two most important questions about their financial health: How much cash does the company have in the bank, and how fast is it burning through it?

The good news for Boston is that it has a lot of companies with a lot of cash. Of the 40 companies that reported quarterly financial results through the end of September, 15 of them had war chests with more than $100 million. A subset of that group—10 companies—are also quite profitable, including Genzyme, Biogen Idec, and Thermo Fisher Scientific, to name a few. By comparison, San Diego has 10 companies with more than $100 million in reserves, and just three companies that are consistently profitable. Seattle has two companies in the $100 million cash club, and just one profitable operation (Sonosite, the ultrasound device maker).

Of course, there’s plenty of misery and anxiety to go around in Boston, too, as you’ll see below. Here’s a rundown of the 40 companies I analyzed, in alphabetical order. It’s not a comprehensive list, so if you’d like to nominate an operation that was left out, please send us a note at editors@xconomy.com.

—Abiomed (NASDAQ: ABMD). The Danvers, MA-based medical device company had $50.6 million in cash and investments at the end of September and a $6.3 million net loss in the third quarter.

—Alkermes (NASDAQ: ALKS). This Cambridge, MA-based company burned through about $47 million of its cash in the first nine months, but it still had $425.8 million left at the end of September.

—Alnylam Pharmaceuticals (NASDAQ: ALNY). The Cambridge, MA-based developer of RNA interference drugs doesn’t have any products on the market, but it actually has more cash now than it did at the beginning of the year because of partnership deals. Alnylam had $520 million in cash and investments at the end of September, and expects to close the year with more than $500 million. … Next Page »

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Hats off to Link Medicine, whose $40 million financing was a nice reminder that the economy still has a pulse. That, and the rest of the week’s Boston-area life sciences news, below.

—In case you missed our forum, How to Build a Life Sciences Company, Ryan did a great round up of the varied and creative strategies that some of the most interesting up-and-coming firms are employing in this difficult economic climate. Among them: The Ensemble Scientific Cast Model, The Big Pharma Checkbook Model, and The David (or Five Davids) Model.

—Natick, MA-based Boston Scientific (NYSE: BSX) won FDA clearance for its Taxus Express2 Atom Stent System, making it the only device approved for propping open clogged heart vessels as small as 2.25 millimeters in diameter.

—Concert Pharmaceuticals of Lexington, MA, launched its first clinical trial of a drug called CTP-347 that’s designed to prevent menopausal hot flashes without the dangerous side effects of hormone replacement therapy. The drug, like the others in Concert’s pipeline, is made by replacing a few hydrogen atoms on an existing drug with deuterium atoms.

—Luke took a quick look at EpiZyme, a stealthy year-old startup backed by MPM Capital and Kleiner Perkins Caufield & Byers. According to the firm’s founding CEO (MPM’s managing director) Kazumi Shiosaki, EpiZyme has hired a “dynamic duo” of executives from two big drugmakers to help lead its efforts to develop drugs based on epigenetics, biological system for turning genes on and off without altering their sequences.

—Lexington, MA-based GI Dynamics unveiled some promising results from a trial of its gut-lining sleeve device that’s designed to mimic the effect of gastric-bypass surgery but spare patients from actually going under the knife. Patients in the trial, which was presented at the International Federation for the Surgery of Obesity and Metabolic Disorders World Congress in Buenos Aires, lost an average of 30 pounds after three months, compared with about 10 pounds for those who dieting.

—Luke explored the strategy that Cambridge, MA-based Genzyme (NASDAQ: GENZ) is building around the cholesterol-lowering drug mipomersen, the co-marketing rights for which Genzyme paid $325 million to Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS). Genzyme typically goes after small patient populations (with very expensive drugs), and that’s where it’s starting with this one, seeking approval for mipomersen for people with an exceedingly rare genetic disorder that causes high cholesterol. But the firm also plans to tackle bigger and bigger markets with mipomersen, which raises a number of questions about how Genzyme will test and price the drug.

—Bermuda-based Covidien, a healthcare products company with a large presence in Massachusetts, announced a restructuring program that includes projects in all four of its business segments and in corporate. The firm says the program will save $50 million to $75 million a year.

—Clinical Data (NASDAQ:CLDA), a biotech firm in Newton, MA, said it will raise some $25 million in a private placement of stock and warrants.

—Luke painted a portrait of CombinatoRx (NASDAQ: CRXX), an eight-year-old firm in Cambridge, MA, that’s nearing an important juncture. CombinatoRx “will find out within the next four weeks whether its experimental combination drug for arthritis is likely to become a multi-billion dollar product, or a big, fat zero,” Luke wrote. If it makes it to market, the drug would be the first of CombinatoRx’s products, which are developed by putting existing drugs together in new combinations.

—Lexington, MA-based Indevus Pharmaceuticals (NASDAQ:IDEV) launched a Phase 3 clinical trial of an implant that delivers a drug to treat the rare condition acromegaly. If it makes it to market, the device could go head-to-head with Novartis’ injectable version of the drug, Sandostatin LAR, which had 2007 sales of $1.027 billion.

—Link Medicine, a Cambridge, MA-based startup developing treatments for Alzheimer’s Disease, ALS, and other neurodegenerative conditions, raised $40 million in a Series C venture round from Clarus Ventures and SV Life Sciences. The firm’s two earlier financing rounds brought in a combined $16.5 million.

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Indevus Pharmaceuticals, a Lexington, MA, maker of specialty drugs, says it has launched a Phase 3 clinical trial of an implant designed to provide long-term treatment of patients with acromegaly, a rare and potentially life-threatening condition caused by the overproduction of growth hormone. The company (NASDAQ:IDEV) plans to use its patented “hydron polymer technology” in the implant to outlast Sandostatin LAR injections, the leading current treatment for acromegaly marketed by Switzerland’s Novartis (NYSE:NVS)—pitting the local biotech firm against a global drug giant.

The Indevus implant is inserted under the skin of a patient’s arm at their doctor’s office and is designed to release octreotide—which is a synthetic peptide designed to replicate the growth-hormone-suppressing properties of a natural hormone—for six months. (Indevus already markets to two treatments—Vantas for advanced prostate cancer and Supprelin for early onset of puberty—that use the same polymer technology to allow for this kind of extended release of the drug.) Sandostatin injections also deliver the octreotide peptide, but must be repeated every month.

In the randomized Phase 3 trial, Indevus plans to recruit 140 patients in the U.S. and Europe to, treat them with either octreotide implants or Sandostatin injections, and compare how well the two treatments suppress growth hormone and insulin-like growth factor. Depending on the results of the trial, Indevus says it may be able to launch the implant by early 2011.

It’s unclear what impact the octreotide implant would have on Novartis, which has managed to stave off competition from generic alternatives to Sandostatin, which had 2007 sales of $1.027 billion out of a market of $1.2 billion for such drugs. “This product represents a large commercial opportunity for the company,” says Glenn Cooper, CEO of Indevus, in a statement. He notes that the company plans to begin a Phase 2 trial of the octreotide implant to treat carcinoid syndrome, which is caused when carcinoid tumors secrete such natural chemicals as serotonin into the bloodstream, in early 2009.

Breaking into a well-trodden market with a longer-acting version of an existing drug has brought mixed results for some biotechs. For example, Cambridge, MA-based Alkermes (NASDAQ:ALKS) has seen slow sales of Vivitrol, a once-per-month injection based on generic drug naltrexone to treat alcohol dependence, which is about 10 times as expensive as generic naltrexone and difficult to get reimbursed by health insurers.

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While many of us were cutting out early for the holiday weekend, and to enjoy the last week of summer, New England tech and life sciences firms were cutting a surprising number of deals.

—Tufts spinoff Quanterix closed the second half of a $15 million financing round from Arch Venture Partners, Bain Capital Ventures, and Flagship Ventures. Luke talked with the Cambridge, MA-based firm’s CEO about its technology for pinpointing minute quantities of proteins in a patient’s blood that might serve as early warning signals for cancer, Alzehimer’s disease, or other ailments.

—Lexington, MA-based Mall Networks, which creates online malls that give loyalty cardholders bonus points for shopping, raised $7 million in a Series B investment led by Dace Ventures and joined by previous investors Flybridge Capital Partners, Venture Capital Fund of New England, and LBO Enterprises.

—Living Proof of Cambridge, MA, raised $7 million Series A-3 financing from Polaris Venture Partners and other investors. Though it tries to keep a low profile, the startup is using the expertise of some very high-profile scientists, investors, and executives to address the multi-billion-dollar market for beauty products.

—Cambridge, MA-based JumpTap, which provides mobile Web search and advertising technology for a variety of phones from AT&T, Alltel, Boost Mobile, U.S. Cellular, and a host of other carriers, closed a $26 million Series D financing round. The deal was led by AllianceBernstein and joined by existing investors General Catalyst Partners, Summerhill Venture Partners, Redpoint Ventures, Valhalla Partners, and WPP.

—Specialty pharmaceutical maker Indevus Pharmaceuticals (NASDAQ:INDEV) raised $105 million in a private placement of notes secured by royalties for Sanctura, the Lexington, MA-based firm’s drug for overactive bladder.

—Software-defined-radio startup Vanu of Cambridge, MA, reportedly took in $32 million a Series B venture round from Charles River Ventures, Norwest Venture Partners, and Tata Capital. The firm’s technology allows wireless operators to broadcast to use multiple standards such as GSM and CDMA.

—Dover, NH-based Salient Surgical Technologies, a maker of blood-vessel-sealing devices, pulled its planned $86.25 million initial public offering.

—Boston-based uLocate inked a deal to provide local information and mapping services for Sprint’s new nationwide WiMax network, XOHM, now under construction.

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There were some exciting venture deals this past week, and some great in-depth reporting about Boston-area life sciences firms on the part of Luke and Ryan. In case you missed any of it….

—Ryan did some sleuthing on a stealthy startup down the street from Xconomy’s headquarters in Kendall Square, MA, and uncovered (at least partially) Living Proof. With a board that includes MIT’s Robert Langer and Polaris Venture Partners as an investor, the startup is leveling some impressive scientific and business firepower against bad hair days and other cosmetic complaints—and it has $7 million in new financing to buoy its quest for beauty.

—Brand-new Boston-area startup Proteostasis Therapeutics closed a massive $45 million Series A financing from HealthCare Ventures, Fidelity BioSciences, New Enterprise Associates, Novartis BioVenture Fund, and Genzyme Ventures. The firm is aiming to develop small-molecule treatments for Alzheimer’s disease, diabetes, emphysema, and other ailments that work by helping the body maintain normal protein production.

—Medical diagnostics startup Quanterix, a Tufts University spinoff in Cambridge, MA, reportedly raised $15 million in a Series A financing from Arch Venture Partners, Bain Capital, and Flagship Ventures. The startup is developing tools capable of identifying single molecules in human blood.

—Just hired to head the Massachusetts Life Sciences Center—the agency that will administer the state’s $1 billion funding initiative—Susan Windham-Bannister shared her goals and plans for the center in a lengthy interview with Luke. (He had the good sense to save the hard questions for part 2.)

—Wondering what happens to the IP when a biotech goes bust? Ryan caught up with Wellesley, MA, accountant Joseph Finn, who puts defunct firms’ patents on the auction block.

—Resolvyx Pharmaceuticals raised $4 million in an add-on to a $25 million Series B financing round that the Bedford, MA-based company closed in April. Atlas Venture, Flagship Ventures, Radius Ventures, CHL Medical Partners, Biogen Idec, and QVT Fund are supporting the startup’s efforts to turn fish-oil science into treatments for a host of inflammatory diseases.

—Genzyme (NASDAQ: GENZ) of Cambridge, MA, and the nonprofit Medicines for Malaria Venture formed an alliance with India’s Advinus Therapeutics to develop new treatments for pregnant women and infants infected with malaria.

—The FDA said that it is working with Biogen Idec (NASDAQ: BIIB) and Elan (NYSE: ELN) to update the labeling for Tysabri following confirmation that two multiple sclerosis patients on the drug had contracted the often-fatal brain infection PML.

—Lexington, MA-based Indevus Pharmaceuticals (NASDAQ: INDEV) raised $105 million in a private placement of notes; the cash is intended to retire existing debt and carry Indevus into calendar 2010.

—Bob gave a sneak peek of our September 23 forum, How to Build a Life Sciences Company. Robert Langer will be a keynoter at the event; I’m betting it will be a good hair day for him.

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Indevus Pharmaceuticals (NASDAQ:INDEV), a Lexington, MA, specialty pharmaceutical firm, announced it has raised $105 million in a private placement of non-recourse notes. The company said the sale of the notes, which are secured by royalties from its overactive bladder drug Sanctura, is intended to retire existing debt due next year and fund operations into calendar 2010.

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Boston-area life sciences firms had mixed success navigating regulatory waters this week. Here’s the skinny on that and the rest of the week’s biomedical news.

—Vertex Pharmaceuticals (NASDAQ: VRTX) sold the rights to its royalty stream on two HIV drugs for $160 million; the Cambridge, MA-based firm plans to use the cash to help bring its hepatitis C drug, telaprevir, to market.

—Syndexa Pharmaceuticals of Cambridge, MA—a spinoff of the Harvard School of Public Health pursuing new treatments for metabolic diseases—announced it has raised $15 million in a Series B financing round.

—The FDA gave Cambridge, MA-based Infinity Pharmaceuticals permission to skip Phase II trials of its drug for stomach cancer, based on a promising early study. The unusual move could shorten by two years the time it takes to bring the drug to market.

—The FDA was less kind to Lexington, MA’s Indevus Pharmaceuticals (NASDAQ: IDEV), requiring that the company complete a new clinical trial of its long-lasting testosterone replacement therapy product, Nebido, before the agency will approve the drug.

—Cambridge, MA-based Alnylam Pharmaceuticals invested $5 million in Tekmira Pharmaceuticals of Vancouver; the deal gives Alnylam access to the Canadian firm’s technology for delivering drugs based on RNA interference.

—Danvers, MA, cardiac device maker Abiomed (NASDAQ: ABMD) won approval for an in-heart pump designed to help critically ill patients for short periods of time.

—Luke took a closer look at Alexandria Real Estate Equities’ recently proposed $1 billion makeover of the Cambridge, MA, neighborhood that is Xconomy’s back yard as an always-open urban mecca for life sciences professionals.

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Indevus Pharmaceuticals got slapped down hard this morning. The Lexington, MA-based company said today it expects the FDA to formally ask for more safety data that will require a new clinical trial before it will approve Nebido, a long-lasting testosterone replacement therapy for men with low levels of the male sex hormone. Shares of the company (NASDAQ: IDEV) sunk 66 percent to $1.40 at noon.

The FDA’s beef with Nebido is that, if injected improperly, it can cause rare, short-term coughing episodes, Indevus said today in a statement. The company’s clinical trials found one coughing episode out of 500 patients. In that case, the side effect resolved within 10 minutes and didn’t require medical attention, Indevus said. “We are very surprised and disappointed by the position the FDA is taking,” said Glenn Cooper, Indevus’ CEO, in the statement.

Indevus isn’t giving up, intending to pump more resources into another study to satisfy the FDA, Cooper said. That should take 18 months, followed by another 6-month review period by the agency before it can be cleared for sale in the U.S. (Indevus already has several other drugs for endocrinology and neurology applications on the market.)

Since Nebido is already approved in Europe and the side effect is described in the product label, the decision “flies in the face of logic,” because the FDA has power to require new surveillance of drug safety once a drug is on the market, said David Miller, president of Biotech Stock Research, an independent research firm in Seattle, in a note to clients this morning. It may be that “this division of FDA has decided they are uncomfortable approving new drugs,” that treat low testosterone levels, Miller wrote.

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