Financing news kept flowing this week from New England startups developing software, medical device, drug, and cleantech products.

—Ziptr, a Burlington, MA-based maker of software focused on business privacy and compliance, pinned down $6.8 million in equity financing from 26 investors.

—Lumicell Diagnostics, a portfolio company of Waltham, MA-based Kodiak Venture Partners that’s developing a cancer diagnostic device, added $2.7 million in equity-based funding.

—Bedford, MA-based Hologic (NASDAQ: HOLX), a developer of medical imaging and diagnostic devices, paid $135 million to acquire Chinese medical products distributor TCT International, which distributes Hologic’s ThinPrep Pap Test.

—General Compression, a Newton, MA-based energy storage technology company, raised a $20.4 million equity financing round from four investors. Its previous backers include Duke Energy, U.S. Renewables Group, and Northwater Intellectual Property Fund.

—Constellation Pharmaceuticals of Cambridge, MA, added another $15 million in Series B extensions from existing investors, including Third Rock Ventures, The Column Group, Venrock Associates, SR One, and Altitude Life Science Ventures. That brings the round to $37 million for Constellation, a developer of drugs for treating cancer, inflammatory and immunologic disorders, and other diseases.

—Concord, MA-based PolyRemedy nabbed $20 million in Series C financing to put towards commercializing its customized wound-healing system. New investor Delphi Ventures led the round, which also included previous PolyRemedy investors MedVenture Associates, Advanced Technology Ventures, and Flybridge Capital Partners. The money will go towards app development, manufacturing, and sales and marketing.

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You wouldn’t know we had a holiday this week, with the rate Boston life sciences companies are pumping out news. They’ve inked partnerships, announced fundings, made acquisitions, and are gearing up for a big medical convention this weekend.

—Cambridge, MA-based Ariad Pharmaceuticals (NASDAQ: ARIA) will reveal data from a clinical trial of its drug ridaforolimus to an eager audience at next week’s American Society of Clinical Oncology’s (ASCO) annual meeting in Chicago, Luke wrote. The drug was developed in a collaboration with Merck and is designed to block a protein that causes tumor growth.

—Woburn, MA-based drug developer Excelimmune said it nabbed $10.5 million in Series B financing, from new and previous individual backers. The money will help advance Staphguard, the company’s treatment for Staph infections resistant to methicillin.

—Aveo Pharmaceuticals of Cambridge said it entered into a partnership with Johnson & Johnson’s (NYSE: JNJ) Centocor Ortho Biotech unit to work together on Aveo’s antibodies targeting a receptor involved in tumor growth. Aveo (NASDAQ: AVEO) received $15 million upfront for this, and could get $540 million more down the road in milestones.

—Cambridge-based Dossia, a nonprofit consortium offering online medical records to employees of its member companies, inked a partnership this spring with Denver-based Health Language. Dossia CEO Michael Critelli says the collaboration will help translate the medical jargon in the clinical records into plain English for patients to better understand and manage their care.

—Luke took a look at Cambridge-based Infinity Pharmaceuticals (NASDAQ: INFI) as it readies itself for a presentation at ASCO. The drug developer will reveal data from the first 16 months of a trial of its new drug candidate for pancreatic cancer, IPI-926.

—My colleague Arlene wrote about Newton, MA-based NeuroHealing, a virtual biotech company that looks for already approved drugs and reformulates them to treat central nervous system disorders. The company has been getting grants and other investments to fund the development of its drugs for treating patients with traumatic brain injuries, Parkinson’s disease, and premature ejaculation.

—Lumicell Diagnostics, a Waltham, MA-based developer of a cancer diagnostic device, took in $2.7 million in equity-based funding.

—Bedford, MA-based diagnostic and medical imaging firm Hologic (NASDAQ: HOLX) announced it had acquired TCT International, a China-based distributor of medical products, for $135 million in cash.

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Hologic (NASDAQ: HOLX), a Bedford, MA-based developer of diagnostic and medical imaging devices, announced today that it has bought Beijing-based TCT International for $135 million in cash, with $35 million of that deferred for one year, plus a two-year contingent earn out. TCT is a distributor of medical products and instruments in China, including Hologic’s ThinPrep Pap Test. “We firmly believe by controlling a distribution channel as extensive as TCT’s, we can better leverage our entire product portfolio to drive growth across multiple market segments,” said Hologic president and CEO Rob Cascella in the announcement of the deal.

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It was a historic week in the Boston biotech field with big acquisition news, but we also saw headlines on stealthier firms and startup financings.

—Ryan took a closer look at H3 Biomedicine, a cancer research house setting up shop in Cambridge, MA, with the support of Japanese drugmaker Eisai. He compared it to the research efforts of other big drugmakers like GlaxoSmithKline, which has also created a entrepreneurial startup in Cambridge, Tempero Pharmaceuticals, to fuel new drug discoveries. Eisai is providing $200 million, access to its scientists, and research and development support to H3.

—Bedford, MA-based Hologic nabbed FDA approval for its 3-D imaging system for breast cancer screening and diagnostics, which is designed to supplement existing scanning technology. The device is said to be the first of its kind to provide 3-D images of the breast.

—Biogen Idec (NASDAQ: BIIB) of Weston, MA, announced that its board of directors had given the drugmaker permission to repurchase 20 million shares of its common stock to offset stock issuances under its share-based compensation plans.

—Beverly, MA-based drug developer Cellceutix settled a compensation dispute with its former CEO George Evans. The company will buy 4.6 million shares of stock held by Evans and/or his sons over the past three years, for $1 million. Evan had previously sought $1.7 million in back salary and future compensation.

—Ryan tracked down a few more details from Tillman Gerngross, co-founder and CEO of Lebanon, NH-based Adimab, about his stealthy new spinout Arsanis. The startup is focused on using Adimab’s yeast-based antibody discovery system to find drugs that could serve as an alternative to antibiotics for infectious diseases.

—Healthcare companies accounted for a 60 percent chunk of the funding raised by Massachusetts startups in January, according to … Next Page »

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Bedford, MA-based Hologic said on Friday it has received approval from the U.S. Food and Drug Administration for its 3-D imaging system for doing breast cancer screening and diagnosis. The company’s X-ray mammography device, called the Selenia Dimensions System, is the first of its kind to provide 3-D images of the breast, according to the FDA. Radiologists in two studies showed a 7 percent improvement in their ability to distinguish between cancerous and non-cancerous cases when they viewed both 3-D and conventional 2-D images, as compared to 2-D images alone. The idea is that Hologic’s 3-D imaging technology can supplement, not replace, conventional breast scanning. The company’s imaging system is already available in more than 40 countries, including Canada and Mexico.

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Bedford, MA-based Hologic, a provider of diagnostics, medical imaging, and surgical products for women, announced today that it has bought Interlace Medical of Framingham, MA, for $125 million in cash. Interlace, which makes a hysteroscopic tissue removal system, will be integrated into Hologic’s (NASDAQ: HOLX) gynecological surgical products business. The deal also includes two annual contingent payments, which will be a “multiple of the incremental revenue growth over the prior year,” according to the announcement.

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Cambridge, MA-based Helicos BioSciences (NASDAQ:HLCS), a developer of genetic analysis technology for molecular diagnostics, said today it has named Ivan Trifunovich as the company’s president and CEO. Trifunovich, who was named the firm’s executive chairman on September 15 and has previously served as its consultant, is a former senior vice president of Third Wave Technologies, a molecular diagnostics company that is now part of Bedford, MA-based Hologic (NASDAQ:HOLX). Helicos’s board of directors asked its former CEO, Ron Lowy, to step down from that post. Lowy has returned to his seat on the firm’s board of directors.

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One day in my high school Spanish class, a kid who I was told had autism started hitting himself on the head repeatedly until our teacher sent him to the nurse. Looking back, I wonder whether he understood how abnormal his behavior was. But 17 years later, I’m encouraged by the growing cluster of outfits in the Boston area that are developing a host of new treatments and medical tests for people like my former classmate.

Autism spectrum disorders—which are brain disorders that make socializing difficult, among other symptoms—are a growing health concern in the United States. And it’s viewed as a huge potential market for drugs and diagnostics. There are an estimated one in 110 children in the country who have autism spectrum disorders, according to the U.S. Centers for Disease Control and Prevention. To date, there are neither approved drugs nor any easy ways to diagnose autism. Yet there have been discoveries at MIT and other research centers in the Boston area in recent years that have given people hope of improved treatments for autism—and reasons for investors to pump capital into startups focused on advancing these treatments.

“What we’re hoping to do is step into a complete void out there in terms of proven medical treatments for the condition,” says George Evans, the chairman and chief executive of Beverly, MA-based Cellceutix, which is seeking capital to advance its experimental compound for autism.

In the Boston area, which is rich with renowned academic centers and biotech companies, there are clusters of companies in almost every kind of disease: cancer, autoimmune diseases, cardiovascular conditions, and on and on. However, there appear to be a particularly high proportion of recent entrants in the area’s budding autism cluster, which tells me that I probably would have had trouble compiling much of a list of such firms back, say, in the early 1990s.

Here’s an alphabetized list of startups and research organizations in the Boston area that are trying to address the unmet medical needs of people with autism:

Affectiva
Waltham, MA

This MIT spin-off is developing the “Q Sensor,” which detects electrical signals on … Next Page »

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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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In remote villages in Africa, clinics are struggling to deliver timely blood tests to help doctors determine the best way to treat HIV patients. But Bill Rodriguez, a Harvard-trained physician, through his new startup Daktari Diagnostics, is working on a handheld device that could someday perform blood tests for HIV patients virtually anywhere within a few minutes.

Cambridge, MA-based Daktari has generated buzz for its technology and social cause from a bevy of Boston-area backers that have invested a total of $2.8 million to complete its Series A round of financing, says Rodriguez, the co-founder and CEO of startup told me in his first in-depth interview about the company. (We wrote a short story last week that the one-year-old startup had raised $2.5 million, based on regulatory filings, but the firm now says it has raised more money than that.) The Boston-area investors in the startup—a few of which we reported last week—include Norwich Ventures, Partners Innovation Fund, Hub Angels, Mass Medical Angels, Launchpad Venture Group, and Boston Harbor Angels.

Daktari (a Swahili word for doctor or caregiver) has a goal with of producing both social and economic benefits. Rodriguez, who was previously chief medical officer of the William J. Clinton Foundation, said that millions of HIV-positive patients in the world aren’t receiving regular tests that measure the number of blood cells with CD4 markers on their surface—a key indicator of a patient’s immune system strength that can inform a doctor’s decisions on how aggressively to treat HIV. Part of the problem is that the blood tests to get CD4 counts typically must be performed by expensive, bulky instruments called flow cytometers. It’s also difficult to obtain and handle the blood samples because many HIV patients live in remote areas.. Daktari may have a solution: a handheld diagnostic device designed to for use in any setting, without having to manually transfer blood with pipettes or other manual steps.

Some serious players in diagnostics and innovation circles are affiliated with Daktari, including Stan … Next Page »

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Perhaps New England’s life sciences companies were busy building arks this past week, because the news flow was a heck of a lot lighter than the rainfall. There are still a few interesting developments to report, though.

—Cambridge, MA-based Biogen Idec (NASDAQ:BIIB) agreed to pay $110 million up front, plus up to $400 million in additional fees, for the rights to develop and commercialize the multiple sclerosis drug Fampridine-SR overseas. The drug’s developer, Hawthorne, NY-based Acorda Therapeutics (NASDAQ:ACOR), will retain U.S. marketing rights.

—Ryan caught up with Xconomist Alexis Borisy, who last week left his post as the CEO of CombinatoRx (NASDAQ:CRXX), the Cambridge, MA-based firm he launched in 2000 to develop novel treatments based on combinations of existing drugs. Borisy spoke candidly about the “miserable” experience of having to lay off about 100 workers after his company’s lead drug failed in a mid-stage clinical trial last October, and about his hopes for the firm’s future, which includes a planned merger with Vancouver’s Neuromed Pharmaceuticals.

—Luke profiled Boston-based Immuneering, the brainchild of 27-year-old CEO Ben Zeskind and 30-year biotech veteran Bob Carpenter who, among other accomplishments, sold one of his companies to Genzyme (NASDAQ: GENZ) for $1 billion. The startup wants to use its proprietary mathematical modeling tools, based on research from the MIT lab of Doug Lauffenburger, to help figure out from blood and biopsy samples which cancer patients will respond to which drugs. This could spare patients the side effects of drugs that won’t work for them and could spare insurance companies the expense of those drugs.

—Hologic (NASDAQ: HOLX), a women’s health-focused firm in Bedford, MA, won FDA approval for a device called Adiana designed to provide a less-invasive alternative to tubal ligation. The permanent contraceptive device was approved for the European market in January.

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Bedford, MA-based Hologic (NASDAQ: HOLX) announced that the FDA has approved its permanent contraception device, called Adiana. Offering a less-invasive alternative to tubal ligation—a surgical procedure that is one of the most common forms of contraception worldwide—the device can be inserted via catheter through the vagina in a 15-minute procedure. Hologic gained European approval for the device this past January.

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It only takes about 30 minutes from downtown Seattle to get to what some people like to call the “Silicon Valley of Ultrasound,” in Bothell, WA. So when I heard about another ultrasound startup company, one with a name that comes from the Latin word for “miraculous,” I figured it was worth checking out.

There’s actually a lot more substance to the story than that. Bothell, WA-based Mirabilis Medica doesn’t claim to have achieved any miracles. But it has a pretty ambitious goal. Its team of engineers are building an ultrasound machine that is supposed to offer a non-invasive way to get rid of uterine fibroids. The technology has potential to help relieve symptoms of these painful growths in the uterus that are the leading reason so many women get hysterectomies after their childbearing years.

The problem, and market opportunity, is a big one. As many as one out of five women in the U.S. suffer from fibroids, according to the National Institutes of Health. Women can take drugs, or get a couple of different surgical procedures, but the only cure is a radical one—complete removal of the uterus, a hysterectomy. About 625,000 women get hysterectomies in the U.S. each year, and about half of the time it is because they have uterine fibroid growths that cause painful cramping and bleeding, says Mirabilis CEO Mike Connolly. So if Mirabilis can come up with a way to get rid of these fibroids, without a doctor having to pull out a scalpel, it forecasts it will tap into a new market worth $1 billion a year.

“Right now, it’s basically like doctors are hitting a fly with a sledgehammer,” Connolly says.

Mirabilis, like practically every ultrasound company in Bothell, can trace its family tree to the University of Washington. The company got started in 2004, by Alex Lebedev on business, Shahram Vaezy on technology, and Michael Lau, a practicing gynecologist in Edmonds, WA, on the medical side. Connolly joined the company in October 2006, after he got an up-close look at the technology when he was a principal with vSpring Capital, an early investor. Besides vSpring, the company has raised about $11 million since the beginning from Charter Life Sciences, Arboretum Ventures, Split Rock Partners, and Dow Chemical.

The Mirabilis technology has two critical components. One uses the diffuse, low-intensity waves of diagnostic ultrasound to help doctors look inside the body and pinpoint the location of the fibroids. The other element is a high-intensity, tightly-focused therapeutic wave of ultrasound. That part is supposed to heat up tissue just enough to kill fibroid cells without causing any collateral damage or side effects.

Mirabilis has about 10 employees, including some engineers from one of the few successful therapeutic ultrasound companies, Liposonix, which uses ultrasound for body sculpting. The technical challenge … Next Page »

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

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

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

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

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

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

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

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

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

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Exact Sciences, a Marlborough, MA, developer of a DNA-based stool test for detecting colorectal cancer, says that its board of directors has replaced the firm’s CEO and chief financial officer. The management changes follow the firm’s successful maneuvering to avoid a takeover by San Diego-based diagnostics firm Sequenom (NASDAQ:SQNM).

The board of Marlborough, MA-based Exact (NASDAQ:EXAS) has named Kevin Conroy as its new chief executive and Maneesh Arora as CFO. Conroy, 43, and Arora, 40, are the former CEO and CFO, respectively, of Third Wave Technologies, a Madison, WI, provider of genetic tests for women’s health and infectious diseases that was sold last year to Bedford, MA-based Hologic (NASDAQ:HOLX) for $582 million. Exact says that previous CEO Jeffrey Luber and CFO Charles Carelli have agreed to resign, and the new top executives will take over their posts April 2.

Luber and Carelli were credited with brokering a $24.5 million deal in January with Cambridge, MA-based biotech powerhouse Genzyme (NASDAQ:GENZ). The deal, which involved the sale prenatal and reproductive health assets to Genzyme, prompted Sequenom to drop its bid to buy Exact for $41 million in Sequenom common stock—an acquisition that Sequenom was pursuing over the objections the Massachusetts firm’s board. Sequenom, a developer of prenatal tests for Down syndrome and other disorders, wanted to buy Exact to improve its footing in the cancer diagnostics market.

Exact has struggled to gain widespread adoption of its DNA-based stool test for colorectal cancer, the second-leading cause of cancer deaths in the U.S., and it plans to seek FDA approval of a new version of the test by 2011. The company’s board members are banking on Conroy and Arora to ensure that the firm realizes its goals. (Hologic is already enjoying the fruits of Conroy and Arora’s labor, winning recent FDA approvals of a pair of human papillomavirus tests previously developed at their former firm Third Wave.)

“[Conroy and Arora's] unique experience with the development of complex molecular diagnostic products and successful management of both clinical and regulatory programs is precisely what Exact needs at this stage in the company’s development,” Patrick Zenner, chairman of Exact’s board of directors, said in a statement.

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The past week saw substantial cuts at two of New England’s biotech firms, but a thorough analysis of the financial reporting for most companies in the sector shows the news isn’t all bad. That and more below.

—Luke delivered the second installment of his Biotech Survival Index, which assesses the financial health of more than 40 of Boston’s public life sciences companies. Things were predictably dire for many of them, but compared to the previous quarter more companies were in the enviable position of having over $100 million squirreled away.

—Cambridge, MA-based Biogen Idec (NASDAQ: BIIB) and partner Genentech were unable to show in a clinical trial that their drug rituximab (Rituxan) is effective as a treatment for lupus nephritis, an inflammatory disease of the kidneys. Rituximab is already approved as a treatment for non-Hodgkin’s lymphoma and rheumatoid arthritis.

—Ryan profiled Aura Biosciences, a startup in Cambridge, MA, that’s out to commercialize drug-delivery technology licensed from European research institutions. Having recently raised over $3 million to fund its efforts, Aura hopes to develop nano-sized particles to ferry cancer drugs directly to tumor cells, say, or to carry RNA-interference-based treatments into the body.

—Epix Pharmaceuticals (NASDAQ:EPIX) of Lexington, MA, announced plans to reduce its staff by half to cut costs. The layoffs, which will affect 44 workers, combined with a reduction in CEO Elkan Gamzu’s base salary, should save Epix $4.4 million a year.

—Epix’s Lexington neighbor, Synta Pharmaceuticals (NASDAQ:SNTA), also announced a planned staff reduction. Cutting 90 workers, or about 41 percent of its staff, should allow the firm to operate for two more years without new funding.

—Wade took a look at a collaboration between IBM and Boston’s Brigham and Women’s Hospital that could give geographically dispersed teams of doctors … Next Page »

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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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Hologic (NASDAQ:HOLX), a Bedford, MA-based provider of women’s healthcare products, says that the FDA has approved two of its “Cervista” tests for detecting human papillomavirus (HPV), a major cause of cervical cancer. One of the tests is intended to identify 14 “high-risk” strains of HPV, according to the firm, and the other test is designed to detect two strains that are linked to 70 percent of cases of cervical cancer in the U.S. Late this morning the firm’s stock had jumped 82 cents per share, or 7.75 percent, to $11.40, on the news.

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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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We’re not a particularly weight-conscious crew, but we at Xconomy have been noticing lately that the ranks of Boston-area firms focusing on obesity seem to be, well, growing. (See page two for our list of such companies.)

Last month, for example, I profiled Lexington, MA-based GI Dynamics, which has reported progress in clinical trials with a device that lines a portion of the small intestine to help block the absorption of calories. Luke chronicled stealthy Cambridge biotech startup Zafgen, which is developing drugs to starve fat cells by cutting their blood supply. Then at our Xconomy Forum at Novartis Institutes of Biomedical Research last month, presenter RXi Pharmaceuticals (NASDAQ:RXII) of Worcester, MA, showed that it’s applying the gene-silencing power of RNA interference to treat obesity.

Even Bedford, MA-based diagnostics giant Hologic (NASDAQ:HOLX) and Wilmington, MA-based lab services behemoth Charles River Laboratories International (NYSE:CRL) are getting in on the action. They’re among the Bay State firms that headed out to Phoenix, AZ this week for the annual meeting of the Obesity Society—Hologic has developed dual energy X-ray machines for measuring body mass and Charles River offers lines of obese mice and rats for pre-clinical studies.

To make sense of this recent flurry of anti-obesity activity, I caught up with obesity market expert Jonas Arenas, an analyst for Boston-based health care investment bank Leerink Swann. What Arenas described was an obesity market with untold billions of dollars in revenue potential but a lack of safe and effective treatment options. According to the U.S. Centers for Disease Control and Prevention, about a third of Americans are obese, and the government is acutely aware of the links between obesity and diabetes, heart diseases and even certain types of cancer. To clarify the regulatory path for experimental obesity treatments, Arenas says, the FDA in February revealed that it would accept impacts on key measurements for diabetes such as blood glucose levels and pancreatic function markers as bases of approval for obesity treatments. This was a major development for drug and device companies aiming for approvals—as well as reimbursements—for weight-loss products.

“As a friend of mine who’s a pharmaceutical executive at a big company that’s involved in this area said,” Arenas says, “The flood gates are now open. It’s not just about losing weight … Next Page »

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