As we wind down the first month of 2012, I thought I’d take the pulse of some of the bigger technology companies around town. In addition to tracking startups and entrepreneurship, this is an important measure of the health and well-being of the Boston tech community.

So here’s a list of 10 well-known public companies, their stock price (as of Friday’s close), most recent financials, and other tidbits. Not comprehensive, of course. But of these firms, you might be surprised whose stock is the highest right now.

Most of these companies will announce their end-of-year financials in the next two weeks…

Akamai (NASDAQ: AKAM)
Stock price: $32.01
2011 stats: Q3 profit of $63M on $282M in revenue; coming off $1B+ revenue in 2010.
Recent news: The company has acquired rival Cotendo and is positioning itself as a platform for businesses to reach customers via Web, mobile, and cloud.
Big question: Why doesn’t Akamai own the cloud (like Amazon)?

Carbonite (NASDAQ: CARB)
Stock price: $10.30
2011 stats: Q3 revenue of $15.9M (net loss of $7.4M); will announce full-year stats on Feb. 9.
Recent news: Coming off its IPO in August, Carbonite is adjusting to life as a public company.
Big question: Is online backup a big enough growth market?

Constant Contact (NASDAQ: CTCT)
Stock price: $25.11
2011 stats: Q3 revenue of $54.3M ($5.4M profit); full-year stats coming Feb. 2.
Recent news: Constant Contact is moving into mobile/social rewards programs with its acquisitions of CardStar and Bantam Networks.
Big question: Can it make a full transition from e-mail to broader online marketing?

EMC (NYSE: EMC)
Stock price: $25.83
2011 stats: Full-year revenue of $20B ($3.4B profit), showing record growth.
Recent news: CEO and chairman Joe Tucci isn’t stepping down this year as planned. (Pat Gelsinger is rumored to be his successor.)
Big question: What is the ultimate future of EMC? In storage, big data, and cloud computing, as EMC goes, so will Massachusetts.

iRobot (NASDAQ: IRBT)
Stock price: $32.88
2011 stats: Q3 revenue of $120.4M ($14.1M profit)
Recent news: iRobot laid off 8 percent of its staff in October but continues to grow.
Big question: Will consumer robotics ever really take off?

LogMeIn (NASDAQ: LOGM)
Stock price: $41.51
2011 stats: Q3 revenues of $31M ($4.4M profit); full-year stats coming Feb. 15.
Recent news: LogMeIn has been expanding to new devices, markets, and geographies.
Big question: Is this still a lifestyle business?

Monster.com (NYSE: MWW)
Stock price: $7.35
2011 stats: $46M profit on roughly $1B revenue, compared to a $9M loss in 2010.
Recent news: Monster Worldwide had layoffs and is restructuring as it continues to expand globally and move into social/mobile technologies.
Big question: Is there a better job site out there?

Nuance (NASDAQ: NUAN)
Stock price: $27.91
2011 stats: Q3 revenue of $400M, and $1.4B revenue for the fiscal year ($38.2M profit).
Recent news: Nuance acquired rival Vlingo in mobile speech recognition; mobile/consumer and healthcare continue to be its biggest markets.
Big question: Can it compete with the big boys (Apple, Google)?

TripAdvisor (NASDAQ: TRIP)
Stock price: $31.24
2011 stats: $3B+ market cap. Year-end stats coming Feb. 8. (2010 revenue of $486M.)
Recent news: After spinning out of Expedia last month, TripAdvisor is New England’s biggest consumer Web company.
Big question: Will it outcompete Google and others in travel search and content?

Zipcar (NASDAQ: ZIP)
Stock price: $16.14
2011 stats: Small profit in Q3 on $68M revenue. Full-year revenue expected to be 240M+ with net loss in $10M range (tune in Feb. 14).
Recent news: Coming off its IPO last spring, Zipcar has been expanding carefully in Europe and on U.S. college campuses.
Big question: Can it reduce costs enough to make a real profit?

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Monster Worldwide (NYSE: MWW), the New York parent company of Maynard, MA-based Monster.com, the jobs and recruiting site, said in a regulatory filing that it has laid off about 400 employees, or 7 percent of its worldwide staff of 5,700.

The layoffs include fewer than 100 job cuts in Massachusetts, according to the Boston Business Journal. No more specifics on that were available.

In the Form 8-K, Monster Worldwide says it is taking a “series of strategic restructuring actions” in 2012 to invest in marketing and sales and “improve its long-term growth prospects and profitability.” The company says it is consolidating some office facilities as part of the restructuring.

Monster reported fourth-quarter 2011 revenues of $250 million and a $13 million profit. The company made a $46 million profit for the year, compared to a loss of $9 million in 2010. Monster’s stock is down about 13 percent to $7.80 this morning.

Last spring, Monster.com spoke with me about its recent efforts in mobile apps and social media partnerships. The company has been investing heavily in R&D to keep up with a slew of newer, hip competitors.

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Cambridge, MA-based Alnylam Pharmaceuticals is getting rid of about one-third of its workforce, as it looks to save cash for clinical trials that it hopes will prove the value of its RNA interference drug technology.

Alnylam (NASDAQ: ALNY) said today it’s cutting 33 percent of its staff, as it looks to concentrate its cash reserves on what it believes are its “highest value opportunities” in its pipeline of experimental RNAi drugs. The company didn’t disclose absolute numbers, but it said in its most recent quarterly report that it had 171 employees at the end of September, so if that number is still current, then 56 people are being let go, and about 115 people will remain at the company.

Alnylam has faced deep skepticism among investors in its RNAi platform, after scientists have struggled to effectively deliver the treatments into cells, and Big Pharma companies like Roche, Novartis, and Merck all scaled back their efforts in the field. But Alnylam, still relatively flush with cash from partnerships it struck years ago, has chosen to forge on by internally developing its own RNAi drugs for a group of liver diseases, where delivery is less of a challenge.

“As we effect our ongoing transformation from a platform company to a product company, now is the time to focus our near-term efforts and resources on what we believe to be our highest value opportunities,” said Alnylam CEO John Maraganore, in a statement.

Alnylam said the cuts are expected to save the company $20 million in cash this year. It ended 2011 with about $260 million of cash and investments in the bank, and said it plans next month to disclose its financial forecast for the coming year.

Alnylam has recently released some preliminary data from clinical trials of a couple RNAi programs that it says have emboldened it to push ahead and become a drug developer on its own. The first is for a rare liver disease called TTR amyloidosis, and the second is for high cholesterol, through hitting a biological target known as PCSK9. The company said today that as part of its restructuring, the TTR program, and another for hemophilia, are now its top two clinical priorities.

This isn’t the first time Alnylam has made layoffs. The company cut 25 to 30 percent of its workforce in September 2010 after Novartis ended a collaboration with the company.

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Founders of Sermo, the Cambridge, MA-based provider of an online community for physicians, are off to a new health-focused Web startup. The news was first reported today at online publication Pharmalot, which noted Sermo CEO Daniel Palestrant’s departure.

Sermo founder and chief medical officer Adam Sharp is also a founder of the new startup, Par8o, according to its website. Par8o seems to be an outgrowth of Sermo, with Palestrant and Sharp stating on the Par8o website that “having built the largest physician community in the world, we’ve seen first-hand what is happening to our profession and understand what it is doing to our colleagues, and most importantly, our patients.” The new startup says it is focused on enabling patients and physicians to collaborate directly on patient care, and is apparently leveraging concepts of efficiency and the allocation of goods from the Italian economist Vilfredo Pareto.

Sermo was founded in late 2005 and hoped to make money by charging financial services firms for access to the doctors in its online community (it stayed away from ads and subscription fees for the physician users). But it struggled to bring cash in that way, and later pivoted to focus on medical device and drug makers as paying customers, as we reported in December 2009. Two days after that report, news surfaced that Sermo laid off about 30 of its employees, reducing a workforce that was previously between 60 and 80 people.

We last heard from Sermo in August, when the company announced a new mobile app that enabled doctors to snap pictures of findings, X-rays, or lab results, and send them to others in the Sermo community for real-time advice. The company also took in another $3.5 million in growth financing from MMV Financial last February. We hope to get more details from Palestrant about the new gig, so stay tuned.

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A lot has happened in the technology world in the past year. So let’s take a minute to reflect on the defining moments of 2011 and where we stand now, as a local tech community with increasingly global impact.

This is by no means comprehensive, or even a summary of the most important stories of the year. It’s just a select few of the biggest highlights and lowlights, organized in spaghetti western fashion (cliché alert).

The Good: Oracle Buys Endeca

Some might argue this wasn’t necessarily “good” for the local tech scene, but Oracle’s $1B+ purchase of Cambridge, MA-based Endeca, the enterprise search and business intelligence firm, was one of the biggest deals of the year, and was kept under wraps pretty well. It will be interesting to watch whether Endeca’s technology and talent give Oracle a leg up in its competition with IBM, SAP, Microsoft, and Google. Endeca, which started in 1999, stands as a testament to the notion that billion-dollar tech companies can be built—and are being built—in Massachusetts. (See Acme Packet, Progress Software, Wayfair, and others on their way.)

Honorable mention: Carbonite, TripAdvisor, and Zipcar each went public with successful IPOs in 2011. That’s three more publicly traded tech companies in Boston that seem to be thriving in a tough market. Who will join them in 2012?

The Bad: RSA Gets Hacked

No one would argue this isn’t bad—and not just for local companies. In March, RSA Security reported a data breach involving its authentication products, which are widely used by big companies and government agencies. The Bedford, MA-based division of data storage giant EMC said it had … Next Page »

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Seattle-based Allozyne has made a small set of job cuts after it was unable to pull the trigger on its plan to go public late last year, Xconomy has learned.

Allozyne has let go some of its scientific staff, according to a source close to the situation. When asked how many jobs were eliminated, and how many employees remain at Allozyne, CEO Meenu Chhabra said there was no downsizing but that “we redistributed functional areas.” That decision came days after Allozyne scrapped a plan to go public through a merger with San Francisco-based Poniard Pharmaceuticals. If the deal had gone through, privately held Allozyne would have gotten a NASDAQ listing that would have enabled it to raise more money from mutual funds, institutions, and hedge funds that only invest in public companies.

“We are gearing up for Phase 3 work and are redistributing the talent to focus on clinical development and regulatory tasks,” Chhabra said via e-mail. “That said, discovery and early stage activities are alive and well.”

She didn’t say exactly how many employees remain at Allozyne, but before Christmas, Chhabra said the company had about 20 employees.

Allozyne has spent about $50 million since its founding in 2005 and was down to its last $1.3 million in cash at the end of June, according to recent regulatory filings. But when Allozyne walked away from the Poniard merger, it raised a still-undisclosed amount of cash from Arch Venture Partners, MPM Capital, and OVP Venture Partners, Chhabra said in a Dec. 22 interview. The money will be used to help the company push ahead with a plan for 2012 to move its lead multiple sclerosis drug into the third and final phase of clinical trials normally required for FDA approval, Chhabra has said.

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Business hasn’t gotten any easier over the past six months for San Diego’s Somaxon Pharmaceuticals (NASDAQ: SOMX), which says it has hired the investment banking firm Stifel Nicolaus Weisel to help the company assess its strategic options. The company also laid off 60 percent of its employees who aren’t out in the field.

The company has struggled to establish itself against lower-cost generics in the sleeping pill market. Somaxon began selling doxepin (Silenor), its prescription drug for insomnia in September 2010. In June, Somaxon filed patent infringement lawsuits against four generic drugmakers that are challenging its patents.

The banking firm was hired to help Somoxon identify alternative strategies, according to Somaxon CEO Richard Pascoe in a statement issued yesterday. That could include “one or more of a sale of the company or assets relating to Silenor, or partnering or other collaboration transactions relating to U.S. or ex-U.S. prescription or over-the-counter rights to Silenor,” Pascoe says.

While the company didn’t say yesterday how many employees were laid off, Somaxon reported in its third-quarter financial results that it had terminated 14 employees in November, after the quarter had ended.

Somaxon reported sales of just $3.7 million for the third quarter that ended Sept. 30, compared with sales of $38,000 in the same quarter last year, when Somaxon began Silenor sales. The company lost $17 million, or 36 cents a share, compared with $12.9 million, or 37 cents a share). Somaxon says it had $34 million in cash and cash equivalents at the end of September.

Somaxon says it intends to allocate significantly more marketing resources to direct-to-consumer marketing in 2012, concentrating in regions where there is a potential for sales growth based on managed care coverage, favorable insomnia demographics, feasible media costs, and in areas where the company has sales representatives. Somaxon says it plans to hire 30 sales reps by the end of the year.

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AVI Biopharma has made some significant job cuts in Washington and Oregon after missing out on a potentially huge federal contract to make an RNA-based treatment against pandemic flu.

The Bothell, WA-based company (NASDAQ: AVII) is cutting the jobs of about 35 of its 125 employees—28 percent of the workforce—according to CEO Chris Garabedian. The company initially announced the job cuts at the bottom of a press release on Friday, without providing further explanation. The cuts will come from AVI’s Seattle-area operations, as well as its operations in Corvallis, OR, Garabedian says.

AVI Biopharma has sought to reinvent itself this year under the new CEO, who has brought in a new management team that has focused on its lead drug candidate for Duchenne Muscular Dystrophy (DMD), as well as biodefense programs to treat the deadly Ebola and Marburg viruses. But the company fell short in its bid to secure a long-term contract to make drugs against pandemic flu, which could have been worth as much as $500 million. Plus, AVI recently disclosed it was unable to overturn a European patent claim by Netherlands-based Prosensa, which claims it owns some intellectual property in AVI’s lead muscular dystrophy program.

“With our stock price at 52-week lows, and the recent disappointing news of not getting the flu contract, combined with Prosensa’s success in defending their patent in Europe related to Exon 51 (our lead program), we felt it was important to reprioritize / refocus on the primary value-driving programs of DMD, Ebola, and Marburg,” Garabedian said in an e-mail today.

AVI stock climbed 2 cents today to 73 cents a share, giving it a market valuation of just under $100 million. The company said in its most recent quarterly report that it expects to burn through about $30 million to $35 million of cash in 2011. AVI reported it had $46.3 million left in the bank at the end of September, in its most recent audited quarterly statement.

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Waltham, MA-based A123 Systems (NASDAQ: AONE), the lithium-ion battery maker, has laid off about 125 employees at its manufacturing facilities in Livonia and Romulus, MI. The news originally broke the week of Thanksgiving and was reported by media outlets including the Observer & Eccentric and Crain’s Detroit Business.

The layoffs are apparently the result of lower demand from Fisker Automotive after its plug-in hybrid sports car ran into production delays. A123 invested in Irvine, CA-based Fisker early last year. Media reports quote Jason Forcier, the vice president and general manager of A123′s automotive group, and PR manager Dan Borgasano as saying the layoffs are temporary and the workers should be hired back within six months.

Forcier spoke with me last year around the opening of the Livonia plant. At the time, he noted that “the battery industry is really a rejuvenation for the whole area. This is extremely important for Michigan from an economic standpoint.”

A123 still employs about 600 people at its two Michigan plants and its research and development center in Ann Arbor, according to the Crain’s report.

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It is a dark time for biofuels companies—and industrial biotech around Boston, more broadly.

Xconomy has learned that Qteros, a heavily funded developer of cellulosic ethanol technology based in Marlborough, MA, has laid off most of its staff, including its CEO John McCarthy. The news was reported earlier today by Dan Primack at Fortune. Xconomy received a tip yesterday from a source with knowledge of the company.

The source said that Qteros “couldn’t raise money” and was “reduced to a skeleton crew to sell anything of value.” Mick Sawka, who is listed on the company’s website as senior vice president, is the acting CEO, according to the source. Messages left with Qteros and Battery Ventures, one of the company’s lead investors, were not returned.

Qteros started in 2006 as SunEthanol (it changed its name in 2008), out of UMass Amherst. Its investors include Battery, Venrock Associates, Long River Ventures, Soros Fund Management, Camros Capital, Valero Energy, and BP. By our count, the company had raised nearly $30 million prior to its most recent financing, which was a $22 million Series C round announced at the beginning of this year.

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It was another big week for life sciences news in San Diego, with interesting developments in agricultural biotech, industrial biotech, and genomic sequencing. This is our wrap up of what you need to know.

—San Diego’s Synthetic Genomics spun out a new San Diego-based agricultural biotech, Agradis, with $20 million in Series A financing and proprietary technology that can be used to develop improved hybrid crops such as castor and sweet sorghum. Mexican investor and businessman Alfonso Romo is a co-founder of Agradis, along with J. Craig Venter, Synthetic Genomics’ chairman and CEO.

—TedMed is underway this week at the Hotel del Coronado. Peter Diamandis, the chairman and co-founder of the X Prize Foundation, took the stage yesterday to announce some changes in its $10 million competition in genomic sequencing. The foundation, based near Los Angeles, says the $10 million Archon Genomics X Prize presented by Medco will be awarded to the first team that accurately sequences the whole genome of 100 people within 30 days for $1,000 or less per genome, and at an error rate no greater than one per million base pairs. The prize is intended to open the way to new era of personalized medicine with unprecedented accuracy.

—San Diego’s Illumina, (NASDAQ: ILMN), the market-leading maker of DNA sequencing equipment, said it’s eliminating 200 jobs, or about 8 percent of its workforce. Illumina said a restructuring of its business is expected to add a $15 million to $17 million charge on the company’s income statement, mostly in the fourth quarter.

—In a separate announcement, GenoLogics of Victoria, BC, said it has raised $8 million through a strategic financing in the company by San Diego’s Illumina. GenoLogics said it plans to develop genomics software tailored for cheaper desktop sequencers, to build up its sales and marketing efforts, and develop new applications.

—The MoneyTree Report on third-quarter venture capital activity found … Next Page »

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[Updated 4:35 pm] Bedford, MA-based iRobot laid off about 55 people last week from its government and industrial robots division, Xconomy has learned. I heard from a source familiar with the company that some of the layoffs came to light because ex-employees posted on social media looking for new positions. An iRobot spokesperson did not immediately respond to a request for comment.

The staff cuts come as the pioneering robotics company (NASDAQ: IRBT) announced its third quarter financial results this afternoon. The press release mentions that the company “implemented a reduction in force” because of “expectations for a reduction in government-funded research in 2012.” There is an earnings conference call scheduled for 8:30 am Eastern Time tomorrow.

The last significant layoff at iRobot was back in 2008, but this one is bigger, according to my source. The latest staff reduction is also notable because it affects the biggest division in the company—the one that houses some of its most famous products, like the PackBot military robot.

I have heard that iRobot has roughly 550 employees, which would make the layoff about 10 percent of the firm’s total workforce. Those numbers are not confirmed, however.

In the past year, Xconomy has reported on iRobot’s progress and expansion in Michigan, among other things. It’s not yet clear in which cities the staff cuts have occurred.

[Updated with comments from iRobot] A company spokesperson just confirmed the layoffs, but with slightly different numbers: “We can confirm that iRobot Corporation has had a reduction in force. This difficult action was taken based on our current view of future defense spending and a shift in program structure. In 2012 we see a significant decrease in our externally funded research and development. This transition from development to production requires our Government and Industrial robot division to reduce the size of its workforce. The reduction accounted for approximately 8 percent of the total workforce.

“We will be addressing this on the call tomorrow.”

[Updated 5:40 pm] iRobot has confirmed that 55 full-time employees were let go from the company’s offices in Bedford, MA; Durham, NC; and San Luis Obispo, CA.

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[Updated: 6:45 am, 10/26] San Diego-based Illumina is doing some restructuring to make up for third-quarter sales that fell way short of investors’ expectations.

The market-leading maker of DNA sequencing instruments (NASDAQ: ILMN) said today it is going to restructure (i.e., make job cuts) that will add up to a $15 million to $17 million charge on the company’s income statement, mostly in the fourth quarter. The disclosure was part of the company’s third-quarter financial report, in which Illumina said it generated $235.5 million in revenue—a 1 percent drop compared with the same period a year ago. The company’s quarterly profits plunged to $20.2 million, a 43 percent decline from $35.4 million a year earlier.

[Updated layoff numbers] Illumina didn’t provide details of its restructuring plan in today’s financial release, although it did say in a subsequent filing it is eliminating 200 jobs, or about 8 percent of its workforce. It also declined to offer a specific revenue forecast, although the company did say it expects sales to be higher this quarter than last quarter because of the commercial rollout of a new desktop sequencing instrument called MiSeq.

News of cutbacks shouldn’t come as a surprise. The company first reported that its sales were falling short—about $40 million short of Wall Street expectations—in an announcement on Oct. 7. Researchers who buy Illumina products are still uncertain about how they will be affected by the possibility of budget cutbacks at the National Institutes of Health.

“We view the move as likely prudent, although the expectation points to a bearish outlook on HiSeq,” said Tycho Peterson, an analyst with JP Morgan, in a note to clients this morning, that referred to the company’s flagship instrument.

Illumina had 2,100 employees as of January 2, according to its annual report filed with the Securities & Exchange Commission.

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Chronically bad unemployment is the biggest story in the U.S. today, and we had some more bad news about jobs being lost this week in Seattle biotech. But there were a few other good things to report, including a story about a new company being born.

—Amgen (NASDAQ: AMGN), the Thousand Oaks, CA-based biotech giant, said this week it is cutting 380 jobs companywide from its R&D operations, which includes 70 people at its sites in Seattle and Bothell, WA. The company plans to say more about the cutbacks Monday on its quarterly financial conference call.

—GlaxoSmithKline made big news in Seattle this week at the Bill & Melinda Gates Foundation‘s malaria forum. The story was about how GSK’s experimental malaria vaccine, supported by the Gates Foundation through the PATH Malaria Vaccine Initiative, was found to protect about half of African children in a Phase III clinical trial. But there’s an elephant in the room about vaccine cost that nobody is really discussing thoroughly in public.

—The latest biotech startup in town has officially spun out of the Fred Hutchinson Cancer Research Center. The company, called Blaze Bioscience, has raised its first $725,000 in angel financing and recruited former ZymoGenetics dealmaker Heather Franklin as its CEO. The idea, from the lab of researcher Jim Olson, is to “paint” tumors so that surgeons can make sure they get rid of the whole tumor, and not leave behind straggler cells that can lead to a recurrence.

—I’ve had Immunex on the mind lately as we prep for our next big Xconomy life sciences event, “The Immunex Impact“ on Dec. 1 in Seattle. Yesterday, I invited Immunoids to bring some old photos and company memorabilia to the event. I also announced the newest addition to the lineup of speakers—Patricia Beckmann. She will join Steve Gillis, Chris Henney, Doug Williams, Stewart Parker and others in this special confab of Immunex alumni. And speaking of Henney, he was honored this week with a biotech “Hall of Fame” award at an annual industry event in Laguna Niguel, CA.

—Bothell, WA-based Marina Biotech (NASDAQ: MRNA) has been running low on cash lately, but it found some support this week from a single investor who agreed to put as much as $15 million into the company over time.

—From the medical device side of town, we had a couple stories about companies going in opposite directions. Kirkland, WA-based Pathway Medical Technologies, acquired in August by Bayer’s Medrad unit, has allowed a lease extension option to expire on its headquarters, suggesting that it may not be interested in keeping operations in Seattle. On a more positive note, Redmond, WA-based Mobisante talked about how it has received more than 300 sales leads for its ultrasound-on-a-smartphone, even before it’s really ready to capture much of the market for this low-cost diagnostic tool.

—I know people have heard a lot of song and dance about genomics revolutionizing healthcare, and the reports have been greatly exaggerated to date. But in this week’s BioBeat I took a moment to marvel at the truly amazing kinds of experiments that are now feasible as scientists have learned how to sequence entire human genomes for $4,000 or less, in a matter of weeks. I’m going to explore this further next Monday at our next event in San Francisco, “Computing in the Age of the $1,000 Genome.”

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Word came out of Amgen last week that it was looking to overhaul its R&D operations, and today the biotech giant confirmed the overhaul is translating into job cuts for 380 people across the company.

Thousand Oaks, CA-based Amgen (NASDAQ: AMGN) notified 380 employees internally today that their jobs are being eliminated as part of the company’s effort to improve focus and re-allocate R&D resources, according to company spokeswoman Mary Klem. Amgen isn’t closing any of its research sites around the world, but people are being laid off at its major U.S. R&D sites in Thousand Oaks, Seattle, San Francisco, and Boston, Klem says.

No sites are being closed, and Amgen isn’t eliminating any therapeutic areas from its research portfolio, she says. Amgen plans to discuss the cuts in some more detail next Monday on its quarterly financial conference call, she says.

“We will continue to invest significantly in R&D,” Klem says. But she added the company needs to shift resources around to support more expensive late-stage development projects. “We will continue to allocate resources in a focused manner,” she says.

Amgen generated about $15.1 billion in revenue last year, and spent what’s generally considered a healthy 19 percent proportion of that revenue ($2.9 billion) on R&D. The company is actively pushing the biggest new innovations from its internal pipeline in years—denosumab, marketed for osteoporosis patients as Prolia, and for cancer-related bone loss as Xgeva. The company has had as many as 20,000 employees in the past, but its latest worldwide headcount is down to about 17,000, according to a recent company fact sheet.

Amgen’s full-year profit was $5.02 billion in 2010, essentially flat compared to $5.01 billion the prior year. In the most recent quarterly report, Amgen said its profits declined about 3 percent compared with the same period a year ago.

Klem didn’t say how much the company expects to save by making the cutbacks.

Here’s the breakdown of job losses at each major Amgen site, according to Klem.

—Thousand Oaks, CA (226)

—Seattle/Bothell, WA (69)

—South San Francisco (37)

—Cambridge, and Woburn, MA (32)

—United Kingdom (the remainder, about 15)

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Mobile technologies were the topic of the week as the wireless industry’s big enterprise & applications conference came to town. But we also had some interesting economic new, and our Xconomy week in review begins now.

—The number of wireless-connected devices around the world will double by 2010, from roughly 12 billion to about 24 billion, according to a study released by the London-based GSMA industry group on the first day of the CTIA Enterprise & Applications Conference in San Diego. About half of the 24 million devices are expected to be machine-to-machine connections, with personal mobile devices making up the other 12 billion.

—A TechCrunch report that Hewlett-Packard was laying off “around 500″ employees and rolling up its entire San Diego Software unit set off a scramble last week among local media, which knocked down much of the report. Mike Freeman of The San Diego Union-Tribune reported that HP is eliminating about 50 jobs at its suburban campus related to help desk and analytics products, which came from HP’s $425 million acquisition of Peregrine Systems in 2005.

—The Ford Motor Co. demonstrated a voice-activated system that could someday help motorists monitor their own health and chronic illnesses on the road. Ford’s prototype uses voice-recognition software to help diabetic motorists who use wireless glucose measurement technology to monitor their blood glucose while driving. K. Venkatesh Prasad, a senior technical leader at Ford Research & Innovation, told the Wireless Health 2011 technical conference that Ford’s in-car health and wellness technology is part of a broader effort to expand the capabilities of Ford’s SYNC in-car connectivity system.

—Local technology industries have had a disproportionate effect in boosting San Diego’s regional economy, according to a study from the National University System Institute for Policy Research. Counting direct, indirect, and induced employment, the study found that San Diego’s 363,000 technology-dependant jobs represent more than 29 percent of all jobs in … Next Page »

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The Seattle biotech community got an energetic new leader this week, but there was also some more grim news about budget cuts coming at one of the biggest local life sciences employers.

—Amgen (NASDAQ: AMGN), the Thousand Oaks, CA-based biotech giant, is looking to “improve focus” and “re-allocate resources” in its $2.9 billion R&D budget, according to a company spokeswoman. The company will have more to say in its quarterly earnings report on Oct. 24. Sounds like there will be some long days of grim speculation for the people at Amgen’s Seattle R&D operation.

—Seattle-based NanoString Technologies rolled out the next-generation version of its genetic analysis instrument at a big scientific conference in Montreal. The new tool is supposed to be able to churn out 50 percent more data, and it’s paired with a more flexible software program. The Broad Institute of Harvard and MIT, one of the world’s leading centers for genomics research, has signed on as the first customer for the Version 2.0 tool from NanoString.

—For the first time, I made an early morning call to Iceland for a story. This was to talk with Kari Stefansson, the prominent geneticist and CEO of deCODE Genetics. The company made the news this week by announcing by announcing a partnership with Pfizer to look for new lupus drug targets. The Seattle angle here is that Arch Venture Partners and its indefatigable managing director Bob Nelsen helped rescue deCODE from bankruptcy in 2010 in a wager that deCODE could thrive in the era of ultra-fast, ultra-cheap gene sequencing.

—Seattle-based Qliance Medical Management, the company that provides direct primary care services on a monthly subscription basis, said this week it has done some management shuffling. Co-founder Erika Bliss, a primary care physician, is stepping up to become president and CEO, while co-founder Norm Wu is stepping aside to serve as a “strategic advisor” working on partnerships. Qliance probably has the investment syndicate with the highest television Q-rating in town—Jeff Bezos, Drew Carey, Michael Dell, and Nick Hanauer are among its backers.

—This week in BioBeat, I offered up a list of five things that the pharmaceutical industry could (and should) do to help the FDA reform itself and restore public confidence in the agency. There are some good comments piling up at the bottom of this story, and you’re always welcome to add your own two cents there.

—Thong Le, the well-wired venture investor at WRF Capital, is going to take on a higher profile in the community next month when he becomes chairman of the Washington Biotechnology & Biomedical Association. Le is replacing Tom Clement, the founder of Pathway Medical Technologies, who is now working to get a couple new startups off the ground—Aqueduct Neurosciences and Cardiac Insight.

—Drew McUsic, a University of Washington graduate student in bioengineering, offered up his view of the opportunity for biotech startups in the world of stem cell R&D. This post was based on a WBBA event in which officials from Geron and Fate Therapeutics offered their view from the trenches.

—Lastly, we had a guest post for the biotech crowd inspired by the life of Steve Jobs, the Apple co-founder who died last week at 56. Christopher Bowe, a healthcare analyst with Informa, sees some lessons in Jobs’ life that might be healthy for a life sciences industry that’s starving for some really exciting new innovations.

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Light Sciences Oncology, the Bellevue, WA-based developer of an unusual drug/device combo treatment for cancer, has failed in a pivotal clinical trial and is preparing to make deep cuts, including layoffs, Xconomy has learned from sources familiar with the situation.

The privately-held company has raised well over $130 million since its founding in 1995, from a big-name group of investors that includes Essex Woodlands Health Ventures, Johnson & Johnson Development Corporation, Novo A/S, Scandinavian Life Science Venture, and the late Microsoft treasurer Craig Watjen—who put more than $50 million of his own money into the company before he died a year ago from cancer. Bob Littauer, the company’s chief financial officer, declined to respond to requests for comment about the outcome of the trials or any subsequent corporate decisions.

The technology at Light Sciences is unlike anything currently on the U.S. market to treat cancer. The company has spent all that time and money developing a drug/device combination therapy against solid tumors that aren’t treated well with conventional drugs that circulate through the body. The Light Sciences therapy uses a catheter with a light-emitting diode on the tip, which a physician sticks into a solid tumor. At the same time, the patient is injected with an inactive drug called talaporfin sodium (Aptocine). The doctor turns on the light, which activates the drug to kill tumors within the specific wavelength of light emitted by the LED. The light stays on for almost three hours while the patient watches TV or reads a magazine, and then goes home. The idea is to fight cancer without damaging the healthy tissue nearby.

The company has had to endure an almost agonizingly long wait to get an answer on whether its strategy really works. Light Sciences Oncology began a pivotal study of more than 200 patients with primary liver cancer back in June 2006, which sought to answer whether the new treatment could help patients live longer—the gold standard measurement of success with cancer drugs. Former CEO Llew Keltner told Xconomy in February 2010 that he expected results from the study in just a few months, saying “the proof for us will be in the pudding this year.” As far back as July 2008, he said that enrollment trends and patient life expectancy meant that clinical trial results could arrive as soon as early 2009.

The results didn’t arrive on schedule. By November 2010, Keltner left Light Sciences Oncology with no official explanation, and the company remained mum on the outcome of the trial. Light Sciences’ only public statement since came in May 2011, when experienced pharmaceutical executive Dennis Langer was named chairman of the company’s executive committee. At that time, the company said it expected to report data in the second half of 2011 on both of its pivotal studies.

The second study is designed to enroll more than 450 patients with cancers that originated somewhere else and have spread (metastasized) into the liver. That study is also designed to show whether the Light Sciences therapy helps patients live longer than they otherwise would on standard chemotherapy.

While the company hasn’t released any results to the scientific community, it did say on its clinicalstrials.gov posting in June that it had reached the final date for collecting data on the trial of 200 patients who cancer is primarily based in the liver. The 450-patient trial, of patients whose cancer had spread to the liver, is expected to yield its full set of data by September 2012, according to the posting on clinicaltrials.gov.

Light Sciences Oncology had 38 employees at the last reported count in March 2010.

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[Updated 2:20 pm PT] Pacific Biosciences (NASDAQ: PACB), the Menlo Park, CA-based maker of a super-fast, super-cheap DNA sequencing instrument for medical, agricultural, and biofuels researchers, disclosed today that it’s laying off 130 employees, or 28 percent of its total workforce. The announcement came today in an 8-K report to the Securities and Exchange Commission.

The company explained that a slower-than-expected adoption rate for its sequencing machine, which it introduced to the market this April, has left it with more employees than it wants or needs. The workforce reduction “will allow the Company to continue support of its growing customer base with improved service and continued product enhancements, while at the same time conserving cash,” PacBio said in the disclosure.

The company says it’s cutting workers across the organization, but that its operations and R&D wings will be most affected. PacBio expects to incur $5.2 million in restructuring charges as a result of the layoffs—mainly compensation and benefits to terminated employees. Hugh Martin, PacBio’s CEO, said in a statement circulated by e-mail today that it has been “an extraordinarily difficult day” for the company given its tight-knit corporate culture. But he said the cuts were necessary to lower the company’s burn rate. Under its new structure, PacBio will have approximately $190 million in cash and investments by the end of the September (down from $217 million at the beginning of the third quarter).

Despite the successful introduction of its “RS” sequencer this spring, PacBio has taken a hammering in the public markets this year, especially after early a disappointing earnings report in early August, which sparked a rout that halved the stock’s value. The company has a backlog of orders for the sequencers, which cost $700,000 each, but there are concerns that dwindling government research budgets will cut into demand for next-generation sequencing devices.

PacBio cited “uncertainties associated with the economic environment” in its 8-K announcement, but said the cuts should “position the company for long-term success.” Martin said in the e-mail statement that “by taking action now, we have given ourselves both the time and flexibility to drive adoption of our product.”

Here’s the full statement from Martin:

Today, we reduced our workforce by approximately 130 employees, or 28%.  Although the cuts were across the company, the groups most affected were Operations and R&D.

Given the uncertainties associated with the economic environment and our desire to position ourselves for long-term success, we have chosen to reorganize the company. Our current infrastructure was staffed to support a faster adoption rate for our products. These changes will allow us to continue to support our growing customer base with improved service and continued product enhancements, while at the same time conserving cash.

For all of us here at PacBio, this is an extraordinarily difficult day.  We have always taken great pride in the talent we have been able to attract, and we value each and every one of our employees. We are known for our emphasis on tight-knit corporate culture, so it is particularly difficult to have to let any employees go.

PacBio is in the process of introducing a game changing, new generation of sequencing technology.  Even in stable, high growth markets, adoption rates of such a disruptive platform can be difficult to predict.  In today’s turbulent economy, it is even more difficult.  We see many of the signs that customers are recognizing the value of our third generation paradigm.  However, we had higher expectations as to the rate with which adoption would occur.  Our internal infrastructure was therefore built to handle a faster generational transition.  Consequently, our burn rate was not in line with the speed with which the business was evolving.  In addition, we are refocusing our resources as we transition from developing and launching a product to establishing the technology in the market and supporting customers as they develop applications and make novel discoveries with the PacBio RS.

We have worked hard to size the company appropriately, while preserving our ability to expand globally and to support current and future customers. Customer satisfaction is our top priority. In addition, we will continue an aggressive program of both increasing the performance of our SMRT technology as well as bringing out new applications that are uniquely enabled by our third generation sequencing platform.

Our cash balance currently is approximately $190 million, and by taking action now, we have given ourselves both the time and flexibility to drive adoption of our product. Given the promise SMRT technology has to greatly impact the future of biology, it is incumbent on us to align and scale the business to enable our platform to have the time to realize its full potential

And here’s the full text of PacBio’s 8-K statement, minus the boilerplate about forward-looking statements.

On September 20, 2011, Pacific Biosciences of California, Inc. (the “Company”) implemented a reduction in its workforce of approximately 130 employees, or approximately 28% of its total workforce. The actions taken were in consideration of uncertainties associated with the economic environment and to position the Company for long-term success. The Company’s current infrastructure was staffed to support a faster adoption rate for its products. The reduction implemented will allow the Company to continue support of its growing customer base with improved service and continued product enhancements, while at the same time conserving cash.

The reduction in workforce was authorized by the Company’s Board of Directors on September 16, 2011 and the employees being terminated received notification on September 20, 2011. Although the cuts were across the organization, the Company’s operations and research and development functions were most effected. In lieu of notice required under the California Worker Adjustment and Retraining Notification Act (the “WARN Act”) and other federal and state law equivalents, as applicable, departing employees will receive salary and benefits for a period of 60 days. In addition, the Company has implemented a severance benefit program that will provide for benefits which are greater than the minimum requirements of the WARN Act, such as additional cash payments determined on the basis of the affected employee’s base salary and tenure with the Company, as well as outplacement services and Company-paid continuation of medical, dental and vision benefits under the Consolidated Omnibus Budget Reconciliation Act (“COBRA”). Payment of the termination benefits in excess of those provided for under the WARN Act is contingent on the departing employee entering into a separation agreement with the Company containing a general release of claims against the Company. As a result of the reductions, the Company expects to record a restructuring charge, comprised mainly of compensation and benefits afforded to terminated employees, of approximately $5.2 million during the third quarter of fiscal 2011. The Company anticipates that the actions associated with the reductions will be substantially completed during September 2011. All cash expenditures for restructuring related charges are expected to be substantially completed during 2011.

The Company’s cash and investments at June 30, 2011 totaled $217 million and the Company expects to end the third quarter with approximately $190 million.

The Company’s estimated restructuring charge is based on a number of assumptions. Actual results may differ materially and additional charges not currently expected may be incurred in connection with or as a result of the reductions.

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The writing was on the wall at Dendreon for weeks, but that didn’t make the bad news of layoffs any easier to stomach.

—Seattle-based Dendreon (NASDAQ: DNDN) said this past week that it is cutting 500 jobs, including about 100 locally, as it seeks to conserve cash in the wake of its sales and marketing stumble. Nothing much more to say other than this hurts those people, especially in a tough job market.

—The new head of global health over at the Bill & Melinda Gates Foundation was named this week, and it’s Trevor Mundel. He’s a former Novartis executive, so his pedigree is similar to that of his predecessor Tachi Yamada, who now works in venture capital with Frazier Healthcare Ventures.

—A couple of sizable financings crossed my desk this week. Seattle-based Theraclone Sciences, the company working to discover new antibody drugs, raised another $10.6 million. And across the lake, Bellevue, WA-based RF Surgical pulled in $12 million for its technology that’s supposed to help surgeons avoid leaving behind sponges inside patients.

—Remember Bothell, WA-based Liposonix, the developer of the ultrasound body sculpting machine? It has been pretty quiet in the three years since it was acquired by Scottsdale, AZ-based Medicis Pharmaceutical for $150 million. But now Liposonix has a new corporate parent in Hayward, CA-based Solta Medical, which paid $35 million in upfront cash and near-term milestones to see what it can do with this technology.

—Seattle-based VentiRx Pharmaceuticals is now just that, Seattle-based. The company said it is closing down its San Diego operations and consolidating its work here around an immune-boosting compound for cancer. Co-founder Rob Hershberg has moved up to the role of president, and remains the chief medical officer.

—This week in BioBeat I tried to show what biotech pros are missing by avoiding the daily conversation on Twitter. So far, at least one local CEO, PhaseRx’s Bob Overell, agreed to give it a shot, and you can follow his comments at @Robert_Overell on Twitter. If there’s more interest among our readers, I might be willing to help with a free Twitter tutorial at one of the local coffee shops. Ping me the old-fashioned way—ltimmerman@xconomy.com—if you’re interested.

—Seattle-based Oncothyreon (NASDAQ: ONTY) said this week that CEO Bob Kirkman is taking a temporary medical leave of absence, and will be replaced on an interim basis by chairman Christopher Henney. Kirkman is expected to return to work in the fourth quarter, a company spokeswoman says.

—Lastly, Bob Nelsen of Arch Venture Partners unloaded on the elected officials in Washington D.C. who voted in favor of a patent reform bill that he says will hurt the little guy inventors out there. There’s a really good thread of comments at the bottom of this post, which I’d encourage you to check if you haven’t already.

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