‘Tis the season to reflect on the past year and take a look at some of Xconomy Boston’s top stories.

As usual, these aren’t necessarily the highest-traffic stories (though in some cases they are). They are stories that exemplify what we are trying to deliver to our readers every day—narratives about the people, companies, and ideas that are shaping the future of technology, life sciences, and cleantech in our region, and across the country.

It was very hard to pick just 20 stories, like I usually do. I guess that’s a good thing. So I fudged it and actually picked slightly more—a dozen tech stories, and a dozen life sciences and cleantech stories.

In any case, our editor’s picks for 2011 span the fields of software, mobile, Internet, security, health IT, biotech, life sciences, energy, and hardware/materials.

They range in topic from people stories (Adriana Jenkins, Steve Jobs) to company strategies (Acme Packet, Vertex) to trends and analysis (big data, biotech risks); from universities (Harvard accelerator) to startups (MedicalRecords, Harvest Power) to big companies (IBM, Pfizer, Biogen Idec); from Q&As (Rob Day, Jim Baum) to company profiles (EnVivo, MC10) to news features (testing the nation’s first car collision-avoidance system); and from big community projects (Entrepreneur Walk of Fame) to cheeky area clusters (top 10 “boring” tech companies).

Here they are in their full glory, our top 20-ish stories of the year, sorted by sector:

Top 12 Tech Stories

Adriana Jenkins, Boston Biotech PR Maven, Dies from Breast Cancer at 41

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The price of shares at San Diego’s Gen-Probe, Amylin Pharmaceuticals, and Optimer were clipped for various reasons over the past week, but several local startups successfully raised capital. Our good news, bad news briefing begins here.

—Rempex Pharmaceuticals, a San Diego biopharmaceutical startup developing a new approach to antibiotics resistance, said it raised $67.5 million in Series B venture funding—bringing total funding for the company to $76 million since its founding less than five months ago. The startup is on a fast track, and plans to use the capital to accelerate the commercialization of its therapies for treating gram-negative bacterial infections. Rempex said it plans to file a new drug application for its first drug candidate in the second half of 2012. New investors Frazier Healthcare Ventures and Vivo Ventures joined existing investors SV Life Sciences, OrbiMed Advisors, and Adams Street Partners in the latest round.

—Cambridge, MA-based Vertex (NASDAQ: VRTX) has held the high ground in hepatitis C therapies since the FDA approved its protease inhibitor drug telaprevir (Incivek) last year. But two rivals are gaining ground. The price of Vertex shares have fallen with the rise of Alpharetta, GA-based Inhibitex (NASDAQ: INHX) and Princeton, NJ-based Pharmasset (NASDAQ: VRUS). Vertex, which has operations in San Diego, hit a 52-week high of $58.87 on May 12, but it has been trading around $31 in recent days.

—Adding to the competition in hepatitis C drugs, San Diego-based iTherX Pharmaceuticals raised almost $3.2 million to advance its development of a prophylactic treatment for Hepatitis C, according to a regulatory filing earlier this week. The startup said in March that its drug candidate TX-5061 appears to prevent the hepatitis C virus from entering liver cells, and has shown “potent preclinical antiviral activity against all HCV genotypes.” Former UCSD virologist Flossie Wong-Staal is a co-founder and chief scientific officer. The company raised $2.8M in 2010.

—San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN) agreed to pay Eli Lilly more than $1.5 billion as it gradually reassumes responsibility for global commercialization of its best-selling diabetes drug in a deal that ends its 10-year partnership with Lilly. Under their agreement, which also ends litigation with Lilly, Amylin will take over sales of exenatide (Byetta) in the U.S. by the end of this month—and global sales of both Byetta and an experimental, extended release version (Bydureon) over the next two years. Amylin shares, which hit a 52-week high of $16.65 on Jan. 27, have been trading around $10 a share over the past few weeks.

—Xconomy east coast biotechnology editor Arlene Weintraub profiled PharmaSecure, a four-year-old startup in Lebanon, NH, with operations in San Diego, Michigan, and India. The company provides machines to drug-makers that print unique bar codes and serial numbers on drug packaging. PharmaSecure raised $3.9 million last month from Innovation Endeavors, Gray Ghost Ventures, Healthtech Capital, and angel investors. The Tech Coast Angels (TCA) participated in … Next Page »

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Drug approvals and advances in new cancer therapies were the prevailing themes in San Diego’s life sciences news over the past week. Our briefing begins now.

—TEDMED, the exclusive medical and healthcare symposium that died in 2004 and was resurrected in 2009, is now the walking TEDMED. The entertaining show with a mix of big ideas, celebrity presentations, humor, and music that played at the Hotel del Coronado for the past three years said it is moving to Washington DC. Playing at the John F. Kennedy Center for the Performing Arts in the nation’s capital will give the $4,000-a-person symposium a bigger stage and a more influential audience, according to Priceline.com founder Jay Walker, who led an investor group that acquired the show in April. About 850 attended last week’s four-day symposium in the San Diego area.

—Federal regulators approved a new pain-killing drug intended to put off the post-surgical need for opioids that was developed by Pacira Pharmaceuticals (NASDAQ: PCRX), the Parsippany, NJ-based drug developer with operations in San Diego. The FDA’s approval marked the end to a protracted drug-development saga for the long-acting form of a pain drug called bupivacaine. Pacira plans to begin marketing the drug, branded as Exparel, in January.

—The FDA approved a new diagnostic test that was developed by San Diego-based Gen-Probe (NASDAQ: GPRO) to detect strains of the human papillomavirus (HPV) that pose a higher risk for cervical cancer and precancerous legions. Gen-Probe said regulators approved its Aptima HPV test to run on TIGRIS, a fully automated, high-throughput molecular diagnostic system. Using a Pap smear sample, the company says its test detects 14 high-risk types of HPV, giving patients and doctors information earlier and more accurately.

—Luke’s BioBeat column focused on several cancer drugs the FDA approved in August, which he suggested could be a turning point in the decades-long battle against cancer. Instead of broad-based anti-cancer drugs, Luke says regulatory approval of vemurafenib (Zelboraf), brentuximab vedotin (Adcetris), and crizotinib (Xalkori) signals the … Next Page »

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If there’s a common thread in San Diego’s biotech news over the past week, it would be perseverance. If you can persist with our briefing, you’ll see what I mean.

—Cambridge, MA-based Vertex, (NASDAQ: VRTX), which has a sizable presence in San Diego, said it generated $74.5 million in second-quarter sales of telaprevir (Incivek), its new drug for treating hepatitis C. Wall Street analysts had expected the number would be less than half that.

—San Diego’s Amylin Pharmaceuticals (NASDAQ: AMLN), Indianapolis-based Eli Lilly (NYSE: LLY), and Waltham, MA-based Alkermes (NASDAQ: ALKS) re-submitted an application to the FDA to market exenatide, its new, once-a-week version of Bydureon.

—San Diego-based Arena Pharmaceuticals, (NASDAQ: ARNA), which sustained a major setback last October when the FDA refused to clear its obesity drug, reported results from a recent study that could address part of the FDA’s objections. Arena said its weight-loss drug lorcaserin (Lorqess) was found in cerebrospinal fluid at much lower concentrations in human beings than in rats. The company plans to address each of the concerns raised by the FDA about its drug.

—San Diego-based BrainCells Inc., which has raised at least $77 million in venture capital since it was founded in 2003, has raised nearly $1 million in a planned financing of $14 million. But BrainCells is moving forward without CEO James Schoeneck, who joined the company more than five years ago, and Carrolee Barlow, who was the chief scientific officer. Consultant Robert Williamson has been serving as the company’s acting CEO.

—There’s a new venture firm in town, called Moore Venture Partners. Terry Moore told me he can make a difference in helping San Diego’s underserved startup community with even a small fund of $10 million to $15 million. Moore plans to invest in both tech and life sciences startups, and participated in last year’s $26.5 million Series B financing at San Diego-based Astute Medical.

—San Diego-based Illumina (NASDAQ: ILMN) said it is working with the University of Oxford to sequence the whole genomes of 500 people with a range of life-threatening genetic diseases or disorders that pose major challenges in diagnosis, treatment, and care. The team plans to recruit patients from Oxford’s clinical community in an effort to identify genetic mutations that could be used to diagnose their diseases and optimize treatment.

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Hold on to your lighter fluid there, Mr. Barbecue. Not so fast, Ms. I’m-Leaving-Early-For-The-Cape. Yes, I’m talking to you, Fourth of July holiday slackers.

Actually, go ahead and slack off—this should go down pretty easy. At the end of each quarter, we like to look back at some of Xconomy’s top stories. These are not necessarily the ones that got the most traffic (though in some cases they are). But they exemplify what we try to deliver day in and day out—real news and stories behind the companies, people, ideas, and trends that are shaping the future of innovation in our network of cities. Basically, they are stories we liked that will stand the test of time.

For the second quarter (April through June), our Boston editor’s picks cut across a wide variety of tech, life sciences, and energy. The topics range from scrappy startups (PerkStreet, Skyhook, SMTP) and midsize successes (Acme Packet, CSN Stores) to giants (Microsoft, Google, Biogen Idec, Genentech/Roche); from venture capitalists (Polaris, Charles River, Braemar) to entrepreneurs (Greentown Labs, Semyon Dukach); from profiles (Harvest Power, Tal Medical) and deals (Forma) to clusters and trends (m-Qube mafia, future of the Web); and from big industry developments (Vertex’s FDA approval) to individual scoops (Robin Chase’s new startup, iPierian shakeout).

Without further ado, here are Xconomy Boston’s top 20 stories of the second quarter, sorted by sector:

Debit Cards Aren’t For Stupid People: Q&A with PerkStreet CEO on Flying Into the Startup Abyss

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Lexington, MA-based Concert Pharmaceuticals announced today that it has moved three novel drug candidates forward in its pipeline—one of which earned it a $4 million milestone payment from GlaxoSmithKline (NYSE: GSK). The European drug giant allied with Concert on an HIV program in 2009, and the molecule, called CTP-298, is now the lead compound in that program.

Glaxo has pledged up to $1 billion in equity and milestone payments to Concert based on the success of its program, which centers on making longer-acting versions of approved HIV treatments by swapping out certain hydrogen atoms in drugs with deuterium atoms. With this last milestone payment, Concert has reaped a total of $50 million from the deal so far.

Concert’s goal is to use its deuterium platform to modify atazanavir, one of the most widely used HIV treatments, which is in the drug class known as protease inhibitors. Currently, atazanavir is commonly given with a boosting agent called ritonavir, which prevents it from getting destroyed by enzymes in the body before it has a chance to be effective. Eliminating the need for ritonavir would simplify the HIV regimen for patients—a big selling point, says Concert CEO Roger Tung.

“Ritonavir is one more pill to remember,” Tung says. “And it’s not a totally benign agent. It causes some patients to get nauseous and it has cardiovascular risk factors. Our goal is to create a drug that can be dosed once a day, without a boosting agent.”

Originally, Concert and Glaxo were counting on a different molecule, CTP-518, to be the lead contender in the HIV program. But CTP-298 “stood out as being preferable” in early human trials, Tung says.

What’s more, Tung says, CTP-298 has the potential to be useful in combination with Glaxo’s experimental treatment called GSK-572, which is an integrase inhibitor that’s now in Phase 3 trials. “Our eventual goal is to have a fixed-dose combo,” Tung says. He adds that Concert and Glaxo have been inspired by the success … Next Page »

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We’ve been seeing some big life sciences deals in recent weeks, the latest being Nestlé’s acquisition of San Diego’s Prometheus Labs. Here’s our wrap-up of the past week.

—Switzerland’s Nestlé Health Science agreed to acquire San Diego’s Prometheus Laboratories in what one analyst estimated as a $1.1 billion deal. The Nestlé subsidiary has been on a buying spree, acquiring CM&D Pharma, which is focused on cancer and inflammatory bowel diseases, in February; and Vitaflo, which develops treatments of inherited metabolic diseases, last August. San Diego’s Prometheus, which has been in registration for an IPO since late 2007, also is a specialty pharma and diagnostics company focused on cancer and gastrointestinal disorders.

—San Diego-based Trius Therapeutics (NASDAQ: TSRX), which is developing a new generation of antibiotics for treating multi-drug resistant infections, surprised me yesterday by disclosing plans to raise $30.2 million through a private stock placement. I recently talked with Trius CEO Jeff Stein about the company’s travails in raising capital through an IPO last year, and how government R&D contracts are supporting the biotech’s early stage drug development.

—La Jolla Pharmaceutical has been an icon of San Diego’s biotech community, but preliminary data from a preclinical study of a compound the company has been studying for repairing scar tissue could spell the end of the company’s 21-year run. In a statement Monday, the biotech says its LJP1485 compound will not show a statistically significant improvement compared to a placebo. CEO Dierdre Gillespie told me in an e-mail yesterday that it will still be a few days before another update is available. The biotech has raised $428.1 million without producing any commercial therapies, according to The San Diego Union-Tribune.

—San Diego-based ResMed ( NYSE: RMD), which provides technology for treating … Next Page »

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Is sentiment coming together to push for FDA regulatory reform? Luke’s BioBeat column described industry efforts to shake up the FDA, and U.S. Rep. Darell Issa convened a hearing in San Diego last to collect life sciences testimony on needed reforms. We have details on all that and more.

—In a run-up to an FDA public advisory meeting today in Silver Springs, MD, Luke reported that an FDA staff analysis of data submitted for a new hepatitis C drug under development at Cambridge, MA-based Vertex shows a cure rate as high as 79 percent among patients getting their first-round of treatment. That’s better than the 75 percent cure rate reported by Vertex, which has substantial operations in San Diego. The question lingering today is whether two side effects cited by the FDA—rash and anemia—will affect the advisory panel’s recommendation concerning the Vertex drug, telaprevir.

—Dow Jones VentureSource provided more details about first-quarter venture capital activity in San Diego, including data about local life sciences deals. In contrast to the MoneyTree Report, which shows a sharp decline, Dow Jones says venture funding in San Diego was relatively flat, with $213.9 million invested in 26 deals. That includes $119.6 million invested in 13 healthcare companies in San Diego, which is almost even with the $121.6 million that was invested in 12 healthcare companies during the same quarter of 2010.

—San Diego’s Polaris Group, which seemed to spring out of nowhere, is moving to begin a late-stage clinical trial of ADI-PEG 20 for treating the most common type of liver cancer. The drug, also known as pegylated arginine deiminase, is intended to deprive tumor cells of arginine, an essential amino acid they need to survive and grow.

—San Diego’s Fate Therapeutics, which is developing stem cell therapies, has increased the size of its current equity round to $36 million and arranged for $1 million in debt financing, according to a couple of recent regulatory filings. Fate said in February that chairman John Mendlein was stepping in to run the company following the departure of CEO Paul Grayson, who is leaving to … Next Page »

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Please excuse this bout of drive-by journalism, but it’s been a very busy couple of weeks for events and news in Xconomy-land. One very impressive local event was the Boston Biotech Business Development Conference on Tuesday (part of the greater Boston Biotech Conference series). The Mandarin Oriental Hotel in Back Bay was full of biotech’s heavy hitters every which way I turned.

I was able to catch a few sessions that focused on the trials and tribulations of large biotech companies, life science venture capitalists, and private startups.

One part I missed, regrettably, was an afternoon chat with veteran investor Peter Brooke of Advent International and Keith Lockhart, the conductor of the Boston Pops, moderated by biotech entrepreneur and venture capitalist Christoph Westphal (see photo above, courtesy of Lacy Roosevelt from Weber Shandwick—you can click on it to see a larger version). Anyone who answers the question “Is the venture capital model broken?” with “There are so many stupid questions,” as Brooke did at another event last week, is OK in my book.

Here are some tidbits from what I saw, heard, and gathered after the fact:

—John Maraganore from Alnylam Pharmaceuticals (NASDAQ: ALNY) quipped that he had a hard time finding his “large biotech” panel (he was moderating) “because it was hard to find a large biotech.”

—Biotechies have a love-hate relationship with Big Pharma—and a hate-hate relationship with the FDA. Matt Emmens from Vertex (NASDAQ: VRTX) noted that he’s hired 600 people in two and a half years, and many have come from pharma. “It’s a good talent pool,” he said. In terms of pharma competing with biotech companies, Richard Pops of Alkermes (NASDAQ: ALKS) said Big Pharma can’t move as quickly to work directly with academic researchers, the way biotechs can. The panel unanimously groused about the challenges of gaining FDA approval for drugs, but they also had some “Stockholm syndrome” sympathy for regulators trying to operate within FDA’s “Byzantine structure.”

—Drug developers can face the dilemma of “turning the corner too early” with new treatments, said Steve Holtzman of Biogen Idec (NASDAQ: BIIB). While these treatments produce short-term praise, patient benefits, and revenue, investors continue to evaluate public-company success on longer-term earnings. So, these companies might encounter difficulty in sustaining profitability.

—More on the evolving relationship between pharma and biotech: Pharma is looking for more external business development opportunities, not wanting to go hostile. Biotech continues to be the first wave of innovation, but it’s struggling to stay small as it becomes big, Emmens said. That is, smaller companies on the verge of going commercial have to either grow into Big Pharma’s shoes, or try to maintain their success through their current collaborative culture and environment.

—Biotech VCs think there’s a new tech bubble, but they don’t agree on its impact. Vaughn Kailian from MPM Capital argued that biotech got spillover from the last bubble and “it was dumb money.” But that was built on lots of companies, versus today’s bubble that’s built on just a few (Facebook, Groupon, Zynga), so he worries about “the dam breaking” and sweeping everything away. Atlas Venture’s J.F. Formela countered that this time, the tech companies have “massive revenues,” so the “bubble has a different shape.” The panel seemed to agree that biotech capital is scarce, and that’s when VCs can get the best returns. (On the other hand, smart observers also realize that no one really knows anything—Venrock’s Bryan Roberts said “companies that succeed end up working on things other than what we invested in.”)

—From the Brooke-Lockhart discussion (with an assist from Weber Shandwick): There is a connection between biotech and the arts, in that opportunity comes out of diversity. It is a tough time for biotech, and it’s always a tough time for the arts; however, it is a great time to look at new ways to deliver products.

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This week we’ve seen news of acquisitions and funding, as well as longer articles on strategy and research moves for New England’s life sciences firms.

—BL Healthcare, a provider of telemedicine products that is based in Foxboro, MA, has bumped its Series A funding round up to $4.9 million, with another $2 million in equity-, debt-, and rights-based financing, an SEC filing showed.

—Luke took a look at the moves that Cambridge, MA-based Epizyme has been making in scoring deals with Big Pharma companies. GlaxoSmithKline (NYSE: GSK) paid the three-year-old biotech $20 million upfront with potentially another $630 million in milestones for a drug discovery partnership, and Japanese firm Eisai Pharmaceuticals will pump $6 million upfront and potentially $200 million in milestones into Epizyme for a collaboration to develop cancer drugs.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) said the Phase III study of its cystic fibrosis drug, VX-770, met its primary goal among patients ages 6 to 11 of improving lung function through 24 weeks, showing that the drug is working about as well in children as it did in older patients with the genetic disorder. The 48-week study of 52 patients is still ongoing, but at 24 weeks, children on the drug showed a mean absolute improvement from baseline in lung function of 12.5 percent.

—Follica, the baldness treatment developer that got started in Boston in 2006, is working to protect its technology that uses lithium treatments to stimulate new hair growth with a patent application, filed in September and published this March. But that’s only one piece of the multiple areas of research that Follica is focusing on, CEO and president William Ju told Ryan.

—Worcester, MA-based RNA interference drug developer RXi Pharmaceuticals (NASDAQ: RXII) announced it has agreed to acquire Scottsdale, AZ-based Apthera, a developer of peptide immunotherapies for cancer. Apthera shareholders will get 4.8 million of RXi’s shares, which were valued at $1.50 before the deal. As part of the agreement, RXi CEO Noah Beerman will resign and will be replaced by RXi board member Mark Ahn.

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Grass is growing. Birds are singing. IPOs are filing. And snow is coming tomorrow. In other words, it’s springtime in New England.

Every so often, we like to take a breath and look back at some of Xconomy’s top stories from the past few months. These are not necessarily the ones that generated the most traffic (though in some cases they are). They are stories that exemplify what we try to deliver to our readers day in and day out—real stories behind the companies, people, ideas, and trends that are shaping the future of innovation in our network of cities. What’s more, they help distinguish us from the media pack—especially the low-level din of incremental tech journalism (not to mention any schmo with a Twitter account).

For this quarter, our Boston editors’ picks range widely in topic from scrappy startups and unsung companies (Dyn, PoKos, Topera) to giants and public firms (IBM/Netezza, Alkermes, Vertex); from personal stories (Adriana Jenkins, Bliss) to broad, sweeping trends (big data, Boston vs. other innovation hubs); from historic developments (Genzyme) to quirky twists (Blank Label); and from the serious (fighting drug addiction) to the humorous (“hold on to your toupees”).

Without further ado, here are Xconomy Boston’s top 20 stories of the first quarter, sorted by sector:

Top 10 Tech Stories:

Yes, Now That Stranger Across the Bar Can Text You. No, It’s Not As Scary As It Sounds, Says Mobile App Developer PoKos

Netezza Chief Talks About “Formative” PTC Days, IBM Deal History, and the Future of Big Data

You Snooze, You Lose: 10 Boring Boston-Area Tech Companies That Are Actually Interesting

The Changing Face of Boston VC: A Chat With NextView Ventures’ David Beisel

Mass Customization, Mystery Developers, and Men’s Shirts: Blank Label Returns to Boston

EveryTrail Was “Unappreciated Gem,” Says TripAdvisor Exec: A Look Inside Today’s Acquisition

MassChallenge, With Lessons Learned, Gears Up for 2011 Startup Competition: A Definitive Debrief

Boston Vs. New York: Tech Startups and Investors Add New Spice to Classic Rivalry

2010 Startup Moves from Boston to San Francisco Offer Insights to the Perennial Coast vs. Coast Debate

Desh Deshpande on Starting Merrimack Valley Innovation Center—and Making a Global Impact from Massachusetts to India

Redstar, From ATG Founders, Reveals Funding Strategy, Sets Up Office Space, Looks to Hire Entrepreneurs

.

Top 10 Life Sciences and Energy Stories:

Former Boston Scientific Exec and UCSD Physician Team Up at Startup Topera Medical

Bill Gates Backs Nimbus, Betting on Computer-Based Drug Discovery

Agrivida, Developer of Cheap Biofuel Tech, Seeks Deals to Broaden Commercial Horizons

Vertex Nails Pivotal Study for Cystic Fibrosis, Racing Toward Market With Second Drug

Alkermes Sees Chance to Reinvent Vivitrol For Fighting Drug Addiction, Not Just Alcoholism

Genzyme, After Months of Holding Out, Agrees to be Sold to Sanofi-Aventis for $20.1B

Adriana Jenkins, Boston Biotech PR Maven, Dies from Breast Cancer at 41

Bliss Healthcare, Founded by MIT Sloan Grad, Starts New Web-Savvy Home Care Service

Amgen’s R&D Chief, Roger Perlmutter, on Why BioVex’s Cancer-Fighting Virus Is Worth $1B

Follica Co-Founder and Team Find New Clues About Male Baldness

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—Cambridge, MA-based Quanterix partnered up with Novartis Diagnostics, the unit of healthcare giant Novartis that tests the safety of 80 percent of the U.S. blood supply. Novartis will run tests to see how effective Quanterix’s device is at pinpointing a protein biomarker in the blood that is linked to an undisclosed neurological disorder. Terms of the arrangement weren’t disclosed.

—New York pharmaceutical company Forest Laboratories (NYSE: FRX) paid $1.2 billion ($30 per share) upfront to acquire Newton, MA-based Clinical Data (NASDAQ: CLDA), a drug developer that won FDA approval last month for its anti-depressant. Forest could pay another $6 per share to Clinical Data shareholders if the drug, vilazodone, hits certain sales goals over the next seven years.

—Watertown, MA-based Athenahealth (NASDAQ: ATHN) formed an alliance with Microsoft (NASDAQ: MSFT) to make the companies’ systems more compatible and easier for healthcare professionals to use together to get a single view of patient records for hospital and outpatient visits.

—Cambridge-based Vertex Pharmaceuticals (NASDAQ: VRTX) announced it had passed a pivotal clinical trial of 161 cystic fibrosis patients who were randomly assigned to the company’s VX-770 pill or  a placebo. Those who received the Vertex drug showed a 17 percent relative improvement in their ability to force out air from their lungs in one second (a measure of lung function). Vertex’s stock shot up 15 percent the morning of the news, to hit $44.03 per share at 10:14am.

—Greg took a look at iAMscientist, a Brookline, MA-based startup developing a global community and resource site for researchers and institutions in science, technology, and medicine. The company has raised $1 million in seed funding from a group that includes famed Harvard chemist George Whitesides, and more than a dozen companies, such as Genzyme.

—Cambridge-based Metamark Genetics is moving out of stealth mode, wrote my colleague Ryan, who caught up with the company’s relatively new CEO Mark Straley. The startup—which was founded by top scientists at Harvard and elsewhere—is out to release a molecular test to provide prognostic information that will help physicians make better treatment decisions.

—Waltham, MA-based lab instruments and services provider Thermo Fisher Scientific (NYSE: TMO) announced it had sold off its Athena Diagnostics and Lancaster Laboratories units for a total of $940 million in cash, to boost shareholder value. Madison, NJ-based lab testing firm Quest Diagnostics is paying $740 million for Athena, and Eurofins Scientific of Brussels, Belgium, will shell out $200 million to acquire Lancaster, a provider of contract testing and analysis services to pharmaceutical companies.

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A series of private announcements and public policy changes in recent days put a spotlight on entrepreneurs nationwide. As Wade wrote in a thoughtful analysis, we seem to have placed a much bigger bet as a nation on early stage startups—and the life sciences news out of San Diego this past week seemed to reflect all the opportunities, risks, and expectations that encompass such bets.

—In an unexpected blow, FDA regulators rejected the new drug application for Contrave, the weight-loss drug developed by San Diego-based Orexigen Therapeutics (NASDAQ: OREX). The FDA said the drugmaker must conduct an extensive new clinical trial of the drug, which is a combination of bupropion and naltrexone, that evaluates the risk of “major cardiovascular events.”

—Across town, San Diego’s Arena Pharmaceuticals (NASDAQ: ARNA) eliminated 66 jobs, or about 25 percent of its workforce. That’s estimated to save the company about $13.5 million a year as Arena works to resurrect the prospects for lorcaserin, another weight-loss drug that was rejected by the FDA last year.

—The Scripps Research Institute’s longtime president, Richard Lerner, is expected to step down soon. No formal announcement has been made, but Luke reported that Berkeley chemist and molecular biologist Michael Marletta may be the leading candidate as Lerner’s successor.

—At a time when California’s biomedical sector lost about 6,000 jobs, a report from the California Healthcare Institute found that San Diego added 678 jobs in 2009, as total employment in San Diego’s biomedical sector hit 24,157. Job gains in San Diego was a surprising theme that emerged in this year’s 2011 California Biomedical Industry Report.

—Kieran Gallahue resigned as … Next Page »

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Most readers will be aware that Vertex announced it is moving from 900,000 square feet of laboratories and offices in Cambridge to over a million square feet in Boston.

Some are asking if this spells serious trouble in Cambridge. This question surprises me. Cambridge is one of the world’s most important sources of next-generation technology and companies, and regularly exports them. A 2009 Kaufmann Foundation study showed that MIT spin-outs alone, if collected together, would rank as the 11th largest economy in the world. Vertex and its Telaprevir hepatitis C drug, which is on the verge of approval by the FDA, follow a time-honored tradition.

Once ideas are proven, those pursuing them should and do move into production mode. Sometimes that means taking larger, cheaper space elsewhere. When this happens, it makes room for another generation of new companies in Cambridge. While nobody wants to lose a taxpayer, Cambridge should feel proud of the contributions it makes to the rest of the world.

For nearly 400 years, Cambridge’s powerful blend of intellectual and entrepreneurial oomph has given the city an enviable self-renewing quality. Let’s look at the record. It starts with the book. Cambridge printed the first book in North America 370 years ago. About that time, it also became home to its first university, Harvard. The first computer (the Mark II) and the Internet (then called the Arpanet) came out of Cambridge. Thomas Watson placed the first two-way telephone call from his lab in Kendall Square, the wires stretching across the river to Alexander Graham Bell’s home on Beacon Hill. Some other Cambridge creations include the microwave oven, the sewing machine, instant photography, ship-to-ship radar, synthesis of penicillin and quinine, fractionation of blood, and deployment of vaccines. Many of Cambridge’s inventions today are so complex, the inventors win Nobel Prizes while most of us don’t even understand them.

(If you want the full background on these inventions and others, you are in luck. The Cambridge Historical Society is readying a comprehensive website on the history of invention in Cambridge. Send a note to innovation@cambridgehistory.org if you’d like to be notified when it’s up.)

Cambridge has launched some pretty interesting ideas in other departments as well. … Next Page »

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With 2010 almost in the books—and a lot of people grounded by the Northeast blizzard—it seems like a good time to take a break and look back at some of Xconomy Boston’s top stories of the year.

These are not necessarily the ones that generated the most traffic (although in some cases they did). Instead, they are stories that best exemplify what we try to deliver to our readers day in and day out—the stories behind the companies, ideas, and people that are helping to create the future of innovation in our network of cities.

Our Boston editor’s picks span a wide range of subjects, from young startups (Baydin, Krush, Energesis) to established public companies (Genzyme, Vertex, Unica, Progress Software), from software and information technology to life sciences, biotech, and energy. They range from unique breaking news stories (Resveratrol) to in-depth features (TripAdvisor), Q&As (John Glaser, Arif Padaria), and commentary/analysis (entrepreneurial Walk of Fame).

Without further ado, here are our top 20 stories of 2010, sorted by sector:

Top 10 Tech Stories

Krush Founder Gina Ashe, Survivor of Horrific Car Crash, Has New Lease on Startup Life

Q&A on Startups and Investing Strategy with Massachusetts Clean Energy Center’s “State Angel” Arif Padaria

Why Rich Levandov Invested Early in Zynga, and Why It Took Off—Lessons Every Entrepreneur Should Consider

Twitter Plea Helps Baydin Get Seed Money from Angel Investor Dave McClure; Startup Moving to the Valley Next Month

Kendall Square Wants an Entrepreneurial Walk of Fame—and So Should Every Innovation Hub

The Unica Story: Yuchun Lee’s Journey from MIT Blackjack Team to IBM Acquisition

Is Boston Becoming a Hub for Female Tech Entrepreneurs? Maybe, and Here’s Why

Tim Berners-Lee and Group of Boston Web Gurus Leading New MIT Class to Get Linked Data to Market

Reinventing Progress Software—Boston’s Next Billion-Dollar Company?

TripAdvisor: The Travel Company That’s Really All About Data

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Top 10 Life Sciences Stories

Avila Therapeutics Pursuing Rival to Lung Cancer Drug in Dana-Farber Lawsuit

Energesis Pharmaceuticals, Co-Founded by Sirtris Vet, Seeks to Tap Power of “Good Fat” in Fighting Obesity and Diabetes

Genzyme Boss Henri Termeer Not Ready to Sell to Sanofi, Ride Into the Sunset, Sources Say

Former Sirtris Execs’ Nonprofit Starts Selling Resveratrol with Potential Anti-Aging Effects Online

John Glaser, Boston’s Top Hospital Geek, Talks About Obama’s Health IT Plan and Getting Booted from Catholic School

Vertex, Worth $7.5B, Eagerly Awaits Final Proof that Hepatitis C Drug Works

Cooking with the Genzyme Recipe: New Players Funding Rare Disease Drugs in Boston

The Genetics Institute Alumni: Where Are They Now?

Prominent Flatley Family Launches Boston Nonprofit for Cystic Fibrosis Drug Research

Chairman Bill Young: Next Biogen Idec CEO May Be a Scientist

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Most of the news from San Diego’s life sciences companies in the week before Thanksgiving was focused on funding deals. And you have our best wishes over the holiday.

—After setting the price for its IPO between $12 and $14 a share earlier this month, San Diego specialty drug developer Zogenix (NASDAQ: ZGNX) priced its initial public offering at $4 a share, a markdown of at least 67 percent. Zogenix also increased its offering from 6 million to 14 million shares, raising a total of about $56 million for the company, which had been shooting for something closer to $84 million. The company is developing drugs for use with its needleless injector.

—Access Scientific, a San Diego startup developing a device for inserting a peripherally inserted central catheter line, has raised an additional $2 million from investors.

—San Diego’s Amira Pharmaceuticals laid off half its staff, leaving 25 employees to concentrate on discovery research and administration as the company reorganizes into more of an early-to-mid-stage drug developer. Founders Peppi Prasit, Jilly Evans, and John Hutchinson are all leaving their jobs, although Prasit will continue as chairman of Amira’s scientific advisory board.

—Shares of San Diego’s Apricus Biosciences (NASDAQ: APRI) gained about 24 percent after the drug development company said it had reached an agreement with the FDA on a plan for conducting a pivotal clinical trial for a potential new treatment for liver cancer. Apricus closed Monday at $3.35 a share after ending Friday at $2.70.

—Vertex (NASDAQ: VRTX), the Cambridge, MA, drug developer with operations in San Diego, filed a new drug application with the U.S. Food and Drug Administration to begin selling telaprevir as a treatment for hepatitis C. The company is seeking a faster-than-usual six-month regulatory process.

—Cambridge, MA-based Genzyme (NASDAQ: GENZ), which has operations in San Diego, disclosed plans to sell its diagnostic products business to Japan’s Sekisui Chemical for $265 million in cash.

—San Diego’s ImThera Medical, which is developing a neuro-stimulation device for treating sleep apnea, has raised $1 million of a planned $2.2 million round from investors.

—San Diego’s BeneChill, which has been developing a portable device that emergency workers can use to lower the temperature of heart attack victims, raised about $600,000 of a planned $1.2 million in debt.

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The third quarter of 2010 is going out with a monsoon in New England. It seems like a good time to hole up indoors and look back at some of the top stories we’ve done at Xconomy Boston over the past three months.

These are our editors’ picks. They aren’t necessarily the ones that got the most traffic or the most attention. Rather, they are stories that highlight our unique style of on-the-scene reporting and in-depth analysis, and will stand the test of time. They range from startup profiles in health IT, security software, and drug development, to analysis pieces on leading companies’ acquisition and expansion strategies, to unique venture capital perspectives and quirky, strange-but-true facts about New England innovation leaders.

So, without further ado, here are our top 20 stories of the third quarter, in reverse chronological order (plus a bonus story, in honor of Unica founder Yuchun Lee, a former member of the MIT Blackjack Team, selling his company to IBM for $21 a share):

Genzyme Boss Henri Termeer Not Ready to Sell to Sanofi, Ride Into the Sunset, Sources Say

MeYou Health Enters Social Gaming Realm with Daily Challenge for Improving Well-Being

IBM’s Software Acquisition Strategy in Massachusetts (Plus Tips on Getting Acquired) From VP Mike Loria

Skyhook, Fighting for Its Life in Suit Against Google, Cries Foul: “Call in the Referees and Review the Tape”

Bluebird Bio, Third Rock & Genzyme’s Gene Therapy Bet, Shows Promise for Blood Disorder

Who Knew? Part 3: Xconomy Uncovers Even More Strange-But-True Facts About Boston’s Innovation Leaders

PerkinElmer Expects to Make Acquisitions After $500M Business Sale: CEO Talks Boston-Area Talent and Growth in Software, Imaging

A123 Opens Lithium Ion Battery Plant in Michigan, Wants to Create Global Hub for Electric Vehicles

Good Start Genetics Emerges from Stealth with $18M Series A Round

Reality Show Project Seeks to Capture MassChallenge Competitors in Their Entrepreneurial Element

Vertex Nails Third Big Trial With Hepatitis C Drug, In Toughest Patients to Treat … Next Page »

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Cambridge, MA-based Vertex Pharmaceuticals’s (NASDAQ:VRTX) stock price has lifted slightly this morning after Merck (NYSE:MRK) reported results of two Phase III trials for its rival protease inhibitor for hepatitis C infection, boceprevir. While Merck’s drug met the primary goals of the trials, it didn’t wipe out the chronic liver disease quite a much as Vertex’s telaprevir did in a pivotal study revealed in May. Vertex’s telaprevir compound, when given in combination with two standard drugs, was able to eliminate any sign of the hepatitis C virus in the blood for 75 percent of patients in that study. By comparison, Whitehouse Station, NJ-based Merck says today that its drug in combination with existing therapies helped eradicate the infection in 66 percent of patients in both of its studies. Vertex’s stock was up 2.67 percent on the day to $36.18 per share as of 11:05 Eastern time. (In case you missed it, our story today chronicles the early history of telaprevir and how drug giant Eli Lilly let this potential billion-dollar molecule slip away.)

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Another week, another cadre of CEOs with big plans for growing their New England life sciences companies even bigger.

—Diagnostics For All CEO Una Ryan talked about her multi-pronged effort to raise money for testing and deployment of her Cambridge, MA-based firm’s affordable diagnostic technology. Developed in the legendary Harvard lab of chemist George Whitesides, the nonprofit’s paper-based, postage stamp-sized devices could begin helping patients in developing countries with HIV/AIDS and other ailments by year’s end, if Ryan has her way.

—Vertex Chief Medical Officer Bob Kauffman told Luke about the biotech’s to develop a drug cocktail to fight hepatitis C virus while avoiding the flu-like symptoms of standard treatments for the infection. Vertex (NASDAQ: VRTX) is poised to begin clinical testing of one such cocktail, which includes its experimental drug telaprevir, even as it pursues approval for telaprevir for use with standard hepatitis drugs—a milestone the company hopes to reach sometime in 2011.

—Cambridge-based Biogen Idec (NASDAQ: BIIB) and its Swiss partner Roche reportedly halted development of ocrelizumab, an experimental drug for rheumatoid arthritis, because of safety concerns. Bloomberg News reported that the drug is still being tested for multiple sclerosis.

—Bob Weiler, chairman and CEO of Waltham, MA-based health IT pioneer Phase Forward (NASDAQ:PFWD) told Ryan about his company’s strategy for maintaining its decade-long growth spurt. Having started out by convincing drug companies to switch from paper records to software for collecting and managing data in clinical trials, Phase Forward is making a series of acquisitions to build up a suite of software products that automate everything from the early clinical development to post-marketing safety studies.

—Swiss pharmaceutical behemoth Novartis signed up to back an online community for organ transplant recipients hosted by Cambridge-based social networking site PatientsLikeMe. Novartis, which has a large R&D organization in Cambridge, previously tapped PatientsLikeMe for information about patients with multiple sclerosis.

—The FDA said it intends to reveal today whether it has approved a once-a-week diabetes drug from Waltham, MA-based Alkermes (NASDAQ: AMLN) and San Diego-based Amylin Pharmaceuticals (NASDAQ: AMLN). Alkermes stands to collect a 7.5 percent royalty on worldwide sales of the drug, an version of exenatide (Byetta) that can be injected just once a week, instead of twice a day.

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New England’s life sciences firms and their investors seemed to be exchanging some early holiday gifts this week.

—Vertex (NASDAQ: VRTX) completed the latest in a string of large financing and licensing deals. In this one, the Cambridge, MA-based developer of drugs for hepatitis C and cystic fibrosis sold a total of $500.5 million worth of new stock in the offering.

—Alkermes (NASDAQ: ALKS) and Acceleron Pharma, both also of Cambridge, struck a deal giving Alkermes access to Acceleron’s technology for boosting biotech drugs’ longevity in the bloodstream. Alkermes will pay $2 million upfront, with the potential for additional milestone payments and royalties, and will make an $8 million equity investment in Acceleron.

—Cambridge-based Biogen Idec (NASDAQ:BIIB) bumped up its bid for Redwood City, CA-based Facet Biotech (NASDAQ:FACT) by 21 percent, to $17.50 per share. Facet rejected Biogen’s earlier buyout offer of $14.50 per share in October.

—Luke profiled NormOxys, a Wellesley, MA-based startup co-founded by French Nobel Laureate Jean-Marie Lehn, as the firm emerged from stealth mode. The startup’s odd name reflects its aim of developing drugs that normalize the amount of oxygen in tissues such as failing heart muscle that are deprived of the vital molecule.

—Luke reported that 28-year-old ImmunoGen (NASDAQ: IMGN) of Waltham, MA, is poised to present data that could indicate its first drug is ready for FDA approval. Developed in partnership with Roche, the drug combines Roche’s breast cancer drug trastuzumab (Herceptin) with a chemical toxin designed to make it an even more effective tumor-cell killer.

—Cambridge-based Gloucester Pharmaceuticals—whose cancer drug romidepsin (Istodax) won FDA approval last month, agreed to a $340 million acquisition by Summit, NJ-based Celgene (NASDAQ: CELG). The deal also includes $300 million in future milestone payments.

—Adelene Perkins took the helm of Cambridge-based Infinity Pharmaceuticals (NASDAQ: INFI). Founding CEO Steve Holtzman will stay on as executive chairman, the company said.

—Cambridge-based Sermo—whose 110,000-plus-member online community for physicians generates potentially valuable information for drug companies, investors, and others–-let go about 30 of its 60 to 80 staffers, according to a source who wished to remain anonymous. In an interview with Ryan, the firm’s founder and CEO, Daniel Palestrant, declined to confirm or deny the cuts, but acknowledged that upheaval in the financial services and pharmaceutical sectors has forced Sermo to adjust its strategy.

—Ryan profiled Cambridge-based Mersana Therapeutics, whose “Fleximer” technology helps ferry otherwise toxic drugs into cells. The startup’s first treatment employing the technology, an anti-cancer agent dubbed XMT-1001, is performing well in a Phase I clinical trial, Mersana CEO Julie Olson told Ryan.

—Cambridge-based Epizyme added $8 million from New Enterprise Associates (NEA) to its Series B venture financing. The new cash brings the total for the round to $40 million.

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