Don’t know about you, but I’m less interested in Facebook’s IPO than I am in the efforts of people trying to find the next Facebook out of Boston/Cambridge. One such effort is the new Experiment Fund, based at Harvard University, which I wrote about earlier this week.

Turns out there’s more to the latest seed-stage fund in Boston than initially meets the eye. I had a chance to speak with the Experiment Fund’s co-founders, Hugo Van Vuuren of Harvard and Patrick Chung, a partner at Silicon Valley-based New Enterprise Associates (not that Patrick Chung, that Patrick Chung).

They clarified the goals of the new fund and provided some more context around how it plans to distinguish itself from other similar efforts. I’ve also talked with a number of other early-stage investors around town and have gotten a better sense of how the Experiment Fund is being received locally (more on that below).

First, some mechanics of the fund, which has been in the works for about two years. Harvard has no financial stake and will have no say in the fund’s investment decisions, but it has provided support and office space, Van Vuuren says. He declined to specify the projected size of the fund, but he said it plans to make four to six new investments over the next two years, each in roughly the $100,000 to $250,000 range.

The Experiment Fund has already invested in four companies: Rock Health (see my colleague Wade’s stories here and here), Omada Health, Punch Media, and Tivli. Interestingly, only Tivli is based in the Boston area. Rock Health and Omada are in San Francisco, and Punch Media is in the DC area. They all were started by Harvard students—the key ingredient for now—but the fund intends to invest in teams from other schools around Boston and the East Coast, as well. So I’m guessing its next four investments will be pretty different from its first four, at least geographically.

“We want to meet them here,” Chung says. “We want to help you right here in Boston where the ideas were first born, where the team was put together.”

One issue they wanted to address was the notion that the fund is … Next Page »

Comments | Reprints | Share:          

There’s a new player in the seed-stage investment game in Boston. As of this week, the Experiment Fund is open for business at Harvard University, backed by the Silicon Valley venture firm New Enterprise Associates (NEA). The startup investment fund is being hosted by Harvard’s School of Engineering and Applied Sciences in Cambridge, MA.

The new fund is led by Hugo Van Vuuren (see photo above), a Harvard graduate student and entrepreneur, and two venture capitalists from NEA, Patrick Chung and Harry Weller (both Harvard alums). David Edwards, a Harvard professor of biomedical engineering, serves as an advisor to the fund. Van Vuuren and NEA did not respond to requests for comment in time for this article.

The basic structure of the Experiment Fund is that selected startups—mostly student-led teams from Cambridge—will receive up to $250,000 in seed funding over the next two years, presumably in exchange for a sizable equity stake in the companies. The fund is based out of Harvard but says it will operate independently of the university and will look at teams from other local schools—and, more broadly, from the East Coast. The sectors targeted are pretty broad as well; they include information technology, healthcare, and energy.

No word yet on the size of the fund or how many companies it will invest in. But Van Vuuren, a recent fellow at Harvard’s Berkman Center for Internet and Society, said in a press release that he and his partners are looking for “smart and resourceful people, zealous full-time teams, and experiments in need of seed funding and hands-on help to get off the ground.”

Not to beat a dead Zuckerberg, but the overarching goal here is to keep the next Facebook in Boston—and, preferably, affiliated with Harvard. “It’s continued growth of the ecosystem for Harvard and beyond,” says Gordon Jones, director of the Harvard Innovation Lab, which is collaborating with the Experiment Fund to provide office space and resources, but is separate from the new fund. Jones calls the Experiment Fund “extremely complementary” to the i-Lab.

One of the first Harvard teams to receive an investment from … Next Page »

Comments | Reprints | Share:          

A dark day in Boston is a little darker now. Jerome Rubin, the publishing executive and inventor who co-founded the display company E Ink and helped commercialize the online database that became LexisNexis, died from a stroke on Monday in New York City, according to a report by the Associated Press. He was 86.

Rubin worked at the MIT Media Lab in the 1990s, where he helped spin out Massachusetts-based E Ink, the electronic-paper company that makes the display in the Amazon Kindle and other e-readers.

Before that, Rubin, a Harvard University alum trained in physics and law, helped launch an Ohio-based research database for lawyers in 1973. The database search and retrieval system eventually became LexisNexis, specializing in news, legal, and public records information. Harvard Magazine wrote about some of Rubin’s achievements back in 2000.

Rubin lived in Manhattan and is survived by his children, Richard Rubin and Alicia Yamin, according to the AP report.

Comments | Reprints | Share:          

Like a lot of biotech executives focused on developing drugs, Martin Tolar has long been skeptical of the value of genomics in bringing about personalized medicine. But over the past few months of scoping out new opportunities, he’s become enough of a believer to jump into genomics with both feet, as the new CEO of Cambridge, MA-based Knome.

“You always hear about genomics and the revolution that never happened,” Tolar says. “There was Millennium and deCode, and others who raised lots of money. But I looked at this and said, ‘No, this is incredible, it’s really happening.’ All the pieces of equation are coming together.’”

Tolar, the former CEO of Wellesley, MA-based NormOxys, is joining Knome just as it has completed its fourth year in business, which was by far its best. The company is announcing today that it has won a new contract to analyze and compare 1,000 genomes for scientists at Johns Hopkins University, who are looking for genetic variants linked to asthma in African American and African Caribbean populations. It’s the latest addition to Knome’s roster of about 100 customers for its genomic-analysis software service, although the Hopkins project is by far the biggest. Knome isn’t disclosing the value of the new project, but the company expects to generate $20 million in revenue in 2012 from academic, biotech, and pharmaceutical industry customers, Tolar says.

Tolar joins Knome after his previous company—which raised $17.5 million in May 2010—discovered in clinical trials that its experimental drug worked in a different way than its scientists thought. The NormOxys drug was shown to alter the PI3 kinase pathway, instead of releasing controlled amounts of oxygen into cells. Tolar didn’t say much about the situation, other than that the NormOxys drug is still moving forward in clinical trials for a different use, and that he was more excited by the task in front of him at Knome.

Martin Tolar

Knome’s previous CEO, Jorge Conde, is staying with the company as chief strategy officer, and will focus on product development, Tolar says. The management team is being further filled out by Jonas Lee, a board member who will now join the company as chief marketing officer, while Marc Rubenfeld, formerly of Beckman Coulter, is joining as vice president of operations.

The timing is right for Knome to grow in 2012, Tolar says, because the torrid pace of innovation with faster/cheaper DNA sequencing hardware has created … Next Page »

Comments | Reprints | Share:          

‘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

Comments | Reprints | Share:          

Fate Therapeutics has been quiet during a down time for the stem cell business, but now it’s making news by luring a big name into its inner management circle.

Bill Rastetter, the CEO of Idec Pharmaceuticals during its long journey to develop the blockbuster lymphoma drug rituximab (Rituxan), has agreed to become the chairman and interim CEO at San Diego-based Fate Therapeutics. Besides being CEO of Fate, Rastetter will remain busy wearing his other hats as a partner at Venrock Associates (an investor in Fate), and through his work as chairman of Illumina (NASDAQ: ILMN), Neurocrine Biosciences (NASDAQ: NBIX), and Receptos.

But the new job at Fate, Rastetter says, will be “my major time commitment.” Fate’s executive chairman, John Mendlein, will now become the vice chairman of the board, and will oversee “scientific excellence” at the company as the chairman of the scientific advisory board, Rastetter says. Mendlein is also executive chairman and CEO of San Diego-based aTyr Pharma. Mendlein replaced Fate’s previous CEO, Paul Grayson, who left the company in February.

“We snagged an industry legend to take Fate that much closer to patient reality,” Mendlein said via e-mail. “Bill has done what few have done before – start and create a biotech to deliver one of the most important medicines today.”

Stem cells have excited scientists for years because of their ability to morph into virtually any type of cell in the body, raising the potential for regenerative medicines against a wide variety of today’s untreatable diseases. Still, no pharmaceutical company has brought forward an FDA-approved medicine based on embryonic stem cells, and drug companies haven’t shelled out big bucks to form alliances with startups working on these types of therapies, or to use the technology to improve the drug discovery process. Last month, a bellwether of the field, Menlo Park, CA-based Geron (NASDAQ: GERN) said it was getting out of the stem cell business altogether so it could focus on cancer drug development.

None of that seemed to deter Rastetter.

“Fate reminds me a lot of Idec back in the early antibody days,” Rastetter says. “I’ve always been very intrigued by new technologies deployed at the right time. I think stem cells are here to stay, and now is the time to invest in them. I’m very excited about the scientific and commercial opportunity here. There’s a passion and cohesion here with the team. I feel energized when I sit down with these guys.”

Bill Rastetter

Fate was founded in 2007 to capitalize on leading-edge stem cell science at Harvard University, Stanford University, the University of Washington, and The Scripps Research Institute. It has raised more than $50 million in venture capital from a group of VCs that includes Arch Venture Partners, Polaris Venture Partners, OVP Venture Partners, and Venrock, as well as Takeda Ventures, Astellas Venture Management, Genzyme Ventures, and one more unnamed company.

Fate announced the addition of Rastetter a day after it released some preliminary clinical trial results from its lead drug candidate, Prohema, formerly known as FT-1050. Instead of injecting embryonic stem cells into the body and hoping they will morph properly into a desired cell type, this program is designed to be much less risky, by operating in a controlled lab environment. The company uses a small molecule to treat umbilical cord blood in a laboratory, in order to coax it to produce more blood-forming stem cells that can then be transplanted into leukemia and lymphoma patients. Many patients with those blood cancers get intense chemotherapy or radiation that wipes out both their cancer and their blood cells, so researchers are constantly looking for safe and effective ways to reconstitute a patient’s bone marrow and immune system.

The data is from a small study, although it suggests … Next Page »

Comments | Reprints | Share:          

[Update: Noon ET, 12/9/11] We’re less than a week away from Xconomy’s biggest event of the year for the Boston biotech community, “The Genetics Institute Impact.”

This is shaping up to be a truly special reunion for the people who built one of Boston’s pioneering life sciences companies, and who are still making waves in the industry today. [Update] More than 270 people have registered, and we are sold out for the festivities next Wednesday evening, Dec. 14, at the Koch Institute for Integrative Cancer Research at MIT.

The agenda will be a little different from some other Xconomy events. We’re going to start off by inviting a handful of Genetics Institute alumni to share a favorite anecdote from their days at GI. These could be tales about ups and downs, thrills, horrors, or just plain funny or embarrassing moments that revealed a lot about what made GI such a great adventure. I don’t know what the speakers plan to say, but I’m sure it will be short and sweet and memorable.

Once those remembrance talks are done, I’ll moderate a 20-minute keynote chat with GI’s longtime CEO Gabe Schmergel and the company’s scientific co-founders—Tom Maniatis and Mark Ptashne.

I’m sure these guys could carry on all night. On yesterday’s prep call, Maniatis and Ptashne started jogging each other’s memory banks, revealing tales about former Harvard University president Derek Bok and legendary former CBS chairman Bill Paley (a GI investor). I could have listened for hours, but the goal is to ask just a few questions, and keep the program brief. That way there will be plenty of time for catching up with old friends.

Besides the talks, we will have a cool memorabilia display to check out thanks to contributions from Dale Blank, Gina Nugent, and others. If you have photos from GI in some kind of electronic format like jpeg or gif, now’s the time to send those my way so I can make this display even better. Just shoot me a note at ltimmerman@xconomy.com. And if you have some favorite music that people at the company used to like to listen to—and it’s on CD, Pandora, or at least something other than vinyl or cassette tapes—let me know. I’m taking suggestions for what ought to be on the GI soundtrack.

Here’s the actual program, which we will print up for those of you there at the event. If you couldn’t tell, I’m looking forward to meeting a lot of fascinating people at this event and learning a bit more about a special time and place in the history of the biotech industry. Those of you who show up early at 4:30 pm can get a jumpstart on networking before the program starts at 5:30 pm. See you there Wednesday evening.

4:30 pm—Registration/networking

5:30 pm—Host welcome, Koch Institute

5:35 pm—Introductions, Xconomy

5:40 pm—Remembrance talks

Adelene Perkins, CEO, Infinity Pharmaceuticals

Tuan Ha-Ngoc, CEO, Aveo Pharmaceuticals

Tony Evnin, partner, Venrock Associates

John Knopf, CEO, Acceleron Pharma

Abbie Celniker, CEO, Eleven Biotherapeutics

Sha Mi, Distinguished Investigator, Biogen Idec

5:55 pm—Keynote chat

Gabe Schmergel, former CEO, Genetics Institute

Mark Ptashne, co-founder, Genetics Institute

Tom Maniatis, co-founder, Genetics Institute

Luke Timmerman, national biotech editor, Xconomy (moderator)

6:15 pm—Networking

7:30 pm—End

Comments | Reprints | Share:          

When last we checked in with Gordon Jones, it was six months ago and he had just been appointed the inaugural director of the Harvard Innovation Lab. It was May, the birds were singing, the Red Sox had pulled out of their season-starting slump, and anything seemed possible.

Now the cold, dark days are upon us, and we need a place to rejuvenate our spirits as we gear up for the holiday season. Students and young entrepreneurs especially need such a place. The Harvard i-lab, as it is called, might be that place—a $20 million center whose mission is to support all Harvard students interested in entrepreneurship. And it is officially open for business as of today, complete with a ribbon-cutting ceremony, school administrators, and politicians.

The important news is that the i-lab is real, and it marks a serious and ambitious effort to foster entrepreneurship on a grand scale. The unstated goal is to keep the next Bill Gates or Mark Zuckerberg from leaving town (and Harvard) and building a multibillion-dollar company somewhere else. Will it work? Who knows, but you have to start somewhere.

Back in May, Jones talked with me about just trying to get his baby to first grade—the idea being, walk before you run. He has been heads-down since then, but I recently caught up with him about the i-lab’s opening, and the progress and challenges to date. (And yes, he hosted Zuckerberg’s recent visit to the lab.)

“I’ve been pleasantly surprised so far,” Jones says. “It’s genuine, the interest here, and the level of engagement across the Harvard schools is strong.” He says that the overall support from the university and the enthusiasm from the academic and business communities “exceeds what I expected.”

Jones adds, “When we first talked six months ago, there was this question of, ‘Is Harvard late to the game?’ I think this is a great time to be doing what Harvard is doing.” And that is, in his words, “trying to bring the best of Harvard’s knowledge and network and make it available to students. And being part of the Boston innovation community.”

Here are my takeaways going into the first day of school at the i-lab:

1. Jones isn’t going anywhere. Yes, he has an extremely challenging job. (You try being accountable to seven different deans across Harvard, for starters.) The fact that he’s still alive and kicking—not to mention attending lots of entrepreneurship events and getting to know students and the local business community at every turn—bodes well for the lab’s future. “You’ve got to pick your battles,” he says.

2. The lab is already active. It officially opens today, but stuff has been happening there for months already: a “startup weekend scramble,” guest speakers (the series includes Eric Ries, Peter Thiel, and Jeff Taylor), Harvard courses on entrepreneurship and global innovation, special panels, startup workshops (Alex Taussig led one about mistakes entrepreneurs make; Eric Paley did one on career choices), and one-on-one consultations with “experts in residence” and “innovation partners” … Next Page »

Comments | Reprints | Share:          

When I entered Harvard as a freshman, there was no central focus on startups or entrepreneurs. Student groups were splintered and stagnating, and there were no main faculty members whom I could approach about entrepreneurship. I was intimidated to approach students or faculty from Harvard’s graduate schools, and there was no cross-campus collaboration. Harvard’s startup scene was almost completely underground. Students worked on their “side projects” alone in their dorm rooms. As far as I can tell, that pattern of the insular Harvard entrepreneur has been true for years.

Yet despite all of these hurdles, Harvard has graduated some of the world’s most successful entrepreneurs. Everyone knows of Zuckerberg and Gates dropping out. But what about Tony Hsieh (College ’95), co-founder of LinkExchange and CEO of Zappos.com? Or Tim O’Reilly (College ’75), founder of O’Reilly Media? And what about Scott McNealy (College ’76), co-founder of Sun Microsystems, or social entrepreneurs like Paul Farmer (HMS ’88, Ph.D. ’90), founder of Partners in Health? Do we consider Trip Hawkins (College ’76), founder of Electronic Arts; Mark Warner (HLS ’80), co-founder of Nextel Communications; or Thomas Stemberg (HBS ’73), co-founder of Staples?

These individuals demonstrate two distinct facts about entrepreneurship: first, it’s not necessary to drop out of school to found and grow an amazingly successful enterprise. Second, Harvard has been the birthplace of innovations across industries since its inception.

On Friday, Harvard enters the next era in its quest to graduate successful entrepreneurs, when the Harvard Innovation Lab officially opens its doors. It is both a new facility and new programming that promises to help Harvard students take their ideas as far as they can go. The 30,000 square foot space features a large and easily re-configured space for students to work on their ideas. Nearly every wall is covered with whiteboard paint for students to sketch out their plans. Conference rooms give students more privacy, and a large classroom will host workshops and classes that help students hone their entrepreneurial abilities. Programs already underway include workshops, classes, access to experts-in-residence, mentoring, and student co-working areas. Many of the events and resources are open to the Boston community as a whole.

There has never been a more exciting time to be a student entrepreneur. College is inherently an environment ripe with new connections. During a conversation at 2 AM or a random meeting with a professor, ideas are born. And in a city as alive with innovation as Boston, students have no excuse not to find an idea and run with it.

It’s easy for new university initiatives to launch and be forgotten. The innovation lab is different. The i-lab wasn’t only created to generate interest in entrepreneurship; it was developed to serve the immense interest already present in the student body. The i-lab is here to stay.

So on Friday, welcome the Harvard innovation lab to the Harvard and Boston communities. Stop by and take a look around. Most importantly, speak to some of the students working there. You’ll like what you hear.

Comments (3) | Reprints | Share:          

Score one for open source startups. Modo Labs, a Cambridge, MA-based mobile software company, is announcing today it has closed a $4 million Series A round from Storm Ventures and New Magellan Ventures. The round includes $2 million that the startup raised last year; the new money ($2 million) comes from Silicon Valley-based Storm, led by founding general partner Tae Hea Nahm.

Modo Labs, which grew out of MIT’s Mobile Framework project, makes an open source software platform called Kurogo, which helps universities and other organizations put their information online and make it quickly available on devices like smartphones, tablets, and so forth. Lots of colleges are already using Kurogo for their mobile sites, including Boston College, Brown University, Harvard University, Middlebury College, University of Vermont, and University of North Carolina at Chapel Hill. Modo Labs says it wants to open up its platform to student developers.

But the 20-person company sees a big opportunity in enterprise apps as well. Specifically, big banks and hospitals need the kind of tech support Modo Labs provides, the company says. And it’s about more than making tools for developers.

“We have some really deep interest in making sure the users’ experience is the best they can be,” says Modo Labs CEO Andrew Yu. That means providing “solid and robust templates” so that enterprises can get their websites and apps up and running fast, he says.

Modo Labs is “aggressively hiring right now for developers” of native and mobile Web software (both iOS and Android), says chief technology officer Marshall Vale. He stresses that business customers “absolutely have to deal with multiple device types” across operating systems, handsets, and tablets, and that his company’s software is optimized for that.

Storm Ventures has a couple of notable companies in its portfolio that are complementary to Modo Labs: MobileIron (mobile device management for businesses) and Appcelerator (enterprise mobile development platform).

On a more human-interest note, Storm Ventures is a particularly apt name. Yu, Modo’s CEO, was scheduled to fly out to the West Coast to pitch the firm in August, but his flight was canceled because of Hurricane Irene. So he had to do the pitch by phone. While there was some concern about the geographic distance from a main investor, Yu emphasizes that Storm “really understood this space and was really willing to work with us.”

Let’s hope the unseasonably early October snow, and future storms, don’t wreak havoc for Modo and its investors. It could be a long winter in Boston.

Comments | Reprints | Share:          

All this talk about quarterly earnings and venture stats reminded me: I never posted my favorite stories from Xconomy Boston’s third quarter.

Yes, I know it’s almost the end of October, and the third quarter ended a month ago. I must have been traumatized by the collapse of the Red Sox or something (is baseball still going on?). Go ahead, run me out of town like Theo and Tito.

This time, I’m not consulting with my colleagues. I’m a rebel, a maverick. I work alone. Without further ado, here are my favorite stories from July through September:

Top 10 Tech Stories:

Comments | Reprints | Share:          

Thong Le, the well-wired venture investor at Seattle-based WRF Capital, is stepping up to become chairman of the Washington Biotechnology & Biomedical Association, the state’s trade organization that represents biotech and medical device companies.

Le will formally replace medical device entrepreneur Tom Clement in the volunteer chairmanship at the WBBA’s annual meeting, which coincides with Gov. Chris Gregoire’s Life Sciences Summit on Nov. 18. Clement, the founder of Kirkland, WA-based Pathway Medical Technologies, is now taking on a new entrepreneurial challenge as CEO of a couple different startups, Aqueduct Neurosciences and Cardiac Insight. He will stay on the WBBA’s executive committee.

Le, 35, has made himself into one of the best-connected people in the local life sciences community since he became a managing director with WRF Capital in 2000. At WRF, he has overseen portfolio investments in Corus Pharma, Alder Biopharmaceuticals, Halosource, Hyperion Therapeutics, Uptake Medical, as well as Accelerator, the venture-backed life sciences startup nurturer. He’s a graduate of Harvard University, and is the Pacific Northwest regional director for the Harvard Alumni Association.

“I’m really thrilled Thong is willing to step up. He’s a very smart guy, a careful thinker and has a lot of energy,” Clement says. Le says he doesn’t see any major strategic changes coming to how the WBBA does business. The role, he says, is about “providing a lot of guidance and support for the president.”

“I’m coming at an exciting time for the organization, with a lot of good things happening in the community,” Le says. “Despite the difficult economy, we’re still a bright spot within the economic ecosystem of the state. Our job is to figure out how we can continue to foster that. We want to help member companies be more successful.”

Clement has been chairman since August 2008, and has overseen the leadership transition at WBBA that occurred later that year when Chris Rivera was brought in as president. Le and Rivera have worked closely for years, not just through WBBA activities, but also through WRF’s investment in South San Francisco-based Hyperion Therapeutics, where Rivera was previously the CEO.

Here’s what Rivera had to say in an e-mail yesterday:

“He is extremely smart, creative and has tremendous industry connections. Since he is an investor in the sector, I think that he brings a different viewpoint to the WBBA. Much of our efforts have been to help support the growth of the sector in WA. We try to do this by the following; 1. Commercialization/Translational research—through our pro-bono consultation, we have helped >55 new companies this year alone, with Chris Porter, Stewart Parker’s and Christiana DeloRusso’s help. 2. Access to Capital—WINGS, VIP Forums and LSINW are our main vehicles. 3. Talent—recruitment, retention and development of the talent needed to grow the sector. 4. Policy—both in Olympia and DC. And, 5. Purchasing Programs—our members have purchased >$30M through our contracts and saved > $4M this year alone.

“Thong is and has been one of our community leaders, will bring some new ideas to the Association, and will help us continue to meet our Mission; help grow life sciences in WA state.

Comments (4) | Reprints | Share:          

There just aren’t that many rich people who want to do scientifically adventurous things like fly in outer space or get their entire genomes sequenced. Fortunately for Cambridge, MA-based Knome, it has found a way to keep its genomic analysis business alive by doing something more than appealing to the curiosity, or vanity, of the mega-rich.

Knome, co-founded in 2007 by Harvard genomics ace George Church, made headlines in its early days when it said it sequenced and analyzed the genomes of three wealthy people for the cool sum of $350,000 each. A year later, the price dropped to $100,000, which meant that a few more folks with genetic diseases in their families were able to afford what it took to scrutinize their genomes. But only now that commercially available sequencers can blaze through an entire 6-billion letter human genome for less than $5,000, Knome has been able to branch out its business to appeal to a whole lot more people.

Molecular biologists and biochemists, for starters, are increasingly becoming curious about using the new tools of genomics for their experiments. But they typically don’t have the math and statistics background to make much sense of the data. People who are trained in bioinformatics who can help analyze and visualize these massive piles of raw data, as you might imagine, are in short supply and high demand these days. As academics start dreaming up all kinds of questions they can realistically ask through sequencing genomes for $5,000 a person, and Big Pharma companies even start to mull whether to sequence patients in their clinical drug trials, it’s created a broader base of interest in the kind of more automated genomic analysis and interpretation that Knome was built to provide.

“We are really working on two fronts now,” says Jorge Conde, Knome’s CEO and co-founder. “We’re trying to make bioinformaticians more efficient, to make it so they can do more with the data. And we are aiming to make the data more accessible to a non-bioinformatician.”

This, of course, is easier said than done. When you start talking to a biologist, or a physician for that matter, about various ways of looking at genomes, transcriptomes, exomes, and the increased or decreased probabilities of disease that might (or might not) stem from those results, eyes glaze quickly. “It’s a foreign language,” Conde says.

Knome is a private company, and doesn’t say much about its finances, but it is showing signs of gaining traction in its fourth year of operations. The company has built up a team of 30 employees in Cambridge, plus another 10 in India. It has recently come out with a version 2.0 of its software. Researchers from Harvard Medical School, the Mayo Clinic, the University of British Columbia, the University of Seoul, have started using the service, among others, Conde says.

Jorge Conde

Knome, financed by the founders in the beginning, has now pulled in a total of $12 million in investment capital from the founders, angels, France-based bioMerieux, and one more unnamed strategic investor. The latest strategic investment, worth $5 million, arrived in July, according to a regulatory filing. Knome now plans to “hire aggressively,” Conde says, and currently lists seven openings on its company site.

Conde wouldn’t disclose actual revenues, or Knome’s growth projections, but he did say in the first quarter of 2011, the company generated more revenue than it had in its cumulative history to that point.

The founding idea in 2007, Conde says, “was to make genomics accessible to the public.” But the cost of the sequencing in the first three years was still so high, there was no way it could be truly accessible, and only a select few genomics experts and bioinformaticians were able to use the Knome service. But now that Illumina, Life Technologies and Complete Genomics have all developed commercial sequencing technologies that can go for less than $5,000 a genome, Knome has found more interest in its software (called kGAP 2.0) that can compare new genomes sequenced on the various instruments vs. what is known in the scientific literature about relationships between DNA and disease.

Now that cost is really less of a barrier, there’s another one standing in the way of making genomics accessible—lack of expertise. Researchers in Big Pharma companies, and academic … Next Page »

Comments | Reprints | Share:          

Ask Jonathan Rothberg a few questions about his new venture in DNA sequencing, and, ever the showman, he find references to a pivotal event in world history while delivering what amounts to a “no comment.”

The questions were basic enough: How many employees do you have in San Francisco and Guilford, CT? How much has your R&D budget grown? How many customers have you signed up in the past nine months? Have you hit any of the milestones outlined in your 2010 merger agreement with Life Technologies?

“Come on, I’m not going to give that information out. This is like 1948 and we’re the Israelis,” Rothberg said with a laugh in a recent phone interview. “We’re still the underdog. Look at how good the other guys are. I respect my competitors too much to give out that information.”

Rothberg and his colleagues at Ion Torrent, the new unit of Carlsbad, CA-based Life Technologies (NASDAQ: LIFE) may be tight-lipped about internal matters at the moment, but they are cutting an increasingly high profile in the world of superfast/cheap genome sequencing. The company introduced its first-of-a-kind DNA sequencing machine based on semiconductor technology in December. Demand has been strong almost right off the bat, as it rang up $13 million in sales in the most recent quarter ended June 30, a 50 percent increase over the prior three-month period. That performance has come even while Ion Torrent has been swimming upstream against government research budgets that are getting nothing but tighter.

The early sales performance is certainly a small sum to a company like Life Technologies, which had $3.6 billion in revenue last year. But there’s undoubtedly a lot more potential for the Ion Torrent machine to drive growth at Life Tech and in the biomedical research world. The earliest version of the machine costs about $49,000, fits on a lab desktop, and reads individual units of DNA in a new way, through semiconductor chips that pick up distinct electron charges from each chemical base of DNA. It’s the first commercial machine of its kind, in an industry where large and heavy sequencing instruments often cost $500,000 or more, and generate their genomes by using fluorescent tags and sophisticated cameras to read the DNA code that varies from species to species and person to person.

San Diego-based Illumina (NASDAQ:ILMN), Menlo Park, CA-based Pacific Biosciences (NASDAQ: PACB) and Mountain View, CA-based Complete Genomics (NASDAQ: GNOM) are a few of the companies deeply invested in fundamentally different kinds of technology for reading DNA at breakneck speed and low cost. Ion Torrent’s Rothberg previously founded another sequencing company, 454 Life Sciences, that was sold to Roche in 2007. There’s no doubting that Rothberg has set some lofty goals for his operation, particularly since he sold Ion Torrent to Life Technologies for $375 million, plus another $350 million in milestone payments, a year ago. Rothberg says the company’s technology is going to bring genome sequencing down to $1,000 per person by 2013; it’s going to continue to help public health officials identify pathogens within hours of outbreaks; it’s going to pave the way for a $100 billion new market.

Jonathan Rothberg

Yeah, Rothberg was quoted in a Forbes story last December saying this would become a $100 billion market. Nine months in to the product launch, he didn’t flinch, making the same prediction.

“It’s like the race to the South Pole 100 years ago,” Rothberg says. “The guys that win now will change healthcare forever. We’re at an amazing point in history.”

No question, a lot has happened for Ion Torrent since it rolled out its first commercial semiconductor sequencer, called the Personal Genome Machine, in December. The original microchip had 1.2 million accessible sensors, which was surpassed in a couple months by a new chip with 6.1 million sensors. The next iteration—expected to come out later this year—is designed to boost capacity to 11 million sensors. After only a few months on the market, the component cost of the mid-range chips dropped in price from $500 to $99. Rothberg isn’t saying yet how much the newest chips will cost.

While capacity is booming and price is falling, scientists are starting to think about experiments that couldn’t have been dreamed of a year or two ago. Ion Torrent isn’t saying how many machines it has sold so far, but, thanks to the global distribution of Life Tech, Ion Torrent’s machine is now established in labs in 40 countries, Rothberg says. The instrument, along with a rival instrument from PacBio, played a starring role in the German E.coli outbreak, helping researchers identify … Next Page »

Comments (1) | Reprints | Share:          

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

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

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

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

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

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

Comments (3) | Reprints | Share:          

Amid all the comings and goings and CEOs changing jobs in the past week—see Rick Reidy of Progress Software (NASDAQ: PRGS), Mara Aspinall of On-Q-ity, and others—one person flew under the radar in Boston.

He is Stéphane Bancel, and until last month he was the CEO of bioMérieux, the microbiology and diagnostics firm based in France. Don’t let the French accent (and fashion sense) fool you, though. Bancel is a Boston guy, he’s been in town since 2007, and he’s here to stay—which is a big deal for the biotech community.

Last week, for example, BG Medicine (NASDAQ: BGMD), a Waltham, MA-based diagnostics company, said it appointed Bancel executive chairman of its board of directors. Bancel also serves as chairman of Cambridge, MA-based Knome, a personal genomics startup co-founded by Harvard’s George Church, which raised some new money this week. (bioMérieux is an investor in Knome.) Bancel is also involved with Cambridge-based ModeRNA, a stealthy therapeutics startup backed by Flagship Ventures.

Bancel had been chief executive of bioMérieux since the beginning of 2007. The billion-dollar company, which has been around since 1963, specializes in molecular diagnostic systems for healthcare, food safety, and industrial applications—like detecting salmonella in food preparation areas or bacterial infections acquired in hospitals. The firm has about 1,500 workers in the U.S., including a small office in Cambridge’s Kendall Square.

“After five years I wanted to move to the startup world,” Bancel told me this week.

Beyond that, Bancel hasn’t said much specifically about his future plans. Bancel is the kind of guy who’s involved in dozens of far-flung projects, but it wouldn’t be surprising if he spent the next part of his career focused on a new startup at the intersection of diagnostics and pharmaceuticals. (He worked for drug giant Eli Lilly from 2000 to 2006.)

Last month, before he left bioMérieux, he sat down with me to talk about the future of diagnostics, and I got the sense that that’s where his heart is. Molecular diagnostics is evolving rapidly, he said, thanks to faster and cheaper genetic sequencing and analysis and new testing approaches. And it’s changing the whole business, he said.

As Bancel put it, diagnostics used to be (and to some extent still is) a “me too” business, full of commoditized offerings from many companies. It also used to require scale—a big testing platform to do lots of similar tests, employing lots of scientists and staff. But now diagnostics is moving “closer to a pharma business,” he said. What’s more, he thinks advances in diagnostics and life sciences … Next Page »

Comments (7) | Reprints | Share:          

Busy day for a couple of well-known cleantech companies around Boston. One public company has signed a big deal in China, while the other, an ambitious upstart, is carefully protecting its intellectual property as it heads toward large-scale commercialization.

—A123 Systems (NASDAQ: AONE), the Waltham, MA-based maker of lithium ion batteries, said today it has won a contract with China’s Dongfang Electric, a large manufacturer of wind turbines and power equipment. A123 will provide an energy storage system for Dongfang’s manufacturing facility in Hangzhou by the end of this year. Financial terms weren’t given. If all goes well, this will be A123’s first storage system installed in China.

A report in CNET today has more context on the deal: A123’s battery bank will be attached to a 1.5-megawatt wind turbine and diesel generator to test how well the batteries can smooth out the dips in wind energy production. A123 has car battery manufacturing facilities in China, but no grid storage systems there yet, the report says.

—Joule Unlimited, the Cambridge, MA-based biofuels startup, said today it has been awarded a pair of U.S. patents that cover its method for producing ethanol at high volumes and high efficiencies. The method involves genetically engineering “photosynthetic bacteria”—microorganisms that convert sunlight and carbon dioxide into ethanol without fermenting sugars from cellulose or other types of biomass. The patents (#7,981,647 and #7,968,321), which were granted in the past month, cover various enzymatic mechanisms that Joule has engineered into cells to maximize their ethanol productivity.

Joule has received plenty of media attention since it started in 2007. The company is also applying its method to produce energy in the form of diesel fuel, which could power trucks and planes. Joule has previously been awarded patents in the area of diesel production. The overarching idea is to replace fossil fuels, but most biofuels makers have found “they can’t compete on a cost basis,” said Joule senior vice president Troy Campione, on a panel at our XSITE conference last month. Joule, of course, believes it is different.

The company has a pilot plant in Texas that has been producing ethanol and is slated to start producing diesel later this year. Joule says it has also signed a lease for land in New Mexico on which it is building a demonstration-scale plant that will begin operations next year.

While the new patents should help distance Joule from some of its competitors, they don’t necessarily get the company to commercialization any faster. George Church, the Harvard geneticist (and chairman of Joule’s technical advisory board), was quoted in the New York Times in March saying, “It’s not a totally obvious organism and they’ve changed it pretty radically, so it’s not clear they can protect everything by patents.”

Comments (1) | Reprints | Share:          

Highland Capital Partners has announced the 10 college startup teams participating in its 10-week Summer@Highland mentorship program in Cambridge, MA, and the San Francisco Bay Area. The venture firm provides coaching, networking, office space, and a $15,000 stipend; the teams don’t give up any equity stake and are under no obligation to Highland afterwards, the firm says. The teams based in Cambridge are: additup (Boston College), ByteLight (Boston University), Tivli (Harvard University and University of Michigan), and Type-U (Babson College). The Bay Area teams are: 27Bards (Stanford University), Adpop (Stanford), Clinkle (Stanford), Imprint Energy (UC Berkeley), Lemonwi.se (University of Pennsylvania), and Waddle (Northwestern University).

Comments | Reprints | Share:          

One of Seattle’s leading scientific entrepreneurs grew up in a working-class home in which neither parent went to college. Ken Stuart‘s family didn’t have enough money to send him to one of the many universities in his hometown of Boston.

When he graduated high school, he had no idea what would come next.

“I wasn’t sure I’d even go to college,” Stuart says. “I never applied. I was sick of school.”

After waiting all the way until May of his senior year, Stuart ended up talking his way into Northeastern University at the last minute and finding a co-op job to help pay the bills. Once there, he got hooked on biology. He soon got on the fast track, and could have had a tenured university faculty job, but decided early on that wasn’t enough. By combining a curiosity for some obscure fields of biology, some entrepreneurial spirit, and really good timing, Stuart ended up building a mini-global health empire at the Seattle Biomedical Research Institute.

Now at 70, after 35 years of building up Seattle Biomedical Research Institute from scratch into a research hotspot with 365 employees and a $52 million annual budget, Stuart is handing over day-to-day leadership to a successor, Alan Aderem. Stuart now says he’s looking forward to returning to more of the science that got him so fired up in the first place.

“There are very few people with the dynamic range to grow an organization from nothing to the state where Seattle Biomed is now,” says John King, a former Merck and Rosetta Inpharmatics executive who served on the institute’s board in the ’80s and ’90s. “Ken learned on the job how to be a startup guy, how to bootstrap an institute based on scientific excellence. He grew into doing things like sophisticated fundraising, marketing—all the kind of things big research institutes have to do.”

Stuart’s journey started in an unusual place. He was born in December 1940, and grew up the youngest of four sons in a working class home in Brighton, MA. His father was a house painter, and his mother was a stay-at-home mom. Stuart found himself interested in the stacks of books that his family kept at home, but he says he wasn’t much of a student. Grammar school was “incredibly easy and boring,” he says.

Stuart didn’t find much that interested him in high school science either, except for physics. It was hard to see where that might lead, though, since Stuart never really saw himself as college-bound. It all changed that one day in May of his senior year, when he recalls going to the school in person, and asking to meet with the dean of admissions. After getting an incredulous look from the secretary, who told him the fall class was full, Stuart persisted in seeing the dean. Within about 10 minutes, he had persuaded the dean to let him in, largely because Stuart had gone to a competitive public high school, he says.

This was the late ’50s, years after Watson and Crick had made the pioneering discovery of the structure of DNA, igniting the modern era of molecular biology. Looking back, Stuart says that moment was lost on him. He found biology more from his personal reading, of a number of books at home that his father accumulated. Pretty soon, Stuart found himself spending long hours not just in the libraries at Northeastern, but at Harvard and MIT libraries, which had reciprocity agreements with Stuart’s school just a few miles across the Charles River. Everything from physiology to biochemistry to frog embryo development, he gobbled up.

“I started studying intensively. I liked it,” Stuart says.

Textbooks soon weren’t enough, and Stuart says he really found his passion … Next Page »

Comments | Reprints | Share:          

The pharmaceutical business tends to split into a couple of camps: Either molecules ought to be small, or large. But some interesting work these days is happening in the middle, where Cambridge, MA-based Ensemble Therapeutics has been carving out its niche.

Ensemble has been toiling away since 2004, based on work in David Liu’s lab at Harvard University, to synthesize a class of mid-sized molecules known as macrocycles. The idea is to try to combine the best of both worlds with small and large molecules. The mid-sized drugs are supposed to have a big advantage of traditional small-molecule drugs-their ability to be made into oral pills-along with the precision targeting capability of large-molecule biotech drugs, like antibodies or other engineered proteins. Ideally, the mid-sized drug candidates should be lean and mean enough to hit biological targets inside cells that bulkier protein drugs can’t reach.

There have been plenty of skeptics. Macrocycles are complex molecules found in nature. Scientists know they can sometimes be made into useful pharmaceuticals, including antibiotics like erythromycin, but no one has developed a fast, cheap, industrialized way to synthesize new macrocycle drugs to fill up a library, like with small molecules. It’s only been in the last year, Ensemble CEO Mike Taylor says, that the company has really hit its groove, developing a method that had created a vast library of about 3 million new macrocycles (soon to be an estimated 4.2 million) with potential to run through screening campaigns against some of biology’s hard-to-reach targets.

All of Ensemble’s molecules are still in their infancy, and need to run the usual gauntlet of tests in animal models before the company even thinks seriously about advancing them into clinical trials. But Ensemble has gotten much positive feedback from its two partners, Pfizer and Bristol-Myers Squibb, and is now in position to add a third or, maybe, fourth partner, Taylor says.

Mike Taylor

“There were a lot of biases against macrocycles when we started, based on historic challenges,” Taylor says. “We had a checklist to work on, to convince people that yes, we could make lots of them, and yes, we can make discrete molecules, and yes, we can make them with drug-like properties, and yes, we can get them into cells. There were about 12 things we had to tick off, which we have essentially done.”

Ensemble recently reported that it had been granted a couple of key patents on its technology. This patented method has put little Ensemble, with a little more than 30 employees, in a position to do what Big Pharma companies do—run industrialized campaigns to see … Next Page »

Comments (1) | Reprints | Share: